Sat Oct 7 23:40:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0050340 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050340/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0050340 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-593 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 60506144 5487704 1778476 0 56894828 -/+ buffers/cache: 3611316 62382532 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: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: ntraut Machine: tars-593 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: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: ntraut Machine: tars-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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: 2017/10/07-21:40:21-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-593 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-6.0.0/0050340 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050340/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050340/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050340/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-6.0.0/0050340/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 23:40:23 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 23:40:31 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/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-593 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 23:40:31 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.9103 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9103/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9103/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.9103/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 23:40:34 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.9103/nu0.mnc ./tmp.mri_nu_correct.mni.9103/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9103/0/ -iterations 1000 -distance 50 [ntraut@tars-593:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/] [2017-10-07 23:40:34] 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.9103/0/ ./tmp.mri_nu_correct.mni.9103/nu0.mnc ./tmp.mri_nu_correct.mni.9103/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 21 CV of field change: 0.000980026 mri_convert ./tmp.mri_nu_correct.mni.9103/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.9103/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.9103/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sat Oct 7 23:41:29 CEST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Oct 7 23:41:29 CEST 2017 Ended at Sat Oct 7 23:42:04 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 23:42:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7747, pval=0.6675 >= threshold=0.0050) awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/transforms/talairach_avi.log TalAviQA: 0.97921 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 23:42:06 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-6.0.0/0050340/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-593 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 23:42:06 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.9640 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9640/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9640/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.9640/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 23:42:09 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.9640/nu0.mnc ./tmp.mri_nu_correct.mni.9640/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9640/0/ [ntraut@tars-593:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/] [2017-10-07 23:42:09] 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.9640/0/ ./tmp.mri_nu_correct.mni.9640/nu0.mnc ./tmp.mri_nu_correct.mni.9640/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 18 CV of field change: 0.000970051 -------------------------------------------------------- Iteration 2 Sat Oct 7 23:42:50 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.9640/nu1.mnc ./tmp.mri_nu_correct.mni.9640/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9640/1/ [ntraut@tars-593:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/] [2017-10-07 23:42:50] 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.9640/1/ ./tmp.mri_nu_correct.mni.9640/nu1.mnc ./tmp.mri_nu_correct.mni.9640/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 10 CV of field change: 0.000990587 mri_binarize --i ./tmp.mri_nu_correct.mni.9640/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9640/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-6.0.0/0050340/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.9640/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9640/ones.mgz sysname Linux hostname tars-593 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.9640/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9640/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.9640/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9640/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9640/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.9640/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9640/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9640/input.mean.dat sysname Linux hostname tars-593 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9640/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.9640/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9640/ones.mgz --i ./tmp.mri_nu_correct.mni.9640/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9640/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9640/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.9640/ones.mgz --i ./tmp.mri_nu_correct.mni.9640/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9640/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9640/output.mean.dat sysname Linux hostname tars-593 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9640/ones.mgz Loading ./tmp.mri_nu_correct.mni.9640/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.9640/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.9640/nu2.mnc ./tmp.mri_nu_correct.mni.9640/nu2.mnc mul 1.00513163083385285011 Saving result to './tmp.mri_nu_correct.mni.9640/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.9640/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.9640/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.9640/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 8 seconds. mapping (10, 109) to ( 3, 110) Sat Oct 7 23:44:11 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 23:44:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 1.09368 0.03463 0.03277 -153.56221; -0.01305 1.02303 0.08753 -155.63049; -0.06859 -0.07832 1.19643 -60.15010; 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 = 19 Starting OpenSpline(): npoints = 19 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 67 (67), valley at 10 (10) csf peak at 34, setting threshold to 56 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 67 (67), valley at 23 (23) csf peak at 34, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 50 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 23:46:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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=16.0 skull bounding box = (41, 55, 28) --> (202, 187, 226) using (95, 99, 127) as brain centroid... mean wm in atlas = 108, using box (75,83,103) --> (114, 115,151) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 4.6 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -4.552 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.433717 @ (9.091, -9.091, -9.091) max log p = -4.336064 @ (-4.545, 4.545, -4.545) max log p = -4.336064 @ (0.000, 0.000, 0.000) max log p = -4.294858 @ (-3.409, 1.136, -1.136) max log p = -4.294858 @ (0.000, 0.000, 0.000) max log p = -4.294858 @ (0.000, 0.000, 0.000) Found translation: (1.1, -3.4, -14.8): log p = -4.295 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.058, old_max_log_p =-4.295 (thresh=-4.3) 1.06375 0.00000 0.00000 -6.75199; 0.00000 1.22567 0.14032 -53.90052; 0.00000 -0.16136 1.06580 -7.05218; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.049, old_max_log_p =-4.058 (thresh=-4.1) 1.14353 0.00000 0.00000 -16.62404; 0.00000 1.22567 0.14032 -53.90052; 0.00000 -0.14926 0.98587 1.79597; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.045, old_max_log_p =-4.049 (thresh=-4.0) 1.05777 0.00000 0.00000 -6.01159; 0.00000 1.23467 0.01043 -37.97911; 0.00000 0.01290 1.07043 -25.39732; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.045, old_max_log_p =-4.045 (thresh=-4.0) 1.05777 0.00000 0.00000 -6.01159; 0.00000 1.23467 0.01043 -37.97911; 0.00000 0.01290 1.07043 -25.39732; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.943, old_max_log_p =-4.045 (thresh=-4.0) 1.05536 0.00158 -0.07148 5.15466; -0.00265 1.30313 0.07503 -55.66413; 0.07234 -0.06454 1.00600 -20.33563; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.932, old_max_log_p =-3.943 (thresh=-3.9) 1.05635 0.04494 -0.03812 -5.60182; -0.04118 1.27934 0.01013 -39.02319; 0.03744 0.02076 1.01055 -28.99963; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.932, old_max_log_p =-3.932 (thresh=-3.9) 1.05635 0.04494 -0.03812 -5.60182; -0.04118 1.27934 0.01013 -39.02319; 0.03744 0.02076 1.01055 -28.99963; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.917, old_max_log_p =-3.932 (thresh=-3.9) 1.05477 0.04472 -0.04635 -4.76688; -0.04122 1.28084 0.01014 -39.23503; 0.04611 0.02115 1.01139 -29.75636; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.916, old_max_log_p =-3.917 (thresh=-3.9) 1.05724 0.04482 -0.04646 -5.07073; -0.04122 1.28084 0.01014 -39.23503; 0.04606 0.02113 1.01020 -29.59150; 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 1.05724 0.04482 -0.04646 -5.07073; -0.04122 1.28084 0.01014 -39.23503; 0.04606 0.02113 1.01020 -29.59150; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.05724 0.04482 -0.04646 -5.07073; -0.04122 1.28084 0.01014 -39.23503; 0.04606 0.02113 1.01020 -29.59150; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05724 0.04482 -0.04646 -5.07073; -0.04122 1.28084 0.01014 -39.23503; 0.04606 0.02113 1.01020 -29.59150; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.916 (old=-4.552) transform before final EM align: 1.05724 0.04482 -0.04646 -5.07073; -0.04122 1.28084 0.01014 -39.23503; 0.04606 0.02113 1.01020 -29.59150; 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 1.05724 0.04482 -0.04646 -5.07073; -0.04122 1.28084 0.01014 -39.23503; 0.04606 0.02113 1.01020 -29.59150; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.05724 0.04482 -0.04646 -5.07073; -0.04122 1.28084 0.01014 -39.23503; 0.04606 0.02113 1.01020 -29.59150; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.3 tol 0.000000 final transform: 1.05724 0.04482 -0.04646 -5.07073; -0.04122 1.28084 0.01014 -39.23503; 0.04606 0.02113 1.01020 -29.59150; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1773.889327 mri_em_register stimesec 1.775730 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 157573 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 440 mri_em_register ru_nivcsw 24920 registration took 15 minutes and 15 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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=124 y=124 z=129 r=67 first estimation of the main basin volume: 1284889 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=103, y=108, z=98, Imax=255 CSF=19, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=8891946141 voxels, voxel volume =1.000 = 8891946141 mmm3 = 8891945.984 cm3 done. PostAnalyze...Basin Prior 66 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=122,y=125, z=122, r=9558 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45440 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1101112322 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1123318834 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1124457339 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1074691960 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1074042714 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 6, 39, 62 after analyzing : 4, 28, 39, 36 RIGHT_CER before analyzing : 3, 4, 41, 72 after analyzing : 3, 28, 41, 39 LEFT_CER before analyzing : 3, 3, 35, 73 after analyzing : 3, 24, 35, 36 RIGHT_BRAIN before analyzing : 4, 6, 38, 62 after analyzing : 4, 27, 38, 35 LEFT_BRAIN before analyzing : 4, 6, 40, 63 after analyzing : 4, 28, 40, 36 OTHER before analyzing : 3, 3, 8, 63 after analyzing : 3, 17, 25, 28 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...67 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 69.123, std = 8.188 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.07, sigma = 4.42 after rotation: sse = 3.07, sigma = 4.42 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.22, its var is 3.96 before Erosion-Dilatation 0.35% 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...37 iterations mri_strip_skull: done peeling brain Brain Size = 1516099 voxels, voxel volume = 1.000 mm3 = 1516099 mmm3 = 1516.099 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 24.747237 mri_watershed stimesec 0.453930 mri_watershed ru_maxrss 818272 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 211536 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2344 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 3134 mri_watershed ru_nivcsw 87 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sun Oct 8 00:01:41 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = (56, 69, 46) --> (184, 176, 212) using (99, 105, 129) as brain centroid... mean wm in atlas = 107, using box (83,92,109) --> (114, 118,149) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 4.7 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.162 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.072098 @ (9.091, -9.091, -9.091) max log p = -3.843884 @ (-4.545, 4.545, -4.545) max log p = -3.788487 @ (-2.273, -2.273, -2.273) max log p = -3.786718 @ (1.136, 1.136, 1.136) max log p = -3.786718 @ (0.000, 0.000, 0.000) max log p = -3.777655 @ (-1.420, -2.557, -1.420) Found translation: (2.0, -8.2, -16.2): log p = -3.778 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.620, old_max_log_p =-3.778 (thresh=-3.8) 1.07500 0.00000 0.00000 -7.36751; 0.00000 1.14016 0.13053 -41.99015; 0.00000 -0.15011 0.99144 3.99015; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.620, old_max_log_p =-3.620 (thresh=-3.6) 1.07500 0.00000 0.00000 -7.36751; 0.00000 1.14016 0.13053 -41.99015; 0.00000 -0.15011 0.99144 3.99015; 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=-3.512, old_max_log_p =-3.620 (thresh=-3.6) 1.05380 -0.00166 -0.03693 1.61059; -0.00526 1.18727 0.09939 -41.68822; 0.03549 -0.11229 1.01274 -7.96986; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.495, old_max_log_p =-3.512 (thresh=-3.5) 1.07355 -0.00169 -0.03762 -0.73553; -0.00526 1.18727 0.09939 -41.68822; 0.03549 -0.11229 1.01274 -7.96986; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.495, old_max_log_p =-3.495 (thresh=-3.5) 1.07355 -0.00169 -0.03762 -0.73553; -0.00526 1.18727 0.09939 -41.68822; 0.03549 -0.11229 1.01274 -7.96986; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.480, old_max_log_p =-3.495 (thresh=-3.5) 1.07082 0.01766 -0.03563 -3.07738; -0.02230 1.18792 0.11682 -40.85401; 0.03549 -0.13139 1.00861 -4.12369; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.467, old_max_log_p =-3.480 (thresh=-3.5) 1.07230 -0.00181 -0.03731 -0.61851; -0.00533 1.18586 0.09935 -41.51546; 0.03499 -0.11155 1.00684 -7.27160; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.462, old_max_log_p =-3.467 (thresh=-3.5) 1.07230 -0.00181 -0.03731 -0.61851; -0.00532 1.18308 0.09912 -41.13857; 0.03495 -0.11142 1.00566 -7.13952; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.462, old_max_log_p =-3.462 (thresh=-3.5) 1.07230 -0.00181 -0.03731 -0.61851; -0.00532 1.18308 0.09912 -41.13857; 0.03495 -0.11142 1.00566 -7.13952; 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 1.07230 -0.00181 -0.03731 -0.61851; -0.00532 1.18308 0.09912 -41.13857; 0.03495 -0.11142 1.00566 -7.13952; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.07230 -0.00181 -0.03731 -0.61851; -0.00532 1.18308 0.09912 -41.13857; 0.03495 -0.11142 1.00566 -7.13952; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07230 -0.00181 -0.03731 -0.61851; -0.00532 1.18308 0.09912 -41.13857; 0.03495 -0.11142 1.00566 -7.13952; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.462 (old=-4.162) transform before final EM align: 1.07230 -0.00181 -0.03731 -0.61851; -0.00532 1.18308 0.09912 -41.13857; 0.03495 -0.11142 1.00566 -7.13952; 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 1.07230 -0.00181 -0.03731 -0.61851; -0.00532 1.18308 0.09912 -41.13857; 0.03495 -0.11142 1.00566 -7.13952; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.07230 -0.00181 -0.03731 -0.61851; -0.00532 1.18308 0.09912 -41.13857; 0.03495 -0.11142 1.00566 -7.13952; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 3.9 tol 0.000000 final transform: 1.07230 -0.00181 -0.03731 -0.61851; -0.00532 1.18308 0.09912 -41.13857; 0.03495 -0.11142 1.00566 -7.13952; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1435.782727 mri_em_register stimesec 1.599756 mri_em_register ru_maxrss 600920 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158949 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 177 mri_em_register ru_nivcsw 14307 registration took 12 minutes and 15 seconds. #-------------------------------------- #@# CA Normalize Sun Oct 8 00:13:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = (56, 69, 46) --> (184, 176, 212) using (99, 105, 129) as brain centroid... mean wm in atlas = 107, using box (83,92,109) --> (114, 118,149) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 4.7 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 using 246344 sample points... INFO: compute sample coordinates transform 1.07230 -0.00181 -0.03731 -0.61851; -0.00532 1.18308 0.09912 -41.13857; 0.03495 -0.11142 1.00566 -7.13952; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (120, 69, 44) --> (184, 169, 209) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0 0 of 3097 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (63, 70, 44) --> (125, 168, 210) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 2973 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (123, 144, 68) --> (168, 180, 122) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 65 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 144, 67) --> (122, 179, 125) Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 26 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 135, 105) --> (139, 195, 134) Brain_Stem: limiting intensities to 97.0 --> 132.0 8 of 96 (8.3%) samples deleted using 6257 total control points for intensity normalization... bias field = 0.942 +- 0.050 34 of 6249 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (120, 69, 44) --> (184, 169, 209) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 3857 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (63, 70, 44) --> (125, 168, 210) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 3774 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (123, 144, 68) --> (168, 180, 122) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 169 (5.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 144, 67) --> (122, 179, 125) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 47 of 104 (45.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 135, 105) --> (139, 195, 134) Brain_Stem: limiting intensities to 88.0 --> 132.0 29 of 177 (16.4%) samples deleted using 8081 total control points for intensity normalization... bias field = 1.034 +- 0.053 35 of 7920 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (120, 69, 44) --> (184, 169, 209) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 3 of 3897 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (63, 70, 44) --> (125, 168, 210) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 3884 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (123, 144, 68) --> (168, 180, 122) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 49 of 217 (22.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 144, 67) --> (122, 179, 125) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 60 of 129 (46.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 135, 105) --> (139, 195, 134) Brain_Stem: limiting intensities to 88.0 --> 132.0 65 of 256 (25.4%) samples deleted using 8383 total control points for intensity normalization... bias field = 1.032 +- 0.052 21 of 8049 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 39 seconds. #-------------------------------------- #@# CA Reg Sun Oct 8 00:15:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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) = 1.29 (predicted orig area = 6.2) 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=0.799, neg=0, invalid=762 0001: dt=205.538462, rms=0.723 (9.536%), neg=0, invalid=762 0002: dt=156.123515, rms=0.703 (2.656%), neg=0, invalid=762 0003: dt=221.952000, rms=0.694 (1.413%), neg=0, invalid=762 0004: dt=134.620690, rms=0.688 (0.768%), neg=0, invalid=762 0005: dt=369.920000, rms=0.683 (0.744%), neg=0, invalid=762 0006: dt=110.976000, rms=0.680 (0.503%), neg=0, invalid=762 0007: dt=517.888000, rms=0.676 (0.600%), neg=0, invalid=762 0008: dt=129.472000, rms=0.674 (0.245%), neg=0, invalid=762 0009: dt=129.472000, rms=0.673 (0.130%), neg=0, invalid=762 0010: dt=129.472000, rms=0.672 (0.184%), neg=0, invalid=762 0011: dt=129.472000, rms=0.670 (0.283%), neg=0, invalid=762 0012: dt=129.472000, rms=0.668 (0.262%), neg=0, invalid=762 0013: dt=129.472000, rms=0.666 (0.269%), neg=0, invalid=762 0014: dt=129.472000, rms=0.665 (0.251%), neg=0, invalid=762 0015: dt=129.472000, rms=0.663 (0.200%), neg=0, invalid=762 0016: dt=129.472000, rms=0.662 (0.188%), neg=0, invalid=762 0017: dt=129.472000, rms=0.661 (0.151%), neg=0, invalid=762 0018: dt=129.472000, rms=0.660 (0.163%), neg=0, invalid=762 0019: dt=129.472000, rms=0.659 (0.132%), neg=0, invalid=762 0020: dt=129.472000, rms=0.658 (0.105%), neg=0, invalid=762 0021: dt=129.472000, rms=0.658 (0.100%), neg=0, invalid=762 0022: dt=1479.680000, rms=0.657 (0.179%), neg=0, invalid=762 0023: dt=92.480000, rms=0.656 (0.083%), neg=0, invalid=762 0024: dt=92.480000, rms=0.656 (0.007%), neg=0, invalid=762 0025: dt=92.480000, rms=0.656 (0.015%), neg=0, invalid=762 0026: dt=92.480000, rms=0.656 (0.018%), neg=0, invalid=762 0027: dt=92.480000, rms=0.656 (0.024%), neg=0, invalid=762 0028: dt=92.480000, rms=0.655 (0.033%), neg=0, invalid=762 0029: dt=92.480000, rms=0.655 (0.047%), neg=0, invalid=762 0030: dt=92.480000, rms=0.655 (0.053%), neg=0, invalid=762 0031: dt=92.480000, rms=0.654 (0.052%), neg=0, invalid=762 0032: dt=92.480000, rms=0.654 (0.046%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.655, neg=0, invalid=762 0033: dt=295.936000, rms=0.653 (0.230%), neg=0, invalid=762 0034: dt=129.472000, rms=0.653 (0.045%), neg=0, invalid=762 0035: dt=129.472000, rms=0.652 (0.033%), neg=0, invalid=762 0036: dt=129.472000, rms=0.652 (0.048%), neg=0, invalid=762 0037: dt=129.472000, rms=0.652 (0.052%), neg=0, invalid=762 0038: dt=129.472000, rms=0.652 (0.053%), neg=0, invalid=762 0039: dt=129.472000, rms=0.651 (0.062%), neg=0, invalid=762 0040: dt=129.472000, rms=0.651 (0.074%), neg=0, invalid=762 0041: dt=129.472000, rms=0.650 (0.074%), neg=0, invalid=762 0042: dt=129.472000, rms=0.650 (0.071%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.653, neg=0, invalid=762 0043: dt=113.053892, rms=0.649 (0.700%), neg=0, invalid=762 0044: dt=248.832000, rms=0.640 (1.396%), neg=0, invalid=762 0045: dt=80.372093, rms=0.637 (0.495%), neg=0, invalid=762 0046: dt=145.152000, rms=0.633 (0.630%), neg=0, invalid=762 0047: dt=36.288000, rms=0.632 (0.174%), neg=0, invalid=762 0048: dt=36.288000, rms=0.631 (0.118%), neg=0, invalid=762 0049: dt=36.288000, rms=0.630 (0.184%), neg=0, invalid=762 0050: dt=36.288000, rms=0.628 (0.283%), neg=0, invalid=762 0051: dt=36.288000, rms=0.626 (0.368%), neg=0, invalid=762 0052: dt=36.288000, rms=0.623 (0.414%), neg=0, invalid=762 0053: dt=36.288000, rms=0.620 (0.409%), neg=0, invalid=762 0054: dt=36.288000, rms=0.618 (0.391%), neg=0, invalid=762 0055: dt=36.288000, rms=0.616 (0.374%), neg=0, invalid=762 0056: dt=36.288000, rms=0.614 (0.338%), neg=0, invalid=762 0057: dt=36.288000, rms=0.612 (0.306%), neg=0, invalid=762 0058: dt=36.288000, rms=0.610 (0.310%), neg=0, invalid=762 0059: dt=36.288000, rms=0.608 (0.296%), neg=0, invalid=762 0060: dt=36.288000, rms=0.606 (0.264%), neg=0, invalid=762 0061: dt=36.288000, rms=0.605 (0.231%), neg=0, invalid=762 0062: dt=36.288000, rms=0.604 (0.199%), neg=0, invalid=762 0063: dt=36.288000, rms=0.603 (0.172%), neg=0, invalid=762 0064: dt=36.288000, rms=0.602 (0.157%), neg=0, invalid=762 0065: dt=36.288000, rms=0.601 (0.152%), neg=0, invalid=762 0066: dt=36.288000, rms=0.600 (0.146%), neg=0, invalid=762 0067: dt=36.288000, rms=0.599 (0.129%), neg=0, invalid=762 0068: dt=36.288000, rms=0.599 (0.117%), neg=0, invalid=762 0069: dt=36.288000, rms=0.598 (0.108%), neg=0, invalid=762 0070: dt=145.152000, rms=0.598 (0.007%), neg=0, invalid=762 0071: dt=145.152000, rms=0.597 (0.102%), neg=0, invalid=762 0072: dt=145.152000, rms=0.597 (-0.067%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.598, neg=0, invalid=762 0073: dt=95.000000, rms=0.596 (0.288%), neg=0, invalid=762 0074: dt=103.680000, rms=0.595 (0.167%), neg=0, invalid=762 0075: dt=103.680000, rms=0.595 (-0.165%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.616, neg=0, invalid=762 0076: dt=9.600000, rms=0.615 (0.201%), neg=0, invalid=762 0077: dt=2.800000, rms=0.615 (0.018%), neg=0, invalid=762 0078: dt=2.800000, rms=0.615 (0.004%), neg=0, invalid=762 0079: dt=2.800000, rms=0.615 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.616, neg=0, invalid=762 0080: dt=2.800000, rms=0.615 (0.093%), neg=0, invalid=762 0081: dt=1.600000, rms=0.615 (0.004%), neg=0, invalid=762 0082: dt=1.600000, rms=0.615 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0083: dt=5.788945, rms=0.652 (1.998%), neg=0, invalid=762 0084: dt=2.785714, rms=0.651 (0.063%), neg=0, invalid=762 0085: dt=2.785714, rms=0.651 (-0.023%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=762 0086: dt=0.000000, rms=0.651 (0.070%), neg=0, invalid=762 0087: dt=0.000000, rms=0.651 (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=0.701, neg=0, invalid=762 0088: dt=0.448000, rms=0.700 (0.203%), neg=0, invalid=762 0089: dt=1.024000, rms=0.699 (0.168%), neg=0, invalid=762 0090: dt=1.024000, rms=0.697 (0.274%), neg=0, invalid=762 0091: dt=1.024000, rms=0.696 (0.127%), neg=0, invalid=762 0092: dt=1.024000, rms=0.696 (-0.283%), neg=0, invalid=762 0093: dt=1.792000, rms=0.695 (0.093%), neg=0, invalid=762 0094: dt=1.792000, rms=0.694 (0.160%), neg=0, invalid=762 0095: dt=0.000000, rms=0.694 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.695, neg=0, invalid=762 0096: dt=0.768000, rms=0.694 (0.126%), neg=0, invalid=762 0097: dt=1.792000, rms=0.693 (0.056%), neg=0, invalid=762 0098: dt=1.792000, rms=0.693 (-0.032%), 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=0.663, neg=0, invalid=762 0099: dt=0.823858, rms=0.646 (2.579%), neg=0, invalid=762 0100: dt=0.080000, rms=0.645 (0.132%), neg=0, invalid=762 0101: dt=0.080000, rms=0.645 (-0.091%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.645, neg=0, invalid=762 0102: dt=0.028000, rms=0.645 (0.094%), neg=0, invalid=762 0103: dt=0.001750, rms=0.645 (-0.002%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.06482 (18) Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (757 voxels, overlap=0.571) Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (757 voxels, peak = 21), gca=21.3 gca peak = 0.15565 (16) mri peak = 0.04843 (17) Right_Lateral_Ventricle (43): linear fit = 2.71 x + 0.0 (722 voxels, overlap=0.432) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (722 voxels, peak = 43), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.08830 (90) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (970 voxels, overlap=0.759) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (970 voxels, peak = 89), gca=88.8 gca peak = 0.20183 (93) mri peak = 0.10163 (93) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (798 voxels, overlap=0.931) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (798 voxels, peak = 90), gca=89.7 gca peak = 0.21683 (55) mri peak = 0.05795 (68) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (946 voxels, overlap=0.033) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (946 voxels, peak = 64), gca=63.5 gca peak = 0.30730 (58) mri peak = 0.07831 (67) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (956 voxels, overlap=0.591) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (956 voxels, peak = 65), gca=64.7 gca peak = 0.11430 (101) mri peak = 0.09138 (101) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (61113 voxels, overlap=0.902) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (61113 voxels, peak = 104), gca=103.5 gca peak = 0.12076 (102) mri peak = 0.08975 (103) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (60832 voxels, overlap=0.779) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (60832 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.03681 (65) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (26709 voxels, overlap=0.905) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (26709 voxels, peak = 63), gca=63.4 gca peak = 0.15082 (58) mri peak = 0.03710 (61) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (27500 voxels, overlap=0.919) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (27500 voxels, peak = 61), gca=60.6 gca peak = 0.14161 (67) mri peak = 0.07219 (74) Right_Caudate (50): linear fit = 1.09 x + 0.0 (980 voxels, overlap=0.863) Right_Caudate (50): linear fit = 1.09 x + 0.0 (980 voxels, peak = 73), gca=72.7 gca peak = 0.15243 (71) mri peak = 0.09621 (79) Left_Caudate (11): linear fit = 1.03 x + 0.0 (972 voxels, overlap=0.887) Left_Caudate (11): linear fit = 1.03 x + 0.0 (972 voxels, peak = 73), gca=73.5 gca peak = 0.13336 (57) mri peak = 0.03916 (56) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (26710 voxels, overlap=0.936) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (26710 voxels, peak = 64), gca=63.6 gca peak = 0.13252 (56) mri peak = 0.03977 (59) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (25021 voxels, overlap=0.886) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (25021 voxels, peak = 62), gca=62.4 gca peak = 0.18181 (84) mri peak = 0.07474 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9145 voxels, overlap=0.784) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9145 voxels, peak = 89), gca=89.5 gca peak = 0.20573 (83) mri peak = 0.05118 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7406 voxels, overlap=0.924) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7406 voxels, peak = 87), gca=86.7 gca peak = 0.21969 (57) mri peak = 0.08525 (75) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (435 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (435 voxels, peak = 74), gca=73.8 gca peak = 0.39313 (56) mri peak = 0.09650 (73) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (516 voxels, overlap=0.021) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (516 voxels, peak = 71), gca=71.4 gca peak = 0.14181 (85) mri peak = 0.06866 (88) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5295 voxels, overlap=0.958) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5295 voxels, peak = 86), gca=86.3 gca peak = 0.11978 (83) mri peak = 0.07183 (87) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4485 voxels, overlap=0.928) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4485 voxels, peak = 85), gca=85.1 gca peak = 0.13399 (79) mri peak = 0.06704 (82) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2313 voxels, overlap=0.919) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2313 voxels, peak = 83), gca=82.6 gca peak = 0.14159 (79) mri peak = 0.07093 (75) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2220 voxels, overlap=1.000) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2220 voxels, peak = 79), gca=78.6 gca peak = 0.10025 (80) mri peak = 0.07865 (88) Brain_Stem (16): linear fit = 1.14 x + 0.0 (10306 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.14 x + 0.0 (10306 voxels, peak = 92), gca=91.6 gca peak = 0.13281 (86) mri peak = 0.07487 (95) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1132 voxels, overlap=0.417) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1132 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.07379 (95) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1420 voxels, overlap=0.502) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1420 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.21881 (14) Fourth_Ventricle (15): linear fit = 0.73 x + 0.0 (305 voxels, overlap=0.458) Fourth_Ventricle (15): linear fit = 0.73 x + 0.0 (305 voxels, peak = 15), gca=15.2 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 1.16 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.10 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=0.645, neg=0, invalid=762 0104: dt=111.325670, rms=0.638 (1.105%), neg=0, invalid=762 0105: dt=221.952000, rms=0.635 (0.511%), neg=0, invalid=762 0106: dt=295.936000, rms=0.632 (0.426%), neg=0, invalid=762 0107: dt=92.480000, rms=0.631 (0.191%), neg=0, invalid=762 0108: dt=517.888000, rms=0.629 (0.247%), neg=0, invalid=762 0109: dt=73.984000, rms=0.629 (0.126%), neg=0, invalid=762 0110: dt=517.888000, rms=0.628 (0.167%), neg=0, invalid=762 0111: dt=129.472000, rms=0.627 (0.123%), neg=0, invalid=762 0112: dt=73.984000, rms=0.627 (0.007%), neg=0, invalid=762 0113: dt=73.984000, rms=0.627 (0.022%), neg=0, invalid=762 0114: dt=73.984000, rms=0.626 (0.038%), neg=0, invalid=762 0115: dt=73.984000, rms=0.626 (0.055%), neg=0, invalid=762 0116: dt=73.984000, rms=0.626 (0.071%), neg=0, invalid=762 0117: dt=73.984000, rms=0.625 (0.078%), neg=0, invalid=762 0118: dt=73.984000, rms=0.625 (0.080%), neg=0, invalid=762 0119: dt=73.984000, rms=0.624 (0.079%), neg=0, invalid=762 0120: dt=73.984000, rms=0.624 (0.075%), neg=0, invalid=762 0121: dt=73.984000, rms=0.623 (0.063%), neg=0, invalid=762 0122: dt=73.984000, rms=0.623 (0.062%), neg=0, invalid=762 0123: dt=73.984000, rms=0.623 (0.056%), neg=0, invalid=762 0124: dt=73.984000, rms=0.622 (0.047%), neg=0, invalid=762 0125: dt=73.984000, rms=0.622 (0.036%), neg=0, invalid=762 0126: dt=73.984000, rms=0.622 (0.031%), neg=0, invalid=762 0127: dt=73.984000, rms=0.622 (0.038%), neg=0, invalid=762 0128: dt=73.984000, rms=0.621 (0.042%), neg=0, invalid=762 0129: dt=73.984000, rms=0.621 (0.041%), neg=0, invalid=762 0130: dt=73.984000, rms=0.621 (0.039%), neg=0, invalid=762 0131: dt=73.984000, rms=0.621 (0.035%), neg=0, invalid=762 0132: dt=73.984000, rms=0.620 (0.032%), neg=0, invalid=762 0133: dt=73.984000, rms=0.620 (0.037%), neg=0, invalid=762 0134: dt=73.984000, rms=0.620 (0.039%), neg=0, invalid=762 0135: dt=73.984000, rms=0.620 (0.039%), neg=0, invalid=762 0136: dt=73.984000, rms=0.620 (0.038%), neg=0, invalid=762 0137: dt=73.984000, rms=0.619 (0.035%), neg=0, invalid=762 0138: dt=73.984000, rms=0.619 (0.036%), neg=0, invalid=762 0139: dt=73.984000, rms=0.619 (0.037%), neg=0, invalid=762 0140: dt=73.984000, rms=0.619 (0.038%), neg=0, invalid=762 0141: dt=73.984000, rms=0.618 (0.037%), neg=0, invalid=762 0142: dt=73.984000, rms=0.618 (0.035%), neg=0, invalid=762 0143: dt=73.984000, rms=0.618 (0.035%), neg=0, invalid=762 0144: dt=73.984000, rms=0.618 (0.033%), neg=0, invalid=762 0145: dt=73.984000, rms=0.618 (0.036%), neg=0, invalid=762 0146: dt=73.984000, rms=0.617 (0.035%), neg=0, invalid=762 0147: dt=73.984000, rms=0.617 (0.035%), neg=0, invalid=762 0148: dt=73.984000, rms=0.617 (0.030%), neg=0, invalid=762 0149: dt=73.984000, rms=0.617 (0.028%), neg=0, invalid=762 0150: dt=73.984000, rms=0.617 (0.028%), neg=0, invalid=762 0151: dt=73.984000, rms=0.616 (0.029%), neg=0, invalid=762 0152: dt=73.984000, rms=0.616 (0.027%), neg=0, invalid=762 0153: dt=73.984000, rms=0.616 (0.025%), neg=0, invalid=762 0154: dt=73.984000, rms=0.616 (0.023%), neg=0, invalid=762 0155: dt=7102.464000, rms=0.615 (0.097%), neg=0, invalid=762 0156: dt=129.472000, rms=0.615 (0.123%), neg=0, invalid=762 0157: dt=0.005645, rms=0.615 (-0.002%), neg=0, invalid=762 0158: dt=0.005645, rms=0.615 (0.000%), neg=0, invalid=762 0159: dt=0.005645, rms=0.615 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.615, neg=0, invalid=762 0160: dt=221.952000, rms=0.613 (0.249%), neg=0, invalid=762 0161: dt=129.472000, rms=0.613 (0.052%), neg=0, invalid=762 0162: dt=369.920000, rms=0.613 (0.046%), neg=0, invalid=762 0163: dt=369.920000, rms=0.613 (-0.142%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.614, neg=0, invalid=762 0164: dt=102.603175, rms=0.610 (0.541%), neg=0, invalid=762 0165: dt=181.020921, rms=0.603 (1.186%), neg=0, invalid=762 0166: dt=57.043478, rms=0.600 (0.505%), neg=0, invalid=762 0167: dt=414.720000, rms=0.594 (1.079%), neg=0, invalid=762 0168: dt=55.752577, rms=0.590 (0.657%), neg=0, invalid=762 0169: dt=145.152000, rms=0.587 (0.486%), neg=0, invalid=762 0170: dt=36.288000, rms=0.586 (0.079%), neg=0, invalid=762 0171: dt=497.664000, rms=0.584 (0.487%), neg=0, invalid=762 0172: dt=64.260516, rms=0.580 (0.570%), neg=0, invalid=762 0173: dt=36.288000, rms=0.580 (0.048%), neg=0, invalid=762 0174: dt=36.288000, rms=0.580 (0.052%), neg=0, invalid=762 0175: dt=36.288000, rms=0.579 (0.094%), neg=0, invalid=762 0176: dt=36.288000, rms=0.578 (0.130%), neg=0, invalid=762 0177: dt=36.288000, rms=0.577 (0.161%), neg=0, invalid=762 0178: dt=36.288000, rms=0.576 (0.182%), neg=0, invalid=762 0179: dt=36.288000, rms=0.575 (0.191%), neg=0, invalid=762 0180: dt=36.288000, rms=0.574 (0.198%), neg=0, invalid=762 0181: dt=36.288000, rms=0.573 (0.192%), neg=0, invalid=762 0182: dt=36.288000, rms=0.572 (0.193%), neg=0, invalid=762 0183: dt=36.288000, rms=0.571 (0.195%), neg=0, invalid=762 0184: dt=36.288000, rms=0.570 (0.193%), neg=0, invalid=762 0185: dt=36.288000, rms=0.569 (0.188%), neg=0, invalid=762 0186: dt=36.288000, rms=0.568 (0.180%), neg=0, invalid=762 0187: dt=36.288000, rms=0.568 (0.017%), neg=0, invalid=762 0188: dt=36.288000, rms=0.567 (0.032%), neg=0, invalid=762 0189: dt=36.288000, rms=0.567 (0.056%), neg=0, invalid=762 0190: dt=36.288000, rms=0.567 (0.075%), neg=0, invalid=762 0191: dt=36.288000, rms=0.566 (0.081%), neg=0, invalid=762 0192: dt=36.288000, rms=0.566 (0.094%), neg=0, invalid=762 0193: dt=36.288000, rms=0.565 (0.095%), neg=0, invalid=762 0194: dt=36.288000, rms=0.565 (0.097%), neg=0, invalid=762 0195: dt=36.288000, rms=0.564 (0.100%), neg=0, invalid=762 0196: dt=36.288000, rms=0.564 (0.013%), neg=0, invalid=762 0197: dt=36.288000, rms=0.564 (0.029%), neg=0, invalid=762 0198: dt=18.144000, rms=0.564 (0.006%), neg=0, invalid=762 0199: dt=9.072000, rms=0.564 (0.004%), neg=0, invalid=762 0200: dt=1.620000, rms=0.564 (0.001%), neg=0, invalid=762 0201: dt=0.050625, rms=0.564 (0.000%), neg=0, invalid=762 0202: dt=0.003164, rms=0.564 (0.000%), neg=0, invalid=762 0203: dt=0.000791, rms=0.564 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.564, neg=0, invalid=762 0204: dt=119.560440, rms=0.561 (0.526%), neg=0, invalid=762 0205: dt=68.682927, rms=0.560 (0.168%), neg=0, invalid=762 0206: dt=145.152000, rms=0.560 (0.123%), neg=0, invalid=762 0207: dt=62.208000, rms=0.559 (0.121%), neg=0, invalid=762 0208: dt=82.944000, rms=0.559 (0.050%), neg=0, invalid=762 0209: dt=82.944000, rms=0.558 (0.077%), neg=0, invalid=762 0210: dt=82.944000, rms=0.558 (0.130%), neg=0, invalid=762 0211: dt=82.944000, rms=0.557 (0.104%), neg=0, invalid=762 0212: dt=82.944000, rms=0.556 (0.211%), neg=0, invalid=762 0213: dt=82.944000, rms=0.555 (0.166%), neg=0, invalid=762 0214: dt=82.944000, rms=0.554 (0.151%), neg=0, invalid=762 0215: dt=20.736000, rms=0.554 (0.029%), neg=0, invalid=762 0216: dt=20.736000, rms=0.554 (0.014%), neg=0, invalid=762 0217: dt=10.368000, rms=0.554 (0.004%), neg=0, invalid=762 0218: dt=2.268000, rms=0.554 (0.002%), neg=0, invalid=762 0219: dt=1.134000, rms=0.554 (0.000%), neg=0, invalid=762 0220: dt=0.567000, rms=0.554 (0.000%), neg=0, invalid=762 0221: dt=0.141750, rms=0.554 (0.000%), neg=0, invalid=762 0222: dt=0.002215, rms=0.554 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.560, neg=0, invalid=762 0223: dt=53.806452, rms=0.554 (0.991%), neg=0, invalid=762 0224: dt=54.914573, rms=0.546 (1.497%), neg=0, invalid=762 0225: dt=22.826667, rms=0.542 (0.649%), neg=0, invalid=762 0226: dt=179.200000, rms=0.532 (1.940%), neg=0, invalid=762 0227: dt=32.000000, rms=0.529 (0.593%), neg=0, invalid=762 0228: dt=38.400000, rms=0.527 (0.321%), neg=0, invalid=762 0229: dt=25.600000, rms=0.526 (0.177%), neg=0, invalid=762 0230: dt=44.800000, rms=0.525 (0.252%), neg=0, invalid=762 0231: dt=25.600000, rms=0.524 (0.109%), neg=0, invalid=762 0232: dt=44.800000, rms=0.523 (0.215%), neg=0, invalid=762 0233: dt=8.000000, rms=0.523 (0.049%), neg=0, invalid=762 0234: dt=0.062500, rms=0.523 (0.016%), neg=0, invalid=762 0235: dt=0.031250, rms=0.523 (0.000%), neg=0, invalid=762 0236: dt=0.003906, rms=0.523 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.523, neg=0, invalid=762 0237: dt=38.400000, rms=0.520 (0.619%), neg=0, invalid=762 0238: dt=32.000000, rms=0.518 (0.326%), neg=0, invalid=762 0239: dt=25.600000, rms=0.517 (0.176%), neg=0, invalid=762 0240: dt=44.800000, rms=0.516 (0.213%), neg=0, invalid=762 0241: dt=24.041451, rms=0.516 (0.126%), neg=0, invalid=762 0242: dt=44.800000, rms=0.515 (0.175%), neg=0, invalid=762 0243: dt=11.200000, rms=0.514 (0.077%), neg=0, invalid=762 0244: dt=44.800000, rms=0.514 (0.119%), neg=0, invalid=762 0245: dt=32.000000, rms=0.513 (0.124%), neg=0, invalid=762 0246: dt=19.200000, rms=0.513 (0.071%), neg=0, invalid=762 0247: dt=102.400000, rms=0.512 (0.233%), neg=0, invalid=762 0248: dt=11.200000, rms=0.511 (0.082%), neg=0, invalid=762 0249: dt=25.600000, rms=0.511 (0.069%), neg=0, invalid=762 0250: dt=32.000000, rms=0.510 (0.095%), neg=0, invalid=762 0251: dt=19.200000, rms=0.510 (0.036%), neg=0, invalid=762 0252: dt=19.200000, rms=0.510 (0.069%), neg=0, invalid=762 0253: dt=19.200000, rms=0.509 (0.082%), neg=0, invalid=762 0254: dt=19.200000, rms=0.509 (0.112%), neg=0, invalid=762 0255: dt=19.200000, rms=0.508 (0.141%), neg=0, invalid=762 0256: dt=19.200000, rms=0.507 (0.164%), neg=0, invalid=762 0257: dt=19.200000, rms=0.506 (0.171%), neg=0, invalid=762 0258: dt=19.200000, rms=0.506 (0.175%), neg=0, invalid=762 0259: dt=19.200000, rms=0.505 (0.174%), neg=0, invalid=762 0260: dt=19.200000, rms=0.504 (0.176%), neg=0, invalid=762 0261: dt=19.200000, rms=0.504 (0.022%), neg=0, invalid=762 0262: dt=19.200000, rms=0.503 (0.039%), neg=0, invalid=762 0263: dt=9.600000, rms=0.503 (0.011%), neg=0, invalid=762 0264: dt=4.800000, rms=0.503 (0.003%), neg=0, invalid=762 0265: dt=0.043750, rms=0.503 (0.001%), neg=0, invalid=762 0266: dt=0.043750, rms=0.503 (0.000%), neg=0, invalid=762 0267: dt=0.021875, rms=0.503 (0.000%), neg=0, invalid=762 0268: dt=0.001367, rms=0.503 (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=0.521, neg=0, invalid=762 0269: dt=0.000000, rms=0.521 (0.103%), neg=0, invalid=762 0270: dt=0.000000, rms=0.521 (0.000%), neg=0, invalid=762 0271: dt=0.150000, rms=0.521 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.521, neg=0, invalid=762 0272: dt=0.000000, rms=0.521 (0.103%), neg=0, invalid=762 0273: dt=0.000000, rms=0.521 (0.000%), neg=0, invalid=762 0274: dt=0.150000, rms=0.521 (-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=0.556, neg=0, invalid=762 0275: dt=1.536000, rms=0.553 (0.575%), neg=0, invalid=762 0276: dt=0.112000, rms=0.553 (0.002%), neg=0, invalid=762 0277: dt=0.112000, rms=0.553 (0.000%), neg=0, invalid=762 0278: dt=0.112000, rms=0.553 (-0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.553, neg=0, invalid=762 0279: dt=1.024000, rms=0.552 (0.185%), neg=0, invalid=762 0280: dt=0.112000, rms=0.552 (0.001%), neg=0, invalid=762 0281: dt=0.112000, rms=0.552 (-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=0.514, neg=0, invalid=762 0282: dt=0.448000, rms=0.501 (2.580%), neg=0, invalid=762 0283: dt=0.448000, rms=0.498 (0.602%), neg=0, invalid=762 0284: dt=0.448000, rms=0.496 (0.338%), neg=0, invalid=762 0285: dt=0.448000, rms=0.495 (0.209%), neg=0, invalid=762 0286: dt=0.466667, rms=0.494 (0.163%), neg=0, invalid=762 0287: dt=0.448000, rms=0.494 (0.106%), neg=0, invalid=762 0288: dt=0.448000, rms=0.493 (0.092%), neg=0, invalid=762 0289: dt=0.448000, rms=0.493 (0.064%), neg=0, invalid=762 0290: dt=0.448000, rms=0.493 (0.061%), neg=0, invalid=762 0291: dt=0.448000, rms=0.492 (0.042%), neg=0, invalid=762 0292: dt=0.448000, rms=0.492 (0.042%), neg=0, invalid=762 0293: dt=0.448000, rms=0.492 (0.068%), neg=0, invalid=762 0294: dt=0.448000, rms=0.491 (0.075%), neg=0, invalid=762 0295: dt=0.448000, rms=0.491 (0.079%), neg=0, invalid=762 0296: dt=0.448000, rms=0.491 (0.007%), neg=0, invalid=762 0297: dt=0.448000, rms=0.491 (0.003%), neg=0, invalid=762 0298: dt=0.384000, rms=0.491 (0.004%), neg=0, invalid=762 0299: dt=0.448000, rms=0.491 (0.005%), neg=0, invalid=762 0300: dt=0.112000, rms=0.491 (-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 0301: dt=0.448000, rms=0.487 (1.014%), neg=0, invalid=762 0302: dt=0.448000, rms=0.486 (0.125%), neg=0, invalid=762 0303: dt=0.448000, rms=0.486 (0.034%), neg=0, invalid=762 0304: dt=0.448000, rms=0.486 (0.018%), neg=0, invalid=762 0305: dt=0.448000, rms=0.486 (0.012%), neg=0, invalid=762 0306: dt=0.448000, rms=0.486 (-0.000%), 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=0.484, neg=0, invalid=762 0307: dt=0.000000, rms=0.483 (0.119%), neg=0, invalid=762 0308: dt=0.000000, rms=0.483 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.484, neg=0, invalid=762 0309: dt=129.472000, rms=0.483 (0.147%), neg=0, invalid=762 0310: dt=110.976000, rms=0.483 (0.010%), neg=0, invalid=762 0311: dt=110.976000, rms=0.483 (0.011%), neg=0, invalid=762 0312: dt=110.976000, rms=0.483 (0.018%), neg=0, invalid=762 0313: dt=110.976000, rms=0.483 (0.013%), neg=0, invalid=762 0314: dt=110.976000, rms=0.483 (0.025%), neg=0, invalid=762 0315: dt=110.976000, rms=0.483 (0.013%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0316: dt=9.072000, rms=0.483 (0.127%), neg=0, invalid=762 0317: dt=9.072000, rms=0.483 (0.004%), neg=0, invalid=762 0318: dt=9.072000, rms=0.483 (0.001%), neg=0, invalid=762 0319: dt=9.072000, rms=0.483 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0320: dt=145.152000, rms=0.481 (0.434%), neg=0, invalid=762 0321: dt=36.288000, rms=0.481 (0.123%), neg=0, invalid=762 0322: dt=36.288000, rms=0.480 (0.038%), neg=0, invalid=762 0323: dt=36.288000, rms=0.480 (0.069%), neg=0, invalid=762 0324: dt=36.288000, rms=0.480 (0.085%), neg=0, invalid=762 0325: dt=36.288000, rms=0.479 (0.102%), neg=0, invalid=762 0326: dt=36.288000, rms=0.479 (0.102%), neg=0, invalid=762 0327: dt=36.288000, rms=0.478 (0.099%), neg=0, invalid=762 0328: dt=124.416000, rms=0.478 (0.034%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.479, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0329: dt=25.456869, rms=0.477 (0.432%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0330: dt=44.800000, rms=0.475 (0.438%), neg=0, invalid=762 0331: dt=25.600000, rms=0.474 (0.211%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0332: dt=25.600000, rms=0.472 (0.287%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0333: dt=25.600000, rms=0.471 (0.281%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 11 iterations, nbhd size=1, neg = 0 0334: dt=25.600000, rms=0.470 (0.250%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0335: dt=25.600000, rms=0.469 (0.237%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 10 iterations, nbhd size=1, neg = 0 0336: dt=25.600000, rms=0.468 (0.165%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0337: dt=25.600000, rms=0.467 (0.158%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 12 iterations, nbhd size=1, neg = 0 0338: dt=25.600000, rms=0.467 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 0339: dt=25.600000, rms=0.466 (0.164%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 0340: dt=25.600000, rms=0.465 (0.133%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0341: dt=25.600000, rms=0.465 (0.153%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0342: dt=25.600000, rms=0.464 (0.128%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 11 iterations, nbhd size=1, neg = 0 0343: dt=25.600000, rms=0.463 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0344: dt=25.600000, rms=0.463 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0345: dt=25.600000, rms=0.462 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0346: dt=38.400000, rms=0.462 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0347: dt=38.400000, rms=0.462 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.463, neg=0, invalid=762 iter 0, gcam->neg = 2 after 11 iterations, nbhd size=1, neg = 0 0348: dt=38.400000, rms=0.459 (0.828%), neg=0, invalid=762 0349: dt=25.600000, rms=0.457 (0.287%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0350: dt=32.000000, rms=0.456 (0.265%), neg=0, invalid=762 0351: dt=19.200000, rms=0.456 (0.099%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0352: dt=19.200000, rms=0.455 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0353: dt=19.200000, rms=0.455 (0.140%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0354: dt=19.200000, rms=0.454 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0355: dt=19.200000, rms=0.453 (0.161%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0356: dt=19.200000, rms=0.453 (0.132%), neg=0, invalid=762 0357: dt=19.200000, rms=0.452 (0.087%), neg=0, invalid=762 0358: dt=19.200000, rms=0.452 (0.060%), neg=0, invalid=762 0359: dt=25.600000, rms=0.452 (0.030%), neg=0, invalid=762 0360: dt=25.600000, rms=0.452 (-0.022%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=762 0361: dt=1.008000, rms=0.458 (0.113%), neg=0, invalid=762 0362: dt=0.720000, rms=0.458 (0.011%), neg=0, invalid=762 0363: dt=0.720000, rms=0.458 (0.002%), neg=0, invalid=762 0364: dt=0.720000, rms=0.458 (-0.009%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0365: dt=4.210526, rms=0.458 (0.180%), neg=0, invalid=762 0366: dt=4.000000, rms=0.458 (0.030%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0367: dt=4.000000, rms=0.458 (0.018%), neg=0, invalid=762 0368: dt=4.000000, rms=0.458 (-0.031%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.467, neg=0, invalid=762 0369: dt=0.000050, rms=0.466 (0.128%), neg=0, invalid=762 0370: dt=0.000000, rms=0.466 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=762 0371: dt=1.024000, rms=0.466 (0.209%), neg=0, invalid=762 0372: dt=0.448000, rms=0.466 (0.013%), neg=0, invalid=762 0373: dt=0.448000, rms=0.466 (-0.002%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 iter 0, gcam->neg = 696 after 11 iterations, nbhd size=1, neg = 0 0374: dt=2.078525, rms=0.428 (6.124%), neg=0, invalid=762 0375: dt=0.028000, rms=0.428 (0.014%), neg=0, invalid=762 0376: dt=0.028000, rms=0.428 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=762 0377: dt=0.080000, rms=0.428 (0.218%), neg=0, invalid=762 0378: dt=0.000000, rms=0.428 (0.002%), neg=0, invalid=762 0379: dt=0.050000, rms=0.428 (-0.019%), 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=0.415, neg=0, invalid=762 0380: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=762 0381: dt=32.368000, rms=0.415 (0.006%), neg=0, invalid=762 0382: dt=32.368000, rms=0.415 (0.001%), neg=0, invalid=762 0383: dt=32.368000, rms=0.415 (0.000%), neg=0, invalid=762 0384: dt=32.368000, rms=0.415 (-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=0.415, neg=0, invalid=762 0385: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=762 0386: dt=36.288000, rms=0.415 (0.025%), neg=0, invalid=762 0387: dt=124.416000, rms=0.414 (0.027%), neg=0, invalid=762 0388: dt=248.832000, rms=0.414 (0.071%), neg=0, invalid=762 0389: dt=31.104000, rms=0.414 (0.007%), neg=0, invalid=762 0390: dt=31.104000, rms=0.414 (0.002%), neg=0, invalid=762 0391: dt=31.104000, rms=0.414 (0.001%), neg=0, invalid=762 0392: dt=31.104000, rms=0.414 (0.004%), neg=0, invalid=762 0393: dt=31.104000, rms=0.414 (0.012%), neg=0, invalid=762 0394: dt=31.104000, rms=0.414 (0.019%), neg=0, invalid=762 0395: dt=31.104000, rms=0.414 (0.020%), neg=0, invalid=762 0396: dt=31.104000, rms=0.414 (0.016%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.414, neg=0, invalid=762 0397: dt=2.800000, rms=0.414 (0.009%), neg=0, invalid=762 0398: dt=2.800000, rms=0.414 (0.003%), neg=0, invalid=762 0399: dt=2.800000, rms=0.414 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.414, neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0400: dt=102.400000, rms=0.412 (0.642%), neg=0, invalid=762 0401: dt=25.600000, rms=0.411 (0.241%), neg=0, invalid=762 0402: dt=25.600000, rms=0.411 (0.071%), neg=0, invalid=762 0403: dt=25.600000, rms=0.410 (0.100%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0404: dt=25.600000, rms=0.409 (0.163%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0405: dt=25.600000, rms=0.409 (0.153%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 10 iterations, nbhd size=1, neg = 0 0406: dt=25.600000, rms=0.408 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 0407: dt=25.600000, rms=0.407 (0.151%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0408: dt=25.600000, rms=0.407 (0.135%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 15 iterations, nbhd size=1, neg = 0 0409: dt=25.600000, rms=0.406 (0.110%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 11 iterations, nbhd size=1, neg = 0 0410: dt=25.600000, rms=0.406 (0.092%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0411: dt=19.200000, rms=0.406 (0.010%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0412: dt=19.200000, rms=0.406 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0413: dt=19.200000, rms=0.406 (0.007%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0414: dt=19.200000, rms=0.406 (0.004%), neg=0, invalid=762 0415: dt=19.200000, rms=0.406 (0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 0416: dt=0.252000, rms=0.410 (0.000%), neg=0, invalid=762 0417: dt=0.027000, rms=0.410 (0.000%), neg=0, invalid=762 0418: dt=0.027000, rms=0.410 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 0419: dt=7.142857, rms=0.410 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0420: dt=11.076923, rms=0.409 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0421: dt=11.076923, rms=0.409 (0.086%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 5 iterations, nbhd size=0, neg = 0 0422: dt=11.076923, rms=0.409 (0.097%), neg=0, invalid=762 iter 0, gcam->neg = 30 after 6 iterations, nbhd size=0, neg = 0 0423: dt=11.076923, rms=0.408 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 6 iterations, nbhd size=0, neg = 0 0424: dt=11.076923, rms=0.408 (0.165%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 12 iterations, nbhd size=1, neg = 0 0425: dt=11.076923, rms=0.407 (0.208%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 10 iterations, nbhd size=0, neg = 0 0426: dt=11.076923, rms=0.406 (0.205%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 18 iterations, nbhd size=1, neg = 0 0427: dt=11.076923, rms=0.405 (0.099%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 14 iterations, nbhd size=1, neg = 0 0428: dt=11.076923, rms=0.405 (-0.007%), neg=0, invalid=762 0429: dt=0.001688, rms=0.405 (0.000%), neg=0, invalid=762 0430: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.412, neg=0, invalid=762 0431: dt=0.000000, 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 0432: dt=0.000000, rms=0.412 (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=0.401, neg=0, invalid=762 iter 0, gcam->neg = 558 after 15 iterations, nbhd size=1, neg = 0 0433: dt=1.280000, rms=0.392 (2.245%), neg=0, invalid=762 0434: dt=0.000023, rms=0.392 (0.000%), neg=0, invalid=762 0435: dt=0.000023, rms=0.392 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=762 0436: dt=0.080000, rms=0.392 (0.032%), neg=0, invalid=762 0437: dt=0.028000, rms=0.392 (0.006%), neg=0, invalid=762 0438: dt=0.028000, rms=0.392 (0.003%), neg=0, invalid=762 0439: dt=0.028000, rms=0.392 (-0.004%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 16 minutes and 44 seconds. mri_ca_register utimesec 9065.639813 mri_ca_register stimesec 8.306737 mri_ca_register ru_maxrss 1334100 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4297014 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 62752 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 4035 mri_ca_register ru_nivcsw 17829 FSRUNTIME@ mri_ca_register 2.2788 hours 2 threads #-------------------------------------- #@# SubCort Seg Sun Oct 8 02:32:19 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-593 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-6.0.0/0050340/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 6.21 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 = 0.06061 (22) Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (179 voxels, overlap=0.669) Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (179 voxels, peak = 19), gca=19.3 gca peak = 0.17677 (13) mri peak = 0.08093 (43) Right_Lateral_Ventricle (43): linear fit = 3.04 x + 0.0 (173 voxels, overlap=0.325) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (173 voxels, peak = 39), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.11229 (90) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (511 voxels, overlap=0.730) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (511 voxels, peak = 91), gca=90.7 gca peak = 0.16930 (96) mri peak = 0.10454 (91) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (504 voxels, overlap=0.870) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (504 voxels, peak = 93), gca=92.6 gca peak = 0.24553 (55) mri peak = 0.09619 (66) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (995 voxels, overlap=0.440) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (995 voxels, peak = 64), gca=63.5 gca peak = 0.30264 (59) mri peak = 0.09011 (67) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (905 voxels, overlap=0.133) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (905 voxels, peak = 67), gca=67.0 gca peak = 0.07580 (103) mri peak = 0.09097 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36647 voxels, overlap=0.824) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36647 voxels, peak = 102), gca=102.5 gca peak = 0.07714 (104) mri peak = 0.09083 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38403 voxels, overlap=0.704) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38403 voxels, peak = 105), gca=104.5 gca peak = 0.09712 (58) mri peak = 0.04402 (62) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (32425 voxels, overlap=0.913) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (32425 voxels, peak = 62), gca=62.4 gca peak = 0.11620 (58) mri peak = 0.04639 (62) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (31653 voxels, overlap=0.944) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (31653 voxels, peak = 61), gca=60.6 gca peak = 0.30970 (66) mri peak = 0.09662 (72) Right_Caudate (50): linear fit = 1.10 x + 0.0 (908 voxels, overlap=0.915) Right_Caudate (50): linear fit = 1.10 x + 0.0 (908 voxels, peak = 72), gca=72.3 gca peak = 0.15280 (69) mri peak = 0.10964 (75) Left_Caudate (11): linear fit = 1.01 x + 0.0 (785 voxels, overlap=1.001) Left_Caudate (11): linear fit = 1.01 x + 0.0 (785 voxels, peak = 70), gca=70.0 gca peak = 0.13902 (56) mri peak = 0.04659 (64) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (27072 voxels, overlap=0.864) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (27072 voxels, peak = 64), gca=63.6 gca peak = 0.14777 (55) mri peak = 0.04750 (63) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (27323 voxels, overlap=0.940) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (27323 voxels, peak = 62), gca=62.4 gca peak = 0.16765 (84) mri peak = 0.10334 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5858 voxels, overlap=0.729) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5858 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.08722 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5855 voxels, overlap=0.910) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5855 voxels, peak = 86), gca=86.1 gca peak = 0.29869 (57) mri peak = 0.09622 (75) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (575 voxels, overlap=0.057) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (575 voxels, peak = 74), gca=73.8 gca peak = 0.33601 (57) mri peak = 0.09966 (72) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (582 voxels, overlap=0.046) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (582 voxels, peak = 70), gca=70.4 gca peak = 0.11131 (90) mri peak = 0.07930 (88) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4616 voxels, overlap=0.995) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4616 voxels, peak = 88), gca=87.8 gca peak = 0.11793 (83) mri peak = 0.07779 (87) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4518 voxels, overlap=0.978) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4518 voxels, peak = 84), gca=84.2 gca peak = 0.08324 (81) mri peak = 0.07834 (79) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2071 voxels, overlap=0.905) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2071 voxels, peak = 81), gca=81.0 gca peak = 0.10360 (77) mri peak = 0.07224 (78) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1842 voxels, overlap=0.950) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1842 voxels, peak = 76), gca=75.8 gca peak = 0.08424 (78) mri peak = 0.07832 (87) Brain_Stem (16): linear fit = 1.11 x + 0.0 (11209 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.11 x + 0.0 (11209 voxels, peak = 86), gca=86.2 gca peak = 0.12631 (89) mri peak = 0.08616 (91) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1526 voxels, overlap=0.568) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1526 voxels, peak = 97), gca=96.6 gca peak = 0.14500 (87) mri peak = 0.08124 (92) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1663 voxels, overlap=0.583) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1663 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19357 (14) mri peak = 0.21461 (14) Fourth_Ventricle (15): linear fit = 0.83 x + 0.0 (323 voxels, overlap=0.642) Fourth_Ventricle (15): linear fit = 0.83 x + 0.0 (323 voxels, peak = 12), gca=11.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.16 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.10 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14846 (20) mri peak = 0.06061 (22) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (179 voxels, overlap=0.708) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (179 voxels, peak = 20), gca=20.5 gca peak = 0.13423 (19) mri peak = 0.08093 (43) Right_Lateral_Ventricle (43): linear fit = 1.82 x + 0.0 (173 voxels, overlap=0.337) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (173 voxels, peak = 34), gca=28.5 gca peak = 0.25462 (90) mri peak = 0.11229 (90) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (511 voxels, overlap=1.005) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (511 voxels, peak = 90), gca=89.6 gca peak = 0.20088 (93) mri peak = 0.10454 (91) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (504 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (504 voxels, peak = 93), gca=92.5 gca peak = 0.24791 (64) mri peak = 0.09619 (66) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (995 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (995 voxels, peak = 64), gca=64.0 gca peak = 0.28088 (67) mri peak = 0.09011 (67) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (905 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (905 voxels, peak = 66), gca=66.0 gca peak = 0.07831 (102) mri peak = 0.09097 (101) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (36647 voxels, overlap=0.804) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (36647 voxels, peak = 104), gca=103.5 gca peak = 0.07908 (105) mri peak = 0.09083 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38403 voxels, overlap=0.724) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38403 voxels, peak = 105), gca=105.0 gca peak = 0.09089 (62) mri peak = 0.04402 (62) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (32425 voxels, overlap=0.984) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (32425 voxels, peak = 64), gca=63.5 gca peak = 0.11303 (61) mri peak = 0.04639 (62) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (31653 voxels, overlap=0.972) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (31653 voxels, peak = 63), gca=62.5 gca peak = 0.25723 (73) mri peak = 0.09662 (72) Right_Caudate (50): linear fit = 0.99 x + 0.0 (908 voxels, overlap=1.008) Right_Caudate (50): linear fit = 0.99 x + 0.0 (908 voxels, peak = 72), gca=71.9 gca peak = 0.15451 (70) mri peak = 0.10964 (75) Left_Caudate (11): linear fit = 1.00 x + 0.0 (785 voxels, overlap=1.002) Left_Caudate (11): linear fit = 1.00 x + 0.0 (785 voxels, peak = 70), gca=70.0 gca peak = 0.12644 (63) mri peak = 0.04659 (64) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (27072 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (27072 voxels, peak = 62), gca=62.1 gca peak = 0.13587 (62) mri peak = 0.04750 (63) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27323 voxels, overlap=0.982) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27323 voxels, peak = 61), gca=61.1 gca peak = 0.15888 (90) mri peak = 0.10334 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5858 voxels, overlap=0.959) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5858 voxels, peak = 90), gca=89.6 gca peak = 0.15827 (86) mri peak = 0.08722 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5855 voxels, overlap=0.966) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5855 voxels, peak = 86), gca=85.6 gca peak = 0.24884 (74) mri peak = 0.09622 (75) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (575 voxels, overlap=0.981) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (575 voxels, peak = 74), gca=74.0 gca peak = 0.29264 (70) mri peak = 0.09966 (72) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (582 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (582 voxels, peak = 72), gca=72.4 gca peak = 0.11017 (86) mri peak = 0.07930 (88) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4616 voxels, overlap=0.995) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4616 voxels, peak = 86), gca=86.0 gca peak = 0.11084 (82) mri peak = 0.07779 (87) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4518 voxels, overlap=0.993) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4518 voxels, peak = 82), gca=81.6 gca peak = 0.08324 (81) mri peak = 0.07834 (79) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2071 voxels, overlap=0.906) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2071 voxels, peak = 81), gca=81.0 gca peak = 0.09873 (76) mri peak = 0.07224 (78) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1842 voxels, overlap=0.939) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1842 voxels, peak = 77), gca=77.1 gca peak = 0.07464 (89) mri peak = 0.07832 (87) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11209 voxels, overlap=0.847) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11209 voxels, peak = 89), gca=88.6 gca peak = 0.11849 (95) mri peak = 0.08616 (91) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1526 voxels, overlap=0.772) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1526 voxels, peak = 95), gca=94.5 gca peak = 0.17000 (92) mri peak = 0.08124 (92) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1663 voxels, overlap=0.888) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1663 voxels, peak = 90), gca=89.7 gca peak = 0.16787 (28) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24326 (13) mri peak = 0.21461 (14) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (323 voxels, overlap=0.795) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (323 voxels, peak = 14), gca=14.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.15127 (30) gca peak Left_Thalamus = 0.36646 (102) gca peak Third_Ventricle = 0.16787 (28) gca peak CSF = 0.24269 (40) gca peak Left_Accumbens_area = 0.76968 (63) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11917 (35) gca peak Right_Inf_Lat_Vent = 0.18678 (27) gca peak Right_Accumbens_area = 0.29943 (71) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14511 (37) gca peak Fifth_Ventricle = 0.65358 (35) gca peak WM_hypointensities = 0.07957 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71063 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.21 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 54951 voxels changed in iteration 0 of unlikely voxel relabeling 272 voxels changed in iteration 1 of unlikely voxel relabeling 23 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 34476 gm and wm labels changed (%32 to gray, %68 to white out of all changed labels) 278 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 61412 changed. image ll: -2.087, PF=0.500 pass 2: 17272 changed. image ll: -2.086, PF=0.500 pass 3: 5205 changed. pass 4: 1884 changed. 38058 voxels changed in iteration 0 of unlikely voxel relabeling 281 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5954 voxels changed in iteration 0 of unlikely voxel relabeling 91 voxels changed in iteration 1 of unlikely voxel relabeling 10 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5152 voxels changed in iteration 0 of unlikely voxel relabeling 60 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4246 voxels changed in iteration 0 of unlikely voxel relabeling 32 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 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 3294.989085 mri_ca_label stimesec 2.100680 mri_ca_label ru_maxrss 2097412 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 682051 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 62744 mri_ca_label ru_oublock 448 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 256 mri_ca_label ru_nivcsw 4136 auto-labeling took 54 minutes and 10 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/transforms/cc_up.lta 0050340 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-6.0.0/0050340/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/norm.mgz 30148 voxels in left wm, 84415 in right wm, xrange [114, 127] searching rotation angles z=[-9 5], y=[-9 5] searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.2 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 global minimum found at slice 123.2, rotations (-2.09, -2.47) final transformation (x=123.2, yr=-2.091, zr=-2.470): 0.99841 0.04310 -0.03646 4.95386; -0.04307 0.99907 0.00157 27.20911; 0.03649 -0.00000 0.99933 0.58773; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 106 123 eigenvectors: -0.00241 -0.01237 0.99992; 0.05919 -0.99817 -0.01220; 0.99824 0.05916 0.00314; writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aseg.auto.mgz... corpus callosum segmentation took 1.2 minutes #-------------------------------------- #@# Merge ASeg Sun Oct 8 03:27:42 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sun Oct 8 03:27:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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... 1012 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 109 gm peak at 65 (65), valley at 33 (33) csf peak at 33, setting threshold to 54 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 65 (65), valley at 32 (32) csf peak at 33, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 55 seconds. #-------------------------------------------- #@# Mask BFS Sun Oct 8 03:30:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1434058 voxels in mask (pct= 8.55) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sun Oct 8 03:30:40 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 (103.0): 103.0 +- 6.4 [79.0 --> 125.0] GM (73.0) : 71.2 +- 10.0 [30.0 --> 95.0] setting bottom of white matter range to 81.1 setting top of gray matter range to 91.1 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... 4187 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3135 filled 1864 bright non-wm voxels segmented. 2164 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 0.53 minutes reading wm segmentation from wm.seg.mgz... 599 voxels added to wm to prevent paths from MTL structures to cortex 2371 additional wm voxels added 0 additional wm voxels added SEG EDIT: 29829 voxels turned on, 41852 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 15 found - 15 modified | TOTAL: 15 pass 2 (xy+): 0 found - 15 modified | TOTAL: 15 pass 1 (xy-): 17 found - 17 modified | TOTAL: 32 pass 2 (xy-): 0 found - 17 modified | TOTAL: 32 pass 1 (yz+): 14 found - 14 modified | TOTAL: 46 pass 2 (yz+): 0 found - 14 modified | TOTAL: 46 pass 1 (yz-): 22 found - 22 modified | TOTAL: 68 pass 2 (yz-): 0 found - 22 modified | TOTAL: 68 pass 1 (xz+): 17 found - 17 modified | TOTAL: 85 pass 2 (xz+): 0 found - 17 modified | TOTAL: 85 pass 1 (xz-): 15 found - 15 modified | TOTAL: 100 pass 2 (xz-): 0 found - 15 modified | TOTAL: 100 Iteration Number : 1 pass 1 (+++): 23 found - 23 modified | TOTAL: 23 pass 2 (+++): 0 found - 23 modified | TOTAL: 23 pass 1 (+++): 22 found - 22 modified | TOTAL: 45 pass 2 (+++): 0 found - 22 modified | TOTAL: 45 pass 1 (+++): 19 found - 19 modified | TOTAL: 64 pass 2 (+++): 0 found - 19 modified | TOTAL: 64 pass 1 (+++): 20 found - 20 modified | TOTAL: 84 pass 2 (+++): 0 found - 20 modified | TOTAL: 84 Iteration Number : 1 pass 1 (++): 47 found - 47 modified | TOTAL: 47 pass 2 (++): 0 found - 47 modified | TOTAL: 47 pass 1 (+-): 49 found - 49 modified | TOTAL: 96 pass 2 (+-): 0 found - 49 modified | TOTAL: 96 pass 1 (--): 62 found - 62 modified | TOTAL: 158 pass 2 (--): 0 found - 62 modified | TOTAL: 158 pass 1 (-+): 43 found - 43 modified | TOTAL: 201 pass 2 (-+): 0 found - 43 modified | TOTAL: 201 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 2 found - 2 modified | TOTAL: 5 pass 2 (xy-): 0 found - 2 modified | TOTAL: 5 pass 1 (yz+): 4 found - 4 modified | TOTAL: 9 pass 2 (yz+): 0 found - 4 modified | TOTAL: 9 pass 1 (yz-): 8 found - 8 modified | TOTAL: 17 pass 2 (yz-): 0 found - 8 modified | TOTAL: 17 pass 1 (xz+): 3 found - 3 modified | TOTAL: 20 pass 2 (xz+): 0 found - 3 modified | TOTAL: 20 pass 1 (xz-): 3 found - 3 modified | TOTAL: 23 pass 2 (xz-): 0 found - 3 modified | TOTAL: 23 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 Iteration Number : 2 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 0 found - 0 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 2 found - 2 modified | TOTAL: 6 pass 2 (-+): 0 found - 2 modified | TOTAL: 6 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 422 (out of 494954: 0.085260) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sun Oct 8 03:32:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 1.07230 -0.00181 -0.03731 -0.61850; -0.00532 1.18308 0.09912 -41.13858; 0.03495 -0.11142 1.00566 -7.13951; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.07230 -0.00181 -0.03731 -0.61850; -0.00532 1.18308 0.09912 -41.13858; 0.03495 -0.11142 1.00566 -7.13951; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1025 (min = 350, max = 1400), aspect = 0.59 (min = 0.10, max = 0.75) no need to search using seed (126, 124, 150), TAL = (2.0, 22.0, 4.0) talairach voxel to voxel transform 0.93148 0.00464 0.03410 1.01048; 0.00684 0.83751 -0.08230 33.87076; -0.03162 0.09263 0.98407 10.81677; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 124, 150) --> (2.0, 22.0, 4.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (2.00, 22.00, 4.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 22.00, 4.00) SRC: (107.30, 126.12, 166.50) search lh wm seed point around talairach space (-16.00, 22.00, 4.00), SRC: (140.83, 126.36, 165.36) 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 03:33:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 4 found - 4 modified | TOTAL: 4 pass 2 (xy-): 0 found - 4 modified | TOTAL: 4 pass 1 (yz+): 7 found - 7 modified | TOTAL: 11 pass 2 (yz+): 0 found - 7 modified | TOTAL: 11 pass 1 (yz-): 0 found - 0 modified | TOTAL: 11 pass 1 (xz+): 2 found - 2 modified | TOTAL: 13 pass 2 (xz+): 0 found - 2 modified | TOTAL: 13 pass 1 (xz-): 1 found - 1 modified | TOTAL: 14 pass 2 (xz-): 0 found - 1 modified | TOTAL: 14 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 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 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 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 = 16 (out of 239828: 0.006671) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 787 vertices, 890 faces slice 60: 5514 vertices, 5712 faces slice 70: 12242 vertices, 12482 faces slice 80: 19881 vertices, 20184 faces slice 90: 28648 vertices, 29000 faces slice 100: 38060 vertices, 38398 faces slice 110: 48321 vertices, 48696 faces slice 120: 59435 vertices, 59822 faces slice 130: 70342 vertices, 70738 faces slice 140: 81018 vertices, 81449 faces slice 150: 91371 vertices, 91757 faces slice 160: 99522 vertices, 99874 faces slice 170: 106595 vertices, 106935 faces slice 180: 113091 vertices, 113384 faces slice 190: 118535 vertices, 118781 faces slice 200: 122980 vertices, 123192 faces slice 210: 124943 vertices, 125045 faces slice 220: 124968 vertices, 125060 faces slice 230: 124968 vertices, 125060 faces slice 240: 124968 vertices, 125060 faces slice 250: 124968 vertices, 125060 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... 124968 voxel in cpt #1: X=-92 [v=124968,e=375180,f=250120] located at (-20.971233, -5.387883, 5.483764) For the whole surface: X=-92 [v=124968,e=375180,f=250120] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sun Oct 8 03:33:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 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 = 3 (out of 235717: 0.001273) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 581 vertices, 641 faces slice 60: 3873 vertices, 4036 faces slice 70: 10230 vertices, 10471 faces slice 80: 18138 vertices, 18446 faces slice 90: 26579 vertices, 26906 faces slice 100: 36547 vertices, 36887 faces slice 110: 46973 vertices, 47374 faces slice 120: 57882 vertices, 58267 faces slice 130: 68735 vertices, 69131 faces slice 140: 79728 vertices, 80161 faces slice 150: 90023 vertices, 90416 faces slice 160: 98279 vertices, 98641 faces slice 170: 105186 vertices, 105520 faces slice 180: 111657 vertices, 111972 faces slice 190: 117191 vertices, 117462 faces slice 200: 121583 vertices, 121815 faces slice 210: 123462 vertices, 123566 faces slice 220: 123462 vertices, 123566 faces slice 230: 123462 vertices, 123566 faces slice 240: 123462 vertices, 123566 faces slice 250: 123462 vertices, 123566 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... 123462 voxel in cpt #1: X=-104 [v=123462,e=370698,f=247132] located at (31.876286, -4.478074, 9.574388) For the whole surface: X=-104 [v=123462,e=370698,f=247132] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sun Oct 8 03:33:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sun Oct 8 03:33:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 24419 of (24419 24422) to complete... Waiting for PID 24422 of (24419 24422) 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 (24419 24422) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sun Oct 8 03:33:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sun Oct 8 03:33:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 24467 of (24467 24470) to complete... Waiting for PID 24470 of (24467 24470) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 45.7 mm, total surface area = 66573 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.160 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.084 (target=0.015) step 020: RMS=0.074 (target=0.015) step 025: RMS=0.069 (target=0.015) step 030: RMS=0.063 (target=0.015) step 035: RMS=0.059 (target=0.015) step 040: RMS=0.057 (target=0.015) step 045: RMS=0.055 (target=0.015) step 050: RMS=0.055 (target=0.015) step 055: RMS=0.054 (target=0.015) step 060: RMS=0.054 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 39.250033 mris_inflate stimesec 0.101984 mris_inflate ru_maxrss 183332 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 26862 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8816 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2141 mris_inflate ru_nivcsw 3069 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 44.8 mm, total surface area = 65650 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.160 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.097 (target=0.015) step 015: RMS=0.084 (target=0.015) step 020: RMS=0.075 (target=0.015) step 025: RMS=0.068 (target=0.015) step 030: RMS=0.063 (target=0.015) step 035: RMS=0.058 (target=0.015) step 040: RMS=0.056 (target=0.015) step 045: RMS=0.054 (target=0.015) step 050: RMS=0.054 (target=0.015) step 055: RMS=0.053 (target=0.015) step 060: RMS=0.052 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 39.031066 mris_inflate stimesec 0.088986 mris_inflate ru_maxrss 181220 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 26333 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8688 mris_inflate ru_oublock 8712 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1948 mris_inflate ru_nivcsw 3063 PIDs (24467 24470) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sun Oct 8 03:34:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sun Oct 8 03:34:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 24538 of (24538 24541) to complete... Waiting for PID 24541 of (24538 24541) 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 1.02 +- 0.60 (0.00-->6.41) (max @ vno 44761 --> 45743) face area 0.03 +- 0.03 (-0.14-->0.50) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.310... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.508, avgs=0 005/300: dt: 0.9000, rms radial error=177.247, avgs=0 010/300: dt: 0.9000, rms radial error=176.686, avgs=0 015/300: dt: 0.9000, rms radial error=175.949, avgs=0 020/300: dt: 0.9000, rms radial error=175.110, avgs=0 025/300: dt: 0.9000, rms radial error=174.217, avgs=0 030/300: dt: 0.9000, rms radial error=173.295, avgs=0 035/300: dt: 0.9000, rms radial error=172.355, avgs=0 040/300: dt: 0.9000, rms radial error=171.409, avgs=0 045/300: dt: 0.9000, rms radial error=170.460, avgs=0 050/300: dt: 0.9000, rms radial error=169.512, avgs=0 055/300: dt: 0.9000, rms radial error=168.566, avgs=0 060/300: dt: 0.9000, rms radial error=167.624, avgs=0 065/300: dt: 0.9000, rms radial error=166.686, avgs=0 070/300: dt: 0.9000, rms radial error=165.753, avgs=0 075/300: dt: 0.9000, rms radial error=164.824, avgs=0 080/300: dt: 0.9000, rms radial error=163.900, avgs=0 085/300: dt: 0.9000, rms radial error=162.980, avgs=0 090/300: dt: 0.9000, rms radial error=162.066, avgs=0 095/300: dt: 0.9000, rms radial error=161.156, avgs=0 100/300: dt: 0.9000, rms radial error=160.251, avgs=0 105/300: dt: 0.9000, rms radial error=159.351, avgs=0 110/300: dt: 0.9000, rms radial error=158.455, avgs=0 115/300: dt: 0.9000, rms radial error=157.564, avgs=0 120/300: dt: 0.9000, rms radial error=156.678, avgs=0 125/300: dt: 0.9000, rms radial error=155.797, avgs=0 130/300: dt: 0.9000, rms radial error=154.921, avgs=0 135/300: dt: 0.9000, rms radial error=154.050, avgs=0 140/300: dt: 0.9000, rms radial error=153.183, avgs=0 145/300: dt: 0.9000, rms radial error=152.321, avgs=0 150/300: dt: 0.9000, rms radial error=151.464, avgs=0 155/300: dt: 0.9000, rms radial error=150.611, avgs=0 160/300: dt: 0.9000, rms radial error=149.763, avgs=0 165/300: dt: 0.9000, rms radial error=148.919, avgs=0 170/300: dt: 0.9000, rms radial error=148.081, avgs=0 175/300: dt: 0.9000, rms radial error=147.246, avgs=0 180/300: dt: 0.9000, rms radial error=146.417, avgs=0 185/300: dt: 0.9000, rms radial error=145.592, avgs=0 190/300: dt: 0.9000, rms radial error=144.771, avgs=0 195/300: dt: 0.9000, rms radial error=143.955, avgs=0 200/300: dt: 0.9000, rms radial error=143.144, avgs=0 205/300: dt: 0.9000, rms radial error=142.337, avgs=0 210/300: dt: 0.9000, rms radial error=141.534, avgs=0 215/300: dt: 0.9000, rms radial error=140.736, avgs=0 220/300: dt: 0.9000, rms radial error=139.942, avgs=0 225/300: dt: 0.9000, rms radial error=139.153, avgs=0 230/300: dt: 0.9000, rms radial error=138.368, avgs=0 235/300: dt: 0.9000, rms radial error=137.587, avgs=0 240/300: dt: 0.9000, rms radial error=136.811, avgs=0 245/300: dt: 0.9000, rms radial error=136.039, avgs=0 250/300: dt: 0.9000, rms radial error=135.271, avgs=0 255/300: dt: 0.9000, rms radial error=134.508, avgs=0 260/300: dt: 0.9000, rms radial error=133.749, avgs=0 265/300: dt: 0.9000, rms radial error=132.994, avgs=0 270/300: dt: 0.9000, rms radial error=132.243, avgs=0 275/300: dt: 0.9000, rms radial error=131.497, avgs=0 280/300: dt: 0.9000, rms radial error=130.754, avgs=0 285/300: dt: 0.9000, rms radial error=130.016, avgs=0 290/300: dt: 0.9000, rms radial error=129.282, avgs=0 295/300: dt: 0.9000, rms radial error=128.552, avgs=0 300/300: dt: 0.9000, rms radial error=127.827, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14622.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2458.43 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 3 (K=160.0), pass 1, starting sse = 271.43 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00624 epoch 4 (K=640.0), pass 1, starting sse = 24.56 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/13 = 0.00931 final distance error %27.23 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 230.699928 mris_sphere stimesec 0.170974 mris_sphere ru_maxrss 183532 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 26916 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 8800 mris_sphere ru_oublock 8840 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8618 mris_sphere ru_nivcsw 16609 FSRUNTIME@ mris_sphere 0.0641 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 1.03 +- 0.59 (0.00-->7.14) (max @ vno 51164 --> 52368) face area 0.03 +- 0.03 (-0.32-->0.77) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.311... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.637, avgs=0 005/300: dt: 0.9000, rms radial error=177.376, avgs=0 010/300: dt: 0.9000, rms radial error=176.817, avgs=0 015/300: dt: 0.9000, rms radial error=176.082, avgs=0 020/300: dt: 0.9000, rms radial error=175.244, avgs=0 025/300: dt: 0.9000, rms radial error=174.349, avgs=0 030/300: dt: 0.9000, rms radial error=173.420, avgs=0 035/300: dt: 0.9000, rms radial error=172.474, avgs=0 040/300: dt: 0.9000, rms radial error=171.524, avgs=0 045/300: dt: 0.9000, rms radial error=170.573, avgs=0 050/300: dt: 0.9000, rms radial error=169.621, avgs=0 055/300: dt: 0.9000, rms radial error=168.673, avgs=0 060/300: dt: 0.9000, rms radial error=167.728, avgs=0 065/300: dt: 0.9000, rms radial error=166.787, avgs=0 070/300: dt: 0.9000, rms radial error=165.851, avgs=0 075/300: dt: 0.9000, rms radial error=164.919, avgs=0 080/300: dt: 0.9000, rms radial error=163.992, avgs=0 085/300: dt: 0.9000, rms radial error=163.070, avgs=0 090/300: dt: 0.9000, rms radial error=162.153, avgs=0 095/300: dt: 0.9000, rms radial error=161.241, avgs=0 100/300: dt: 0.9000, rms radial error=160.334, avgs=0 105/300: dt: 0.9000, rms radial error=159.432, avgs=0 110/300: dt: 0.9000, rms radial error=158.535, avgs=0 115/300: dt: 0.9000, rms radial error=157.642, avgs=0 120/300: dt: 0.9000, rms radial error=156.755, avgs=0 125/300: dt: 0.9000, rms radial error=155.872, avgs=0 130/300: dt: 0.9000, rms radial error=154.994, avgs=0 135/300: dt: 0.9000, rms radial error=154.121, avgs=0 140/300: dt: 0.9000, rms radial error=153.253, avgs=0 145/300: dt: 0.9000, rms radial error=152.389, avgs=0 150/300: dt: 0.9000, rms radial error=151.531, avgs=0 155/300: dt: 0.9000, rms radial error=150.677, avgs=0 160/300: dt: 0.9000, rms radial error=149.828, avgs=0 165/300: dt: 0.9000, rms radial error=148.984, avgs=0 170/300: dt: 0.9000, rms radial error=148.144, avgs=0 175/300: dt: 0.9000, rms radial error=147.309, avgs=0 180/300: dt: 0.9000, rms radial error=146.479, avgs=0 185/300: dt: 0.9000, rms radial error=145.653, avgs=0 190/300: dt: 0.9000, rms radial error=144.832, avgs=0 195/300: dt: 0.9000, rms radial error=144.015, avgs=0 200/300: dt: 0.9000, rms radial error=143.203, avgs=0 205/300: dt: 0.9000, rms radial error=142.395, avgs=0 210/300: dt: 0.9000, rms radial error=141.592, avgs=0 215/300: dt: 0.9000, rms radial error=140.794, avgs=0 220/300: dt: 0.9000, rms radial error=140.000, avgs=0 225/300: dt: 0.9000, rms radial error=139.210, avgs=0 230/300: dt: 0.9000, rms radial error=138.424, avgs=0 235/300: dt: 0.9000, rms radial error=137.644, avgs=0 240/300: dt: 0.9000, rms radial error=136.867, avgs=0 245/300: dt: 0.9000, rms radial error=136.095, avgs=0 250/300: dt: 0.9000, rms radial error=135.327, avgs=0 255/300: dt: 0.9000, rms radial error=134.563, avgs=0 260/300: dt: 0.9000, rms radial error=133.804, avgs=0 265/300: dt: 0.9000, rms radial error=133.049, avgs=0 270/300: dt: 0.9000, rms radial error=132.298, avgs=0 275/300: dt: 0.9000, rms radial error=131.551, avgs=0 280/300: dt: 0.9000, rms radial error=130.809, avgs=0 285/300: dt: 0.9000, rms radial error=130.070, avgs=0 290/300: dt: 0.9000, rms radial error=129.336, avgs=0 295/300: dt: 0.9000, rms radial error=128.606, avgs=0 300/300: dt: 0.9000, rms radial error=127.880, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14404.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 2387.69 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 3 (K=160.0), pass 1, starting sse = 253.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00535 epoch 4 (K=640.0), pass 1, starting sse = 23.20 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/14 = 0.00944 final distance error %26.27 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 231.958736 mris_sphere stimesec 0.164974 mris_sphere ru_maxrss 181424 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 26390 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 8696 mris_sphere ru_oublock 8736 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8905 mris_sphere ru_nivcsw 16881 FSRUNTIME@ mris_sphere 0.0644 hours 1 threads PIDs (24538 24541) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sun Oct 8 03:38:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sun Oct 8 03:38:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sun Oct 8 03:38:12 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050340 lh #@# Fix Topology rh Sun Oct 8 03:38:12 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050340 rh Waiting for PID 24728 of (24728 24731) to complete... Waiting for PID 24731 of (24728 24731) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050340 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=-92 (nv=124968, nf=250120, ne=375180, g=47) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 7832 ambiguous faces found in tessellation segmenting defects... 55 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 5 -merging segment 7 into 5 -merging segment 27 into 22 52 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0920 (-4.5460) -vertex loglikelihood: -6.0931 (-3.0466) -normal dot loglikelihood: -3.6001 (-3.6001) -quad curv loglikelihood: -6.1614 (-3.0807) Total Loglikelihood : -24.9466 CORRECTING DEFECT 0 (vertices=122, convex hull=159, v0=4) After retessellation of defect 0 (v0=4), euler #=-49 (120306,359259,238904) : difference with theory (-49) = 0 CORRECTING DEFECT 1 (vertices=36, convex hull=60, v0=745) After retessellation of defect 1 (v0=745), euler #=-48 (120324,359336,238964) : difference with theory (-48) = 0 CORRECTING DEFECT 2 (vertices=51, convex hull=52, v0=3297) After retessellation of defect 2 (v0=3297), euler #=-47 (120336,359393,239010) : difference with theory (-47) = 0 CORRECTING DEFECT 3 (vertices=71, convex hull=107, v0=4039) After retessellation of defect 3 (v0=4039), euler #=-46 (120377,359566,239143) : difference with theory (-46) = 0 CORRECTING DEFECT 4 (vertices=202, convex hull=181, v0=5987) After retessellation of defect 4 (v0=5987), euler #=-45 (120459,359892,239388) : difference with theory (-45) = 0 CORRECTING DEFECT 5 (vertices=102, convex hull=95, v0=9623) After retessellation of defect 5 (v0=9623), euler #=-42 (120476,359986,239468) : difference with theory (-44) = -2 CORRECTING DEFECT 6 (vertices=25, convex hull=20, v0=12249) After retessellation of defect 6 (v0=12249), euler #=-41 (120478,359997,239478) : difference with theory (-43) = -2 CORRECTING DEFECT 7 (vertices=6, convex hull=20, v0=20649) After retessellation of defect 7 (v0=20649), euler #=-40 (120479,360006,239487) : difference with theory (-42) = -2 CORRECTING DEFECT 8 (vertices=42, convex hull=80, v0=24189) After retessellation of defect 8 (v0=24189), euler #=-39 (120505,360116,239572) : difference with theory (-41) = -2 CORRECTING DEFECT 9 (vertices=78, convex hull=89, v0=25556) After retessellation of defect 9 (v0=25556), euler #=-38 (120529,360224,239657) : difference with theory (-40) = -2 CORRECTING DEFECT 10 (vertices=16, convex hull=49, v0=27582) After retessellation of defect 10 (v0=27582), euler #=-37 (120539,360272,239696) : difference with theory (-39) = -2 CORRECTING DEFECT 11 (vertices=29, convex hull=34, v0=30291) After retessellation of defect 11 (v0=30291), euler #=-36 (120543,360293,239714) : difference with theory (-38) = -2 CORRECTING DEFECT 12 (vertices=158, convex hull=135, v0=41134) After retessellation of defect 12 (v0=41134), euler #=-35 (120577,360467,239855) : difference with theory (-37) = -2 CORRECTING DEFECT 13 (vertices=307, convex hull=180, v0=41862) After retessellation of defect 13 (v0=41862), euler #=-35 (120695,360908,240178) : difference with theory (-36) = -1 CORRECTING DEFECT 14 (vertices=75, convex hull=104, v0=42564) After retessellation of defect 14 (v0=42564), euler #=-34 (120739,361087,240314) : difference with theory (-35) = -1 CORRECTING DEFECT 15 (vertices=16, convex hull=32, v0=48028) After retessellation of defect 15 (v0=48028), euler #=-33 (120742,361111,240336) : difference with theory (-34) = -1 CORRECTING DEFECT 16 (vertices=39, convex hull=31, v0=50635) After retessellation of defect 16 (v0=50635), euler #=-32 (120745,361131,240354) : difference with theory (-33) = -1 CORRECTING DEFECT 17 (vertices=44, convex hull=60, v0=55166) After retessellation of defect 17 (v0=55166), euler #=-31 (120763,361209,240415) : difference with theory (-32) = -1 CORRECTING DEFECT 18 (vertices=10, convex hull=22, v0=57249) After retessellation of defect 18 (v0=57249), euler #=-30 (120764,361222,240428) : difference with theory (-31) = -1 CORRECTING DEFECT 19 (vertices=6, convex hull=25, v0=60336) After retessellation of defect 19 (v0=60336), euler #=-29 (120767,361240,240444) : difference with theory (-30) = -1 CORRECTING DEFECT 20 (vertices=64, convex hull=125, v0=62696) After retessellation of defect 20 (v0=62696), euler #=-27 (120805,361410,240578) : difference with theory (-29) = -2 CORRECTING DEFECT 21 (vertices=73, convex hull=37, v0=64923) After retessellation of defect 21 (v0=64923), euler #=-26 (120813,361446,240607) : difference with theory (-28) = -2 CORRECTING DEFECT 22 (vertices=23, convex hull=43, v0=67088) After retessellation of defect 22 (v0=67088), euler #=-25 (120815,361467,240627) : difference with theory (-27) = -2 CORRECTING DEFECT 23 (vertices=18, convex hull=58, v0=67435) After retessellation of defect 23 (v0=67435), euler #=-24 (120824,361516,240668) : difference with theory (-26) = -2 CORRECTING DEFECT 24 (vertices=57, convex hull=57, v0=67848) After retessellation of defect 24 (v0=67848), euler #=-23 (120833,361567,240711) : difference with theory (-25) = -2 CORRECTING DEFECT 25 (vertices=54, convex hull=98, v0=70710) After retessellation of defect 25 (v0=70710), euler #=-22 (120868,361712,240822) : difference with theory (-24) = -2 CORRECTING DEFECT 26 (vertices=76, convex hull=49, v0=73412) After retessellation of defect 26 (v0=73412), euler #=-21 (120879,361765,240865) : difference with theory (-23) = -2 CORRECTING DEFECT 27 (vertices=1168, convex hull=358, v0=75111) L defect detected... After retessellation of defect 27 (v0=75111), euler #=-22 (121120,362692,241550) : difference with theory (-22) = 0 CORRECTING DEFECT 28 (vertices=15, convex hull=28, v0=75460) After retessellation of defect 28 (v0=75460), euler #=-21 (121122,362711,241568) : difference with theory (-21) = 0 CORRECTING DEFECT 29 (vertices=37, convex hull=58, v0=75477) After retessellation of defect 29 (v0=75477), euler #=-20 (121136,362778,241622) : difference with theory (-20) = 0 CORRECTING DEFECT 30 (vertices=59, convex hull=44, v0=76462) After retessellation of defect 30 (v0=76462), euler #=-19 (121144,362818,241655) : difference with theory (-19) = 0 CORRECTING DEFECT 31 (vertices=32, convex hull=69, v0=79845) After retessellation of defect 31 (v0=79845), euler #=-18 (121160,362897,241719) : difference with theory (-18) = 0 CORRECTING DEFECT 32 (vertices=34, convex hull=27, v0=79857) After retessellation of defect 32 (v0=79857), euler #=-17 (121165,362922,241740) : difference with theory (-17) = 0 CORRECTING DEFECT 33 (vertices=51, convex hull=60, v0=81033) After retessellation of defect 33 (v0=81033), euler #=-16 (121193,363030,241821) : difference with theory (-16) = 0 CORRECTING DEFECT 34 (vertices=40, convex hull=60, v0=81921) After retessellation of defect 34 (v0=81921), euler #=-15 (121207,363092,241870) : difference with theory (-15) = 0 CORRECTING DEFECT 35 (vertices=50, convex hull=33, v0=84494) After retessellation of defect 35 (v0=84494), euler #=-14 (121217,363137,241906) : difference with theory (-14) = 0 CORRECTING DEFECT 36 (vertices=87, convex hull=89, v0=88513) After retessellation of defect 36 (v0=88513), euler #=-13 (121257,363296,242026) : difference with theory (-13) = 0 CORRECTING DEFECT 37 (vertices=149, convex hull=79, v0=89545) After retessellation of defect 37 (v0=89545), euler #=-12 (121293,363448,242143) : difference with theory (-12) = 0 CORRECTING DEFECT 38 (vertices=59, convex hull=73, v0=89949) After retessellation of defect 38 (v0=89949), euler #=-11 (121307,363524,242206) : difference with theory (-11) = 0 CORRECTING DEFECT 39 (vertices=69, convex hull=52, v0=90096) After retessellation of defect 39 (v0=90096), euler #=-10 (121314,363564,242240) : difference with theory (-10) = 0 CORRECTING DEFECT 40 (vertices=26, convex hull=37, v0=90120) After retessellation of defect 40 (v0=90120), euler #=-9 (121317,363582,242256) : difference with theory (-9) = 0 CORRECTING DEFECT 41 (vertices=98, convex hull=108, v0=90982) After retessellation of defect 41 (v0=90982), euler #=-8 (121347,363718,242363) : difference with theory (-8) = 0 CORRECTING DEFECT 42 (vertices=72, convex hull=86, v0=95506) After retessellation of defect 42 (v0=95506), euler #=-7 (121376,363842,242459) : difference with theory (-7) = 0 CORRECTING DEFECT 43 (vertices=478, convex hull=206, v0=97016) After retessellation of defect 43 (v0=97016), euler #=-6 (121519,364376,242851) : difference with theory (-6) = 0 CORRECTING DEFECT 44 (vertices=159, convex hull=118, v0=97136) After retessellation of defect 44 (v0=97136), euler #=-5 (121572,364595,243018) : difference with theory (-5) = 0 CORRECTING DEFECT 45 (vertices=25, convex hull=37, v0=100921) After retessellation of defect 45 (v0=100921), euler #=-4 (121578,364626,243044) : difference with theory (-4) = 0 CORRECTING DEFECT 46 (vertices=39, convex hull=41, v0=105880) After retessellation of defect 46 (v0=105880), euler #=-3 (121585,364661,243073) : difference with theory (-3) = 0 CORRECTING DEFECT 47 (vertices=25, convex hull=23, v0=108565) After retessellation of defect 47 (v0=108565), euler #=-2 (121586,364672,243084) : difference with theory (-2) = 0 CORRECTING DEFECT 48 (vertices=38, convex hull=85, v0=116217) After retessellation of defect 48 (v0=116217), euler #=-1 (121609,364779,243169) : difference with theory (-1) = 0 CORRECTING DEFECT 49 (vertices=36, convex hull=81, v0=121942) After retessellation of defect 49 (v0=121942), euler #=0 (121620,364845,243225) : difference with theory (0) = 0 CORRECTING DEFECT 50 (vertices=6, convex hull=13, v0=124753) After retessellation of defect 50 (v0=124753), euler #=1 (121620,364848,243229) : difference with theory (1) = 0 CORRECTING DEFECT 51 (vertices=56, convex hull=22, v0=124828) After retessellation of defect 51 (v0=124828), euler #=2 (121622,364860,243240) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.07-->8.69) (max @ vno 6316 --> 10975) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.07-->8.69) (max @ vno 6316 --> 10975) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 179 mutations (35.0%), 333 crossovers (65.0%), 127 vertices were eliminated building final representation... 3346 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=121622, nf=243240, ne=364860, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.9 minutes 0 defective edges removing intersecting faces 000: 413 intersecting 001: 5 intersecting mris_fix_topology utimesec 1615.864351 mris_fix_topology stimesec 0.318951 mris_fix_topology ru_maxrss 404520 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 54583 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 24160 mris_fix_topology ru_oublock 11784 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 415 mris_fix_topology ru_nivcsw 3476 FSRUNTIME@ mris_fix_topology lh 0.4488 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050340 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=-104 (nv=123462, nf=247132, ne=370698, g=53) 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... 7258 ambiguous faces found in tessellation segmenting defects... 55 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 5 -merging segment 32 into 26 -merging segment 42 into 40 52 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0936 (-4.5468) -vertex loglikelihood: -6.0727 (-3.0363) -normal dot loglikelihood: -3.5928 (-3.5928) -quad curv loglikelihood: -6.1123 (-3.0562) Total Loglikelihood : -24.8713 CORRECTING DEFECT 0 (vertices=191, convex hull=97, v0=0) After retessellation of defect 0 (v0=0), euler #=-49 (119160,355975,236766) : difference with theory (-49) = 0 CORRECTING DEFECT 1 (vertices=140, convex hull=147, v0=231) After retessellation of defect 1 (v0=231), euler #=-49 (119206,356192,236937) : difference with theory (-48) = 1 CORRECTING DEFECT 2 (vertices=6, convex hull=35, v0=349) After retessellation of defect 2 (v0=349), euler #=-48 (119208,356208,236952) : difference with theory (-47) = 1 CORRECTING DEFECT 3 (vertices=32, convex hull=44, v0=509) After retessellation of defect 3 (v0=509), euler #=-47 (119213,356244,236984) : difference with theory (-46) = 1 CORRECTING DEFECT 4 (vertices=77, convex hull=126, v0=1062) After retessellation of defect 4 (v0=1062), euler #=-46 (119261,356445,237138) : difference with theory (-45) = 1 CORRECTING DEFECT 5 (vertices=65, convex hull=111, v0=6450) After retessellation of defect 5 (v0=6450), euler #=-44 (119279,356539,237216) : difference with theory (-44) = 0 CORRECTING DEFECT 6 (vertices=55, convex hull=87, v0=10951) After retessellation of defect 6 (v0=10951), euler #=-43 (119294,356623,237286) : difference with theory (-43) = 0 CORRECTING DEFECT 7 (vertices=24, convex hull=52, v0=12493) After retessellation of defect 7 (v0=12493), euler #=-42 (119309,356690,237339) : difference with theory (-42) = 0 CORRECTING DEFECT 8 (vertices=131, convex hull=134, v0=14566) After retessellation of defect 8 (v0=14566), euler #=-41 (119344,356857,237472) : difference with theory (-41) = 0 CORRECTING DEFECT 9 (vertices=35, convex hull=74, v0=17414) After retessellation of defect 9 (v0=17414), euler #=-40 (119368,356955,237547) : difference with theory (-40) = 0 CORRECTING DEFECT 10 (vertices=36, convex hull=64, v0=20478) After retessellation of defect 10 (v0=20478), euler #=-39 (119391,357049,237619) : difference with theory (-39) = 0 CORRECTING DEFECT 11 (vertices=29, convex hull=61, v0=22052) After retessellation of defect 11 (v0=22052), euler #=-38 (119400,357101,237663) : difference with theory (-38) = 0 CORRECTING DEFECT 12 (vertices=36, convex hull=79, v0=27589) After retessellation of defect 12 (v0=27589), euler #=-37 (119411,357164,237716) : difference with theory (-37) = 0 CORRECTING DEFECT 13 (vertices=441, convex hull=224, v0=41063) normal vector of length zero at vertex 120259 with 3 faces After retessellation of defect 13 (v0=41063), euler #=-36 (119434,357344,237874) : difference with theory (-36) = 0 CORRECTING DEFECT 14 (vertices=22, convex hull=63, v0=41688) After retessellation of defect 14 (v0=41688), euler #=-35 (119443,357397,237919) : difference with theory (-35) = 0 CORRECTING DEFECT 15 (vertices=26, convex hull=20, v0=43681) After retessellation of defect 15 (v0=43681), euler #=-34 (119444,357402,237924) : difference with theory (-34) = 0 CORRECTING DEFECT 16 (vertices=30, convex hull=58, v0=51313) After retessellation of defect 16 (v0=51313), euler #=-33 (119453,357449,237963) : difference with theory (-33) = 0 CORRECTING DEFECT 17 (vertices=33, convex hull=27, v0=56426) After retessellation of defect 17 (v0=56426), euler #=-32 (119454,357462,237976) : difference with theory (-32) = 0 CORRECTING DEFECT 18 (vertices=32, convex hull=49, v0=57780) After retessellation of defect 18 (v0=57780), euler #=-31 (119464,357508,238013) : difference with theory (-31) = 0 CORRECTING DEFECT 19 (vertices=23, convex hull=52, v0=57915) After retessellation of defect 19 (v0=57915), euler #=-30 (119473,357555,238052) : difference with theory (-30) = 0 CORRECTING DEFECT 20 (vertices=15, convex hull=36, v0=58898) After retessellation of defect 20 (v0=58898), euler #=-29 (119476,357578,238073) : difference with theory (-29) = 0 CORRECTING DEFECT 21 (vertices=14, convex hull=34, v0=60079) After retessellation of defect 21 (v0=60079), euler #=-28 (119478,357592,238086) : difference with theory (-28) = 0 CORRECTING DEFECT 22 (vertices=64, convex hull=105, v0=63718) After retessellation of defect 22 (v0=63718), euler #=-27 (119501,357710,238182) : difference with theory (-27) = 0 CORRECTING DEFECT 23 (vertices=11, convex hull=32, v0=65605) After retessellation of defect 23 (v0=65605), euler #=-26 (119502,357723,238195) : difference with theory (-26) = 0 CORRECTING DEFECT 24 (vertices=54, convex hull=38, v0=67771) After retessellation of defect 24 (v0=67771), euler #=-25 (119506,357749,238218) : difference with theory (-25) = 0 CORRECTING DEFECT 25 (vertices=128, convex hull=141, v0=70958) After retessellation of defect 25 (v0=70958), euler #=-23 (119576,358033,238434) : difference with theory (-24) = -1 CORRECTING DEFECT 26 (vertices=15, convex hull=25, v0=70962) After retessellation of defect 26 (v0=70962), euler #=-22 (119578,358047,238447) : difference with theory (-23) = -1 CORRECTING DEFECT 27 (vertices=56, convex hull=55, v0=73069) After retessellation of defect 27 (v0=73069), euler #=-21 (119585,358088,238482) : difference with theory (-22) = -1 CORRECTING DEFECT 28 (vertices=34, convex hull=70, v0=73739) After retessellation of defect 28 (v0=73739), euler #=-20 (119599,358158,238539) : difference with theory (-21) = -1 CORRECTING DEFECT 29 (vertices=1386, convex hull=428, v0=74973) L defect detected... After retessellation of defect 29 (v0=74973), euler #=-21 (119682,358647,238944) : difference with theory (-20) = 1 CORRECTING DEFECT 30 (vertices=46, convex hull=24, v0=75296) After retessellation of defect 30 (v0=75296), euler #=-20 (119688,358672,238964) : difference with theory (-19) = 1 CORRECTING DEFECT 31 (vertices=24, convex hull=32, v0=79165) After retessellation of defect 31 (v0=79165), euler #=-19 (119692,358695,238984) : difference with theory (-18) = 1 CORRECTING DEFECT 32 (vertices=18, convex hull=45, v0=85108) After retessellation of defect 32 (v0=85108), euler #=-18 (119702,358737,239017) : difference with theory (-17) = 1 CORRECTING DEFECT 33 (vertices=30, convex hull=30, v0=89829) After retessellation of defect 33 (v0=89829), euler #=-17 (119707,358763,239039) : difference with theory (-16) = 1 CORRECTING DEFECT 34 (vertices=10, convex hull=17, v0=90543) After retessellation of defect 34 (v0=90543), euler #=-16 (119709,358774,239049) : difference with theory (-15) = 1 CORRECTING DEFECT 35 (vertices=20, convex hull=23, v0=92414) After retessellation of defect 35 (v0=92414), euler #=-15 (119713,358792,239064) : difference with theory (-14) = 1 CORRECTING DEFECT 36 (vertices=45, convex hull=65, v0=93547) After retessellation of defect 36 (v0=93547), euler #=-14 (119731,358869,239124) : difference with theory (-13) = 1 CORRECTING DEFECT 37 (vertices=269, convex hull=73, v0=95882) After retessellation of defect 37 (v0=95882), euler #=-13 (119750,358958,239195) : difference with theory (-12) = 1 CORRECTING DEFECT 38 (vertices=120, convex hull=102, v0=96542) After retessellation of defect 38 (v0=96542), euler #=-11 (119795,359143,239337) : difference with theory (-11) = 0 CORRECTING DEFECT 39 (vertices=5, convex hull=22, v0=96568) After retessellation of defect 39 (v0=96568), euler #=-10 (119795,359154,239349) : difference with theory (-10) = 0 CORRECTING DEFECT 40 (vertices=30, convex hull=76, v0=98999) After retessellation of defect 40 (v0=98999), euler #=-9 (119811,359231,239411) : difference with theory (-9) = 0 CORRECTING DEFECT 41 (vertices=17, convex hull=50, v0=101119) After retessellation of defect 41 (v0=101119), euler #=-8 (119819,359271,239444) : difference with theory (-8) = 0 CORRECTING DEFECT 42 (vertices=10, convex hull=20, v0=103651) After retessellation of defect 42 (v0=103651), euler #=-7 (119819,359276,239450) : difference with theory (-7) = 0 CORRECTING DEFECT 43 (vertices=75, convex hull=28, v0=107800) After retessellation of defect 43 (v0=107800), euler #=-6 (119823,359297,239468) : difference with theory (-6) = 0 CORRECTING DEFECT 44 (vertices=22, convex hull=43, v0=110408) After retessellation of defect 44 (v0=110408), euler #=-5 (119832,359337,239500) : difference with theory (-5) = 0 CORRECTING DEFECT 45 (vertices=6, convex hull=23, v0=110985) After retessellation of defect 45 (v0=110985), euler #=-4 (119834,359348,239510) : difference with theory (-4) = 0 CORRECTING DEFECT 46 (vertices=41, convex hull=67, v0=112905) After retessellation of defect 46 (v0=112905), euler #=-3 (119849,359421,239569) : difference with theory (-3) = 0 CORRECTING DEFECT 47 (vertices=53, convex hull=25, v0=115711) After retessellation of defect 47 (v0=115711), euler #=-2 (119852,359438,239584) : difference with theory (-2) = 0 CORRECTING DEFECT 48 (vertices=47, convex hull=80, v0=119603) After retessellation of defect 48 (v0=119603), euler #=-1 (119874,359537,239662) : difference with theory (-1) = 0 CORRECTING DEFECT 49 (vertices=55, convex hull=75, v0=122019) After retessellation of defect 49 (v0=122019), euler #=0 (119891,359621,239730) : difference with theory (0) = 0 CORRECTING DEFECT 50 (vertices=88, convex hull=39, v0=122736) After retessellation of defect 50 (v0=122736), euler #=1 (119898,359657,239760) : difference with theory (1) = 0 CORRECTING DEFECT 51 (vertices=38, convex hull=78, v0=122896) After retessellation of defect 51 (v0=122896), euler #=2 (119917,359745,239830) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.26 (0.14-->15.24) (max @ vno 83046 --> 86613) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.26 (0.14-->15.24) (max @ vno 83046 --> 86613) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 176 mutations (33.0%), 357 crossovers (67.0%), 469 vertices were eliminated building final representation... 3545 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=119917, nf=239830, ne=359745, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 31.2 minutes 0 defective edges removing intersecting faces 000: 374 intersecting mris_fix_topology utimesec 1875.103940 mris_fix_topology stimesec 0.196970 mris_fix_topology ru_maxrss 409812 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 57561 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 16376 mris_fix_topology ru_oublock 11600 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 565 mris_fix_topology ru_nivcsw 7201 FSRUNTIME@ mris_fix_topology rh 0.5207 hours 1 threads PIDs (24728 24731) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 121622 - 364860 + 243240 = 2 --> 0 holes F =2V-4: 243240 = 243244-4 (0) 2E=3F: 729720 = 729720 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 119917 - 359745 + 239830 = 2 --> 0 holes F =2V-4: 239830 = 239834-4 (0) 2E=3F: 719490 = 719490 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 125 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 52 intersecting 001: 5 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Oct 8 04:09:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050340 lh #-------------------------------------------- #@# Make White Surf rh Sun Oct 8 04:09:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050340 rh Waiting for PID 26761 of (26761 26764) to complete... Waiting for PID 26764 of (26761 26764) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050340 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-6.0.0/0050340/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... 13065 bright wm thresholded. 2133 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.orig... computing class statistics... border white: 229073 voxels (1.37%) border gray 266822 voxels (1.59%) WM (97.0): 97.6 +- 7.9 [70.0 --> 110.0] GM (75.0) : 73.5 +- 10.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70) setting MAX_BORDER_WHITE to 109.9 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 48.3 (was 40) setting MAX_GRAY to 94.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 58.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.0 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.03-->4.63) (max @ vno 120951 --> 121071) face area 0.28 +- 0.13 (0.00-->4.36) mean absolute distance = 0.73 +- 0.85 3853 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-5.2, GM=69+-9.6 mean inside = 93.9, mean outside = 77.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=80.8, 102 (102) missing vertices, mean dist 0.4 [0.6 (%32.7)->0.8 (%67.3))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.25 (0.09-->4.63) (max @ vno 120951 --> 121071) face area 0.28 +- 0.13 (0.00-->3.34) mean absolute distance = 0.39 +- 0.60 4015 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2746584.2, rms=9.776 001: dt: 0.5000, sse=1626610.5, rms=6.996 (28.438%) 002: dt: 0.5000, sse=1104060.8, rms=5.161 (26.232%) 003: dt: 0.5000, sse=862365.1, rms=4.024 (22.022%) 004: dt: 0.5000, sse=754096.2, rms=3.382 (15.959%) 005: dt: 0.5000, sse=704332.4, rms=3.082 (8.857%) 006: dt: 0.5000, sse=683768.4, rms=2.925 (5.115%) rms = 2.89, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=678478.6, rms=2.888 (1.249%) 008: dt: 0.2500, sse=571379.4, rms=1.808 (37.387%) 009: dt: 0.2500, sse=553200.4, rms=1.561 (13.704%) 010: dt: 0.2500, sse=549665.9, rms=1.504 (3.629%) rms = 1.49, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=560378.8, rms=1.486 (1.176%) rms = 1.46, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=546839.4, rms=1.463 (1.578%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=83.8, 83 (26) missing vertices, mean dist -0.2 [0.4 (%71.7)->0.3 (%28.3))] %79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.10-->4.45) (max @ vno 120627 --> 120657) face area 0.36 +- 0.17 (0.00-->4.82) mean absolute distance = 0.28 +- 0.43 3692 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1099073.4, rms=4.521 013: dt: 0.5000, sse=806503.6, rms=2.806 (37.934%) 014: dt: 0.5000, sse=767579.4, rms=2.483 (11.513%) 015: dt: 0.5000, sse=758735.9, rms=2.429 (2.182%) rms = 2.56, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=697135.8, rms=1.770 (27.130%) 017: dt: 0.2500, sse=676110.3, rms=1.432 (19.063%) 018: dt: 0.2500, sse=670977.6, rms=1.331 (7.065%) rms = 1.29, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=662942.6, rms=1.294 (2.827%) rms = 1.26, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=660612.9, rms=1.256 (2.942%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=85.4, 78 (9) 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 0.90 +- 0.25 (0.08-->4.62) (max @ vno 120627 --> 120657) face area 0.34 +- 0.16 (0.00-->4.66) mean absolute distance = 0.26 +- 0.37 3091 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=771860.5, rms=2.696 021: dt: 0.5000, sse=699218.4, rms=1.979 (26.588%) rms = 2.04, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=656842.6, rms=1.500 (24.239%) 023: dt: 0.2500, sse=644564.8, rms=1.227 (18.153%) 024: dt: 0.2500, sse=636800.9, rms=1.162 (5.311%) rms = 1.15, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=640807.5, rms=1.152 (0.831%) rms = 1.12, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=632838.9, rms=1.120 (2.806%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.2, 109 (6) missing vertices, mean dist -0.0 [0.3 (%55.2)->0.2 (%44.8))] %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-6.0.0/0050340/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=652593.0, rms=1.570 027: dt: 0.5000, sse=645520.1, rms=1.372 (12.608%) rms = 1.73, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=619799.9, rms=1.015 (26.038%) 029: dt: 0.2500, sse=617971.4, rms=0.952 (6.240%) 030: dt: 0.2500, sse=612071.6, rms=0.896 (5.849%) rms = 0.93, time step reduction 2 of 3 to 0.125... rms = 0.88, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=610472.5, rms=0.882 (1.613%) positioning took 0.6 minutes generating cortex label... 9 non-cortical segments detected only using segment with 6934 vertices erasing segment 1 (vno[0] = 56818) erasing segment 2 (vno[0] = 75289) erasing segment 3 (vno[0] = 84321) erasing segment 4 (vno[0] = 86043) erasing segment 5 (vno[0] = 87596) erasing segment 6 (vno[0] = 88421) erasing segment 7 (vno[0] = 90040) erasing segment 8 (vno[0] = 121233) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.area vertex spacing 0.90 +- 0.25 (0.04-->4.62) (max @ vno 120627 --> 120657) face area 0.34 +- 0.16 (0.00-->4.88) refinement took 4.6 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050340 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-6.0.0/0050340/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... 13065 bright wm thresholded. 2133 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.orig... computing class statistics... border white: 229073 voxels (1.37%) border gray 266822 voxels (1.59%) WM (97.0): 97.6 +- 7.9 [70.0 --> 110.0] GM (75.0) : 73.5 +- 10.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.7 (was 70) setting MAX_BORDER_WHITE to 108.9 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 49.3 (was 40) setting MAX_GRAY to 93.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 59.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.0 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->5.47) (max @ vno 42316 --> 46682) face area 0.28 +- 0.13 (0.00-->4.77) mean absolute distance = 0.72 +- 0.86 3702 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+-5.2, GM=70+-8.7 mean inside = 93.6, mean outside = 77.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=81.1, 116 (116) missing vertices, mean dist 0.3 [0.6 (%34.0)->0.8 (%66.0))] %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.08-->7.09) (max @ vno 46682 --> 47728) face area 0.28 +- 0.13 (0.00-->6.30) mean absolute distance = 0.39 +- 0.62 4170 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2599617.2, rms=9.523 001: dt: 0.5000, sse=1566268.5, rms=6.868 (27.875%) 002: dt: 0.5000, sse=1106555.0, rms=5.155 (24.945%) 003: dt: 0.5000, sse=870905.3, rms=4.062 (21.204%) 004: dt: 0.5000, sse=746163.3, rms=3.420 (15.810%) 005: dt: 0.5000, sse=703175.2, rms=3.127 (8.547%) 006: dt: 0.5000, sse=684637.7, rms=2.967 (5.138%) 007: dt: 0.5000, sse=677518.5, rms=2.912 (1.857%) rms = 2.87, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=669398.0, rms=2.872 (1.373%) 009: dt: 0.2500, sse=566995.4, rms=1.832 (36.217%) 010: dt: 0.2500, sse=551777.8, rms=1.613 (11.960%) 011: dt: 0.2500, sse=546699.8, rms=1.549 (3.962%) rms = 1.51, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=548308.3, rms=1.513 (2.319%) 013: dt: 0.1250, sse=539852.9, rms=1.454 (3.869%) rms = 1.45, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=539366.5, rms=1.450 (0.312%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=83.9, 94 (30) missing vertices, mean dist -0.2 [0.4 (%70.8)->0.3 (%29.2))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.10-->7.72) (max @ vno 46682 --> 47728) face area 0.35 +- 0.17 (0.00-->9.41) mean absolute distance = 0.29 +- 0.42 3484 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1061727.9, rms=4.416 015: dt: 0.5000, sse=798493.4, rms=2.820 (36.140%) 016: dt: 0.5000, sse=758405.8, rms=2.454 (12.987%) 017: dt: 0.5000, sse=740733.5, rms=2.393 (2.495%) rms = 2.51, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=685772.3, rms=1.796 (24.955%) 019: dt: 0.2500, sse=666773.1, rms=1.497 (16.618%) 020: dt: 0.2500, sse=667121.5, rms=1.414 (5.537%) rms = 1.37, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=662307.4, rms=1.370 (3.105%) 022: dt: 0.1250, sse=655670.6, rms=1.318 (3.856%) rms = 1.29, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=652869.2, rms=1.288 (2.259%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=85.6, 113 (14) missing vertices, mean dist -0.1 [0.3 (%64.5)->0.2 (%35.5))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.04-->7.97) (max @ vno 46682 --> 47728) face area 0.34 +- 0.17 (0.00-->9.66) mean absolute distance = 0.26 +- 0.37 2954 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=766610.9, rms=2.717 024: dt: 0.5000, sse=694328.2, rms=1.990 (26.756%) rms = 1.99, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=652750.6, rms=1.528 (23.221%) 026: dt: 0.2500, sse=648584.2, rms=1.290 (15.590%) 027: dt: 0.2500, sse=642024.5, rms=1.235 (4.228%) rms = 1.21, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=638528.4, rms=1.209 (2.130%) rms = 1.16, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=629913.1, rms=1.161 (3.911%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.3, 142 (7) missing vertices, mean dist -0.0 [0.3 (%55.3)->0.2 (%44.7))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=649883.4, rms=1.598 030: dt: 0.5000, sse=642397.1, rms=1.449 (9.338%) rms = 1.72, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=618278.2, rms=1.094 (24.465%) rms = 1.05, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=621372.2, rms=1.048 (4.263%) 033: dt: 0.1250, sse=609836.7, rms=0.958 (8.598%) rms = 0.93, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=607845.2, rms=0.933 (2.586%) positioning took 0.5 minutes generating cortex label... 7 non-cortical segments detected only using segment with 6462 vertices erasing segment 1 (vno[0] = 87194) erasing segment 2 (vno[0] = 87252) erasing segment 3 (vno[0] = 88984) erasing segment 4 (vno[0] = 89863) erasing segment 5 (vno[0] = 91509) erasing segment 6 (vno[0] = 95241) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.area vertex spacing 0.90 +- 0.26 (0.03-->7.83) (max @ vno 46682 --> 47728) face area 0.34 +- 0.16 (0.00-->9.86) refinement took 4.7 minutes PIDs (26761 26764) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sun Oct 8 04:14:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sun Oct 8 04:14:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 27050 of (27050 27053) to complete... Waiting for PID 27053 of (27050 27053) 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 (27050 27053) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sun Oct 8 04:14:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sun Oct 8 04:14:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 27099 of (27099 27102) to complete... Waiting for PID 27102 of (27099 27102) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 45.7 mm, total surface area = 74672 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.178 (target=0.015) step 005: RMS=0.126 (target=0.015) step 010: RMS=0.094 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.041 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 38.788103 mris_inflate stimesec 0.092985 mris_inflate ru_maxrss 178600 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 26319 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8560 mris_inflate ru_oublock 9528 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2211 mris_inflate ru_nivcsw 4472 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.0 mm, total surface area = 73818 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.177 (target=0.015) step 005: RMS=0.126 (target=0.015) step 010: RMS=0.095 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 38.224189 mris_inflate stimesec 0.118981 mris_inflate ru_maxrss 176072 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 25685 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8440 mris_inflate ru_oublock 9400 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3989 mris_inflate ru_nivcsw 2933 PIDs (27099 27102) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sun Oct 8 04:15:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 04:15:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 27200 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... Waiting for PID 27203 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... Waiting for PID 27206 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... Waiting for PID 27209 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... Waiting for PID 27212 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... Waiting for PID 27215 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... Waiting for PID 27218 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... Waiting for PID 27221 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... Waiting for PID 27224 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... Waiting for PID 27227 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... Waiting for PID 27232 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... Waiting for PID 27235 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 11.904*4pi (149.589) --> -11 handles ICI = 171.9, FI = 1511.8, variation=24637.630 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 134 vertices thresholded to be in k1 ~ [-0.58 0.37], k2 ~ [-0.09 0.83] total integrated curvature = 0.523*4pi (6.577) --> 0 handles ICI = 1.3, FI = 7.6, variation=133.905 125 vertices thresholded to be in [-0.06 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 96 vertices thresholded to be in [-0.17 0.17] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.021 done. mris_curvature -w rh.white.preaparc total integrated curvature = 18.379*4pi (230.956) --> -17 handles ICI = 173.7, FI = 1503.7, variation=24493.355 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 127 vertices thresholded to be in k1 ~ [-0.34 0.31], k2 ~ [-0.11 0.08] total integrated curvature = 0.595*4pi (7.480) --> 0 handles ICI = 1.3, FI = 6.9, variation=122.386 89 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 113 vertices thresholded to be in [-0.14 0.15] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.020 done. PIDs (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sun Oct 8 04:16:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050340 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 [ 0050340/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 [ 210 ] Gb_filter = 0 WARN: S lookup min: -0.397253 WARN: S explicit min: 0.000000 vertex = 336 WARN: C lookup max: 176.346786 WARN: C explicit max: 89.507462 vertex = 120614 #----------------------------------------- #@# Curvature Stats rh Sun Oct 8 04:16:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050340 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 [ 0050340/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 [ 210 ] Gb_filter = 0 WARN: S lookup min: -1.274895 WARN: S explicit min: 0.000000 vertex = 2 #-------------------------------------------- #@# Sphere lh Sun Oct 8 04:16:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sun Oct 8 04:16:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 27458 of (27458 27462) to complete... Waiting for PID 27462 of (27458 27462) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0.293... 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 %41.86 pass 1: epoch 2 of 3 starting distance error %19.72 unfolding complete - removing small folds... starting distance error %19.58 removing remaining folds... final distance error %19.61 MRISunfold() return, current seed 1234 -01: dt=0.0000, 193 negative triangles 160: dt=0.9900, 193 negative triangles 161: dt=0.9900, 121 negative triangles 162: dt=0.9900, 84 negative triangles 163: dt=0.9900, 63 negative triangles 164: dt=0.9900, 55 negative triangles 165: dt=0.9900, 37 negative triangles 166: dt=0.9900, 38 negative triangles 167: dt=0.9900, 35 negative triangles 168: dt=0.9900, 23 negative triangles 169: dt=0.9900, 29 negative triangles 170: dt=0.9900, 25 negative triangles 171: dt=0.9900, 22 negative triangles 172: dt=0.9900, 13 negative triangles 173: dt=0.9900, 22 negative triangles 174: dt=0.9900, 12 negative triangles 175: dt=0.9900, 11 negative triangles 176: dt=0.9900, 9 negative triangles 177: dt=0.9900, 14 negative triangles 178: dt=0.9900, 7 negative triangles 179: dt=0.9900, 3 negative triangles 180: dt=0.9900, 8 negative triangles 181: dt=0.9900, 4 negative triangles 182: dt=0.9900, 8 negative triangles 183: dt=0.9900, 4 negative triangles 184: dt=0.9900, 4 negative triangles 185: dt=0.9900, 4 negative triangles 186: dt=0.9900, 1 negative triangles 187: dt=0.9900, 1 negative triangles 188: dt=0.9900, 3 negative triangles 189: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.53 hours mris_sphere utimesec 1919.457198 mris_sphere stimesec 0.946856 mris_sphere ru_maxrss 250772 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 44474 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 8600 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 85386 mris_sphere ru_nivcsw 158905 FSRUNTIME@ mris_sphere 0.5340 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0.296... 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 %40.31 pass 1: epoch 2 of 3 starting distance error %19.26 unfolding complete - removing small folds... starting distance error %19.15 removing remaining folds... final distance error %19.17 MRISunfold() return, current seed 1234 -01: dt=0.0000, 183 negative triangles 137: dt=0.9900, 183 negative triangles 138: dt=0.9900, 101 negative triangles 139: dt=0.9900, 73 negative triangles 140: dt=0.9900, 54 negative triangles 141: dt=0.9900, 65 negative triangles 142: dt=0.9900, 55 negative triangles 143: dt=0.9900, 52 negative triangles 144: dt=0.9900, 54 negative triangles 145: dt=0.9900, 41 negative triangles 146: dt=0.9900, 44 negative triangles 147: dt=0.9900, 36 negative triangles 148: dt=0.9900, 36 negative triangles 149: dt=0.9900, 25 negative triangles 150: dt=0.9900, 23 negative triangles 151: dt=0.9900, 27 negative triangles 152: dt=0.9900, 21 negative triangles 153: dt=0.9900, 30 negative triangles 154: dt=0.9900, 27 negative triangles 155: dt=0.9900, 29 negative triangles 156: dt=0.9900, 33 negative triangles 157: dt=0.9900, 28 negative triangles 158: dt=0.9900, 32 negative triangles 159: dt=0.9900, 34 negative triangles 160: dt=0.9900, 33 negative triangles 161: dt=0.9900, 32 negative triangles 162: dt=0.9405, 31 negative triangles 163: dt=0.9405, 32 negative triangles 164: dt=0.9405, 35 negative triangles 165: dt=0.9405, 36 negative triangles 166: dt=0.9405, 33 negative triangles 167: dt=0.9405, 32 negative triangles 168: dt=0.9405, 34 negative triangles 169: dt=0.9405, 34 negative triangles 170: dt=0.9405, 41 negative triangles 171: dt=0.9405, 36 negative triangles 172: dt=0.8935, 33 negative triangles 173: dt=0.8935, 36 negative triangles 174: dt=0.8935, 34 negative triangles 175: dt=0.8935, 30 negative triangles 176: dt=0.8935, 31 negative triangles 177: dt=0.8935, 34 negative triangles 178: dt=0.8935, 35 negative triangles 179: dt=0.8935, 31 negative triangles 180: dt=0.8935, 31 negative triangles 181: dt=0.8935, 32 negative triangles 182: dt=0.8488, 34 negative triangles 183: dt=0.8488, 34 negative triangles 184: dt=0.8488, 34 negative triangles 185: dt=0.8488, 32 negative triangles 186: dt=0.8488, 30 negative triangles 187: dt=0.8488, 30 negative triangles 188: dt=0.8488, 33 negative triangles 189: dt=0.8488, 34 negative triangles 190: dt=0.8488, 30 negative triangles 191: dt=0.8488, 32 negative triangles 192: dt=0.8064, 30 negative triangles 193: dt=0.8064, 29 negative triangles 194: dt=0.8064, 34 negative triangles 195: dt=0.8064, 30 negative triangles 196: dt=0.8064, 34 negative triangles 197: dt=0.8064, 31 negative triangles 198: dt=0.8064, 29 negative triangles 199: dt=0.8064, 31 negative triangles 200: dt=0.8064, 31 negative triangles 201: dt=0.8064, 35 negative triangles 202: dt=0.7660, 27 negative triangles expanding nbhd size to 1 203: dt=0.9900, 25 negative triangles 204: dt=0.9900, 25 negative triangles 205: dt=0.9900, 27 negative triangles 206: dt=0.9900, 24 negative triangles 207: dt=0.9900, 24 negative triangles 208: dt=0.9900, 23 negative triangles 209: dt=0.9900, 21 negative triangles 210: dt=0.9900, 19 negative triangles 211: dt=0.9900, 17 negative triangles 212: dt=0.9900, 17 negative triangles 213: dt=0.9900, 19 negative triangles 214: dt=0.9900, 15 negative triangles 215: dt=0.9900, 17 negative triangles 216: dt=0.9900, 15 negative triangles 217: dt=0.9900, 15 negative triangles 218: dt=0.9900, 15 negative triangles 219: dt=0.9900, 21 negative triangles 220: dt=0.9900, 18 negative triangles 221: dt=0.9900, 16 negative triangles 222: dt=0.9900, 14 negative triangles 223: dt=0.9900, 12 negative triangles 224: dt=0.9900, 12 negative triangles 225: dt=0.9900, 12 negative triangles 226: dt=0.9900, 17 negative triangles 227: dt=0.9900, 16 negative triangles 228: dt=0.9900, 12 negative triangles 229: dt=0.9900, 13 negative triangles 230: dt=0.9900, 11 negative triangles 231: dt=0.9900, 10 negative triangles 232: dt=0.9900, 10 negative triangles 233: dt=0.9900, 11 negative triangles 234: dt=0.9900, 11 negative triangles 235: dt=0.9900, 8 negative triangles 236: dt=0.9900, 6 negative triangles 237: dt=0.9900, 4 negative triangles 238: dt=0.9900, 4 negative triangles 239: dt=0.9900, 9 negative triangles 240: dt=0.9900, 5 negative triangles 241: dt=0.9900, 5 negative triangles 242: dt=0.9900, 2 negative triangles 243: dt=0.9900, 6 negative triangles 244: dt=0.9900, 7 negative triangles 245: dt=0.9900, 4 negative triangles 246: dt=0.9900, 3 negative triangles 247: dt=0.9900, 4 negative triangles 248: dt=0.9900, 3 negative triangles 249: dt=0.9900, 6 negative triangles 250: dt=0.9900, 4 negative triangles 251: dt=0.9900, 1 negative triangles 252: dt=0.9900, 4 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.54 hours mris_sphere utimesec 1938.191350 mris_sphere stimesec 0.959854 mris_sphere ru_maxrss 247496 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 43693 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 8536 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 80589 mris_sphere ru_nivcsw 160401 FSRUNTIME@ mris_sphere 0.5359 hours 1 threads PIDs (27458 27462) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sun Oct 8 04:48:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 04:48:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 29979 of (29979 29982) to complete... Waiting for PID 29982 of (29979 29982) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 5.558 curvature mean = 0.041, std = 0.819 curvature mean = 0.015, std = 0.876 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 297716.6, tmin=0.9265 d=32.00 min @ (0.00, 8.00, -8.00) sse = 196049.1, tmin=1.8791 d=16.00 min @ (4.00, 0.00, 0.00) sse = 178781.0, tmin=2.8414 d=8.00 min @ (-2.00, -2.00, 0.00) sse = 171298.6, tmin=3.8091 d=4.00 min @ (0.00, 0.00, 1.00) sse = 169980.9, tmin=4.7873 d=2.00 min @ (0.50, 0.00, -0.50) sse = 169696.5, tmin=5.7678 d=1.00 min @ (-0.25, -0.25, 0.25) sse = 169489.6, tmin=6.7435 d=0.50 min @ (0.12, 0.00, 0.00) sse = 169476.8, tmin=7.7337 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 = 0.007, std = 0.837 curvature mean = 0.005, std = 0.955 curvature mean = 0.003, std = 0.848 curvature mean = 0.001, std = 0.983 curvature mean = 0.001, std = 0.850 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.035, std = 0.320 curvature mean = 0.040, std = 0.249 curvature mean = 0.058, std = 0.337 curvature mean = 0.033, std = 0.310 curvature mean = 0.039, std = 0.499 curvature mean = 0.032, std = 0.337 curvature mean = 0.024, std = 0.615 curvature mean = 0.031, std = 0.349 curvature mean = 0.010, std = 0.708 MRISregister() return, current seed 0 -01: dt=0.0000, 93 negative triangles 112: dt=0.9900, 93 negative triangles expanding nbhd size to 1 113: dt=0.9900, 120 negative triangles 114: dt=0.9900, 97 negative triangles 115: dt=0.9900, 84 negative triangles 116: dt=0.9900, 85 negative triangles 117: dt=0.9900, 82 negative triangles 118: dt=0.9900, 79 negative triangles 119: dt=0.9900, 72 negative triangles 120: dt=0.9900, 69 negative triangles 121: dt=0.9900, 70 negative triangles 122: dt=0.9900, 68 negative triangles 123: dt=0.9900, 55 negative triangles 124: dt=0.9900, 51 negative triangles 125: dt=0.9900, 50 negative triangles 126: dt=0.9900, 46 negative triangles 127: dt=0.9900, 48 negative triangles 128: dt=0.9900, 49 negative triangles 129: dt=0.9900, 45 negative triangles 130: dt=0.9900, 43 negative triangles 131: dt=0.9900, 38 negative triangles 132: dt=0.9900, 32 negative triangles 133: dt=0.9900, 32 negative triangles 134: dt=0.9900, 29 negative triangles 135: dt=0.9900, 30 negative triangles 136: dt=0.9900, 22 negative triangles 137: dt=0.9900, 24 negative triangles 138: dt=0.9900, 20 negative triangles 139: dt=0.9900, 15 negative triangles 140: dt=0.9900, 13 negative triangles 141: dt=0.9900, 9 negative triangles 142: dt=0.9900, 10 negative triangles 143: dt=0.9900, 7 negative triangles 144: dt=0.9900, 8 negative triangles 145: dt=0.9900, 6 negative triangles 146: dt=0.9900, 7 negative triangles 147: dt=0.9900, 8 negative triangles 148: dt=0.9900, 6 negative triangles 149: dt=0.9900, 4 negative triangles 150: dt=0.9900, 2 negative triangles 151: dt=0.9900, 1 negative triangles 152: dt=0.9900, 1 negative triangles 153: dt=0.9900, 1 negative triangles 154: dt=0.9900, 1 negative triangles 155: dt=0.9900, 1 negative triangles 156: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.00 hours mris_register utimesec 3609.329298 mris_register stimesec 1.776729 mris_register ru_maxrss 233648 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 33881 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 8560 mris_register ru_oublock 8656 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 277355 mris_register ru_nivcsw 194898 FSRUNTIME@ mris_register 1.0026 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 5.661 curvature mean = 0.038, std = 0.815 curvature mean = 0.016, std = 0.875 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 312917.3, tmin=0.9132 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 207337.7, tmin=1.8509 d=16.00 min @ (0.00, -4.00, -4.00) sse = 197683.1, tmin=2.7981 d=8.00 min @ (2.00, 2.00, 2.00) sse = 184871.0, tmin=3.7635 d=4.00 min @ (0.00, 0.00, -1.00) sse = 184833.0, tmin=4.7407 d=2.00 min @ (-0.50, 0.00, 0.50) sse = 183780.2, tmin=5.7201 d=0.50 min @ (0.12, 0.00, 0.00) sse = 183765.7, tmin=7.6560 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 7.66 min curvature mean = 0.009, std = 0.833 curvature mean = 0.005, std = 0.955 curvature mean = 0.006, std = 0.844 curvature mean = 0.002, std = 0.983 curvature mean = 0.005, std = 0.847 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.033, std = 0.309 curvature mean = 0.036, std = 0.245 curvature mean = 0.060, std = 0.350 curvature mean = 0.030, std = 0.304 curvature mean = 0.041, std = 0.516 curvature mean = 0.029, std = 0.331 curvature mean = 0.025, std = 0.638 curvature mean = 0.029, std = 0.343 curvature mean = 0.011, std = 0.739 MRISregister() return, current seed 0 -01: dt=0.0000, 57 negative triangles 104: dt=0.9900, 57 negative triangles expanding nbhd size to 1 105: dt=0.9900, 80 negative triangles 106: dt=0.9900, 58 negative triangles 107: dt=0.9900, 67 negative triangles 108: dt=0.9900, 61 negative triangles 109: dt=0.9900, 61 negative triangles 110: dt=0.9405, 63 negative triangles 111: dt=0.9405, 56 negative triangles 112: dt=0.9405, 51 negative triangles 113: dt=0.9405, 54 negative triangles 114: dt=0.9405, 53 negative triangles 115: dt=0.9405, 46 negative triangles 116: dt=0.9405, 41 negative triangles 117: dt=0.9405, 38 negative triangles 118: dt=0.9405, 31 negative triangles 119: dt=0.9405, 33 negative triangles 120: dt=0.9405, 28 negative triangles 121: dt=0.9405, 31 negative triangles 122: dt=0.9405, 28 negative triangles 123: dt=0.9405, 25 negative triangles 124: dt=0.9405, 22 negative triangles 125: dt=0.9405, 22 negative triangles 126: dt=0.9405, 22 negative triangles 127: dt=0.9405, 20 negative triangles 128: dt=0.9405, 15 negative triangles 129: dt=0.9405, 17 negative triangles 130: dt=0.9405, 17 negative triangles 131: dt=0.9405, 17 negative triangles 132: dt=0.9405, 14 negative triangles 133: dt=0.9405, 12 negative triangles 134: dt=0.9405, 14 negative triangles 135: dt=0.9405, 10 negative triangles 136: dt=0.9405, 9 negative triangles 137: dt=0.9405, 8 negative triangles 138: dt=0.9405, 7 negative triangles 139: dt=0.9405, 11 negative triangles 140: dt=0.9405, 8 negative triangles 141: dt=0.9405, 7 negative triangles 142: dt=0.9405, 5 negative triangles 143: dt=0.9405, 9 negative triangles 144: dt=0.9405, 7 negative triangles 145: dt=0.9405, 6 negative triangles 146: dt=0.9405, 4 negative triangles 147: dt=0.9405, 5 negative triangles 148: dt=0.9405, 4 negative triangles 149: dt=0.9405, 6 negative triangles 150: dt=0.9405, 4 negative triangles 151: dt=0.9405, 6 negative triangles 152: dt=0.9405, 4 negative triangles 153: dt=0.9405, 2 negative triangles 154: dt=0.9405, 2 negative triangles 155: dt=0.9405, 4 negative triangles 156: dt=0.9405, 1 negative triangles 157: dt=0.9405, 2 negative triangles 158: dt=0.9405, 1 negative triangles 159: dt=0.9405, 3 negative triangles 160: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.07 hours mris_register utimesec 4019.939876 mris_register stimesec 2.327646 mris_register ru_maxrss 230776 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 32363 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 8528 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 315355 mris_register ru_nivcsw 195696 FSRUNTIME@ mris_register 1.0735 hours 1 threads PIDs (29979 29982) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 05:53:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 05:53:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 1232 of (1232 1235) to complete... Waiting for PID 1235 of (1232 1235) 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 (1232 1235) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 05:53:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 05:53:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 1282 of (1282 1285) to complete... Waiting for PID 1285 of (1282 1285) 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 (1282 1285) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 05:53:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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 05:53:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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 1328 of (1328 1331) to complete... Waiting for PID 1331 of (1328 1331) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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... 1354 labels changed using aseg relabeling using gibbs priors... 000: 2712 changed, 121622 examined... 001: 691 changed, 11595 examined... 002: 179 changed, 3844 examined... 003: 53 changed, 1032 examined... 004: 16 changed, 341 examined... 005: 9 changed, 93 examined... 006: 9 changed, 58 examined... 007: 3 changed, 52 examined... 008: 1 changed, 23 examined... 009: 1 changed, 7 examined... 010: 0 changed, 6 examined... 198 labels changed using aseg 000: 117 total segments, 75 labels (307 vertices) changed 001: 44 total segments, 3 labels (5 vertices) changed 002: 41 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... 1931 vertices marked for relabeling... 1931 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 0050340 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... 1241 labels changed using aseg relabeling using gibbs priors... 000: 2457 changed, 119917 examined... 001: 569 changed, 10741 examined... 002: 138 changed, 3215 examined... 003: 60 changed, 843 examined... 004: 21 changed, 370 examined... 005: 5 changed, 124 examined... 006: 2 changed, 38 examined... 007: 0 changed, 16 examined... 164 labels changed using aseg 000: 97 total segments, 60 labels (224 vertices) changed 001: 39 total segments, 2 labels (6 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1611 vertices marked for relabeling... 1611 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 12 seconds. PIDs (1328 1331) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 05:53:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050340 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 05:53:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050340 rh Waiting for PID 1380 of (1380 1383) to complete... Waiting for PID 1383 of (1380 1383) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050340 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-6.0.0/0050340/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... 13065 bright wm thresholded. 2133 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.orig... computing class statistics... border white: 229073 voxels (1.37%) border gray 266822 voxels (1.59%) WM (97.0): 97.6 +- 7.9 [70.0 --> 110.0] GM (75.0) : 73.5 +- 10.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70) setting MAX_BORDER_WHITE to 109.9 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 48.3 (was 40) setting MAX_GRAY to 94.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 58.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.0 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-5.2, GM=69+-9.6 mean inside = 93.9, mean outside = 77.5 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.25 (0.04-->4.62) (max @ vno 120627 --> 120657) face area 0.34 +- 0.16 (0.00-->4.84) mean absolute distance = 0.62 +- 0.85 3268 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 3 with 150 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 18 points - only 0.00% unknown mean border=80.5, 132 (132) missing vertices, mean dist 0.4 [0.7 (%17.0)->0.6 (%83.0))] %67 local maxima, %29 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 +- 0.26 (0.06-->4.51) (max @ vno 120627 --> 120657) face area 0.34 +- 0.16 (0.00-->4.46) mean absolute distance = 0.39 +- 0.60 3656 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1899366.5, rms=7.518 001: dt: 0.5000, sse=1105996.0, rms=4.697 (37.518%) 002: dt: 0.5000, sse=837870.1, rms=3.306 (29.611%) 003: dt: 0.5000, sse=772723.8, rms=2.863 (13.416%) 004: dt: 0.5000, sse=749067.6, rms=2.661 (7.045%) rms = 2.69, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=681018.9, rms=2.003 (24.736%) 006: dt: 0.2500, sse=656116.5, rms=1.654 (17.402%) 007: dt: 0.2500, sse=646690.6, rms=1.552 (6.157%) rms = 1.50, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=643855.6, rms=1.503 (3.195%) rms = 1.46, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=640965.1, rms=1.463 (2.623%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 2 with 44 points - only 0.00% unknown deleting segment 3 with 19 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown mean border=83.7, 81 (35) missing vertices, mean dist -0.3 [0.4 (%72.8)->0.2 (%27.2))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.08-->4.68) (max @ vno 46767 --> 46768) face area 0.36 +- 0.18 (0.00-->4.98) mean absolute distance = 0.28 +- 0.42 3523 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1106662.9, rms=4.515 010: dt: 0.5000, sse=816369.9, rms=2.788 (38.251%) 011: dt: 0.5000, sse=769132.4, rms=2.406 (13.680%) 012: dt: 0.5000, sse=762395.7, rms=2.342 (2.686%) rms = 2.47, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=698470.7, rms=1.678 (28.351%) 014: dt: 0.2500, sse=675869.6, rms=1.324 (21.104%) 015: dt: 0.2500, sse=674159.1, rms=1.235 (6.739%) rms = 1.21, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=669123.4, rms=1.211 (1.937%) rms = 1.18, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=666462.9, rms=1.181 (2.444%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 54 points - only 0.00% unknown deleting segment 2 with 22 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown mean border=85.4, 109 (21) 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 0.90 +- 0.26 (0.06-->4.71) (max @ vno 46767 --> 46768) face area 0.35 +- 0.17 (0.00-->4.85) mean absolute distance = 0.26 +- 0.37 3047 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=775504.8, rms=2.691 018: dt: 0.5000, sse=702740.1, rms=1.955 (27.353%) rms = 2.02, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=659749.4, rms=1.465 (25.043%) 020: dt: 0.2500, sse=649105.2, rms=1.197 (18.325%) 021: dt: 0.2500, sse=639712.9, rms=1.129 (5.666%) rms = 1.12, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=639633.2, rms=1.124 (0.451%) rms = 1.09, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=637053.0, rms=1.088 (3.170%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 50 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 24 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown mean border=86.1, 113 (15) missing vertices, mean dist -0.0 [0.3 (%55.1)->0.2 (%44.9))] %87 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-6.0.0/0050340/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=654481.8, rms=1.525 024: dt: 0.5000, sse=646804.1, rms=1.355 (11.189%) rms = 1.72, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=622425.6, rms=0.998 (26.306%) 026: dt: 0.2500, sse=619401.9, rms=0.936 (6.293%) 027: dt: 0.2500, sse=616626.1, rms=0.885 (5.399%) rms = 0.91, time step reduction 2 of 3 to 0.125... rms = 0.87, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=614792.2, rms=0.869 (1.796%) positioning took 0.6 minutes generating cortex label... 10 non-cortical segments detected only using segment with 6925 vertices erasing segment 1 (vno[0] = 74227) erasing segment 2 (vno[0] = 78908) erasing segment 3 (vno[0] = 81531) erasing segment 4 (vno[0] = 84321) erasing segment 5 (vno[0] = 86043) erasing segment 6 (vno[0] = 87596) erasing segment 7 (vno[0] = 88421) erasing segment 8 (vno[0] = 90040) erasing segment 9 (vno[0] = 121233) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.area vertex spacing 0.90 +- 0.26 (0.04-->4.77) (max @ vno 46767 --> 46768) face area 0.34 +- 0.17 (0.00-->4.90) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=56.8, 129 (129) missing vertices, mean dist 1.8 [0.8 (%0.1)->3.0 (%99.9))] %14 local maxima, %43 large gradients and %38 min vals, 566 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=21580402.0, rms=30.076 001: dt: 0.0500, sse=19365454.0, rms=28.445 (5.423%) 002: dt: 0.0500, sse=17761332.0, rms=27.203 (4.368%) 003: dt: 0.0500, sse=16516768.0, rms=26.198 (3.693%) 004: dt: 0.0500, sse=15496659.0, rms=25.345 (3.257%) 005: dt: 0.0500, sse=14626565.0, rms=24.594 (2.964%) 006: dt: 0.0500, sse=13863962.0, rms=23.916 (2.756%) 007: dt: 0.0500, sse=13181819.0, rms=23.293 (2.606%) 008: dt: 0.0500, sse=12562952.0, rms=22.713 (2.491%) 009: dt: 0.0500, sse=11994850.0, rms=22.167 (2.404%) 010: dt: 0.0500, sse=11470442.0, rms=21.650 (2.329%) positioning took 0.8 minutes mean border=56.6, 102 (61) missing vertices, mean dist 1.5 [0.4 (%0.1)->2.5 (%99.9))] %15 local maxima, %43 large gradients and %37 min vals, 538 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=12146528.0, rms=22.311 011: dt: 0.0500, sse=11654303.0, rms=21.830 (2.155%) 012: dt: 0.0500, sse=11195148.0, rms=21.372 (2.100%) 013: dt: 0.0500, sse=10764958.0, rms=20.933 (2.052%) 014: dt: 0.0500, sse=10361075.0, rms=20.513 (2.008%) 015: dt: 0.0500, sse=9981607.0, rms=20.109 (1.965%) 016: dt: 0.0500, sse=9625494.0, rms=19.724 (1.919%) 017: dt: 0.0500, sse=9290741.0, rms=19.354 (1.875%) 018: dt: 0.0500, sse=8976233.0, rms=19.000 (1.829%) 019: dt: 0.0500, sse=8679966.0, rms=18.660 (1.788%) 020: dt: 0.0500, sse=8401549.0, rms=18.335 (1.742%) positioning took 0.8 minutes mean border=56.5, 130 (51) missing vertices, mean dist 1.3 [0.1 (%1.0)->2.2 (%99.0))] %16 local maxima, %43 large gradients and %37 min vals, 524 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=8499231.0, rms=18.454 021: dt: 0.0500, sse=8231438.0, rms=18.138 (1.714%) 022: dt: 0.0500, sse=7980170.0, rms=17.836 (1.664%) 023: dt: 0.0500, sse=7742240.0, rms=17.545 (1.630%) 024: dt: 0.0500, sse=7518705.0, rms=17.268 (1.583%) 025: dt: 0.0500, sse=7309095.0, rms=17.003 (1.532%) 026: dt: 0.0500, sse=7111351.0, rms=16.749 (1.491%) 027: dt: 0.0500, sse=6924478.0, rms=16.506 (1.453%) 028: dt: 0.0500, sse=6746713.0, rms=16.271 (1.423%) 029: dt: 0.0500, sse=6577139.5, rms=16.044 (1.397%) 030: dt: 0.0500, sse=6415323.0, rms=15.824 (1.372%) positioning took 0.8 minutes mean border=56.4, 172 (46) missing vertices, mean dist 1.1 [0.1 (%7.8)->2.0 (%92.2))] %16 local maxima, %43 large gradients and %36 min vals, 474 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=6491114.0, rms=15.926 031: dt: 0.5000, sse=5368080.0, rms=14.317 (10.103%) 032: dt: 0.5000, sse=4558397.5, rms=13.027 (9.010%) 033: dt: 0.5000, sse=3914014.2, rms=11.902 (8.642%) 034: dt: 0.5000, sse=3387371.8, rms=10.890 (8.499%) 035: dt: 0.5000, sse=2939488.8, rms=9.951 (8.623%) 036: dt: 0.5000, sse=2561440.2, rms=9.080 (8.748%) 037: dt: 0.5000, sse=2233541.8, rms=8.255 (9.089%) 038: dt: 0.5000, sse=1966830.9, rms=7.515 (8.963%) 039: dt: 0.5000, sse=1752777.1, rms=6.868 (8.616%) 040: dt: 0.5000, sse=1602711.6, rms=6.372 (7.222%) 041: dt: 0.5000, sse=1493620.2, rms=5.989 (6.003%) 042: dt: 0.5000, sse=1425187.8, rms=5.733 (4.270%) 043: dt: 0.5000, sse=1377356.4, rms=5.549 (3.219%) 044: dt: 0.5000, sse=1344583.4, rms=5.418 (2.365%) 045: dt: 0.5000, sse=1318798.0, rms=5.314 (1.917%) 046: dt: 0.5000, sse=1306892.4, rms=5.262 (0.970%) 047: dt: 0.5000, sse=1291795.0, rms=5.202 (1.147%) rms = 5.16, time step reduction 1 of 3 to 0.250... 048: dt: 0.5000, sse=1282866.6, rms=5.162 (0.769%) 049: dt: 0.2500, sse=1198317.6, rms=4.749 (7.992%) 050: dt: 0.2500, sse=1173798.0, rms=4.634 (2.421%) rms = 4.63, time step reduction 2 of 3 to 0.125... 051: dt: 0.2500, sse=1174079.8, rms=4.633 (0.022%) 052: dt: 0.1250, sse=1155451.9, rms=4.540 (2.026%) rms = 4.52, time step reduction 3 of 3 to 0.062... 053: dt: 0.1250, sse=1151561.5, rms=4.521 (0.408%) positioning took 2.6 minutes mean border=55.1, 1889 (23) missing vertices, mean dist 0.2 [0.2 (%43.5)->0.6 (%56.5))] %28 local maxima, %34 large gradients and %32 min vals, 233 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=1460955.1, rms=5.073 054: dt: 0.5000, sse=1355623.0, rms=4.610 (9.119%) 055: dt: 0.5000, sse=1291179.2, rms=4.327 (6.137%) rms = 4.45, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=1201828.1, rms=3.809 (11.981%) 057: dt: 0.2500, sse=1178547.9, rms=3.656 (4.025%) rms = 3.64, time step reduction 2 of 3 to 0.125... 058: dt: 0.2500, sse=1174891.4, rms=3.635 (0.555%) 059: dt: 0.1250, sse=1150706.1, rms=3.477 (4.354%) rms = 3.45, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1146255.9, rms=3.450 (0.776%) positioning took 1.0 minutes mean border=54.4, 2176 (17) missing vertices, mean dist 0.1 [0.2 (%46.2)->0.4 (%53.8))] %35 local maxima, %27 large gradients and %31 min vals, 274 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=1189576.4, rms=3.700 rms = 4.07, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1163811.5, rms=3.540 (4.316%) rms = 3.49, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1155400.2, rms=3.494 (1.306%) 063: dt: 0.1250, sse=1146441.6, rms=3.434 (1.726%) rms = 3.41, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1142229.1, rms=3.410 (0.697%) positioning took 0.7 minutes mean border=53.8, 4561 (16) missing vertices, mean dist 0.1 [0.2 (%46.8)->0.3 (%53.2))] %39 local maxima, %23 large gradients and %30 min vals, 265 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-6.0.0/0050340/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1153928.2, rms=3.474 rms = 3.71, time step reduction 1 of 3 to 0.250... 065: dt: 0.2500, sse=1138889.1, rms=3.378 (2.761%) 066: dt: 0.2500, sse=1128137.5, rms=3.326 (1.533%) rms = 3.32, time step reduction 2 of 3 to 0.125... 067: dt: 0.2500, sse=1125477.4, rms=3.320 (0.194%) 068: dt: 0.1250, sse=1109833.0, rms=3.212 (3.245%) rms = 3.18, time step reduction 3 of 3 to 0.062... 069: dt: 0.1250, sse=1105193.0, rms=3.185 (0.842%) positioning took 0.8 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.area.pial vertex spacing 1.04 +- 0.47 (0.05-->7.86) (max @ vno 45749 --> 46752) face area 0.43 +- 0.35 (0.00-->6.92) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 121622 vertices processed 25000 of 121622 vertices processed 50000 of 121622 vertices processed 75000 of 121622 vertices processed 100000 of 121622 vertices processed 0 of 121622 vertices processed 25000 of 121622 vertices processed 50000 of 121622 vertices processed 75000 of 121622 vertices processed 100000 of 121622 vertices processed thickness calculation complete, 452:1401 truncations. 24624 vertices at 0 distance 78087 vertices at 1 distance 74655 vertices at 2 distance 35625 vertices at 3 distance 12538 vertices at 4 distance 4179 vertices at 5 distance 1433 vertices at 6 distance 521 vertices at 7 distance 239 vertices at 8 distance 148 vertices at 9 distance 67 vertices at 10 distance 50 vertices at 11 distance 24 vertices at 12 distance 21 vertices at 13 distance 12 vertices at 14 distance 9 vertices at 15 distance 15 vertices at 16 distance 14 vertices at 17 distance 10 vertices at 18 distance 14 vertices at 19 distance 19 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.thickness positioning took 13.9 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050340 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-6.0.0/0050340/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... 13065 bright wm thresholded. 2133 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.orig... computing class statistics... border white: 229073 voxels (1.37%) border gray 266822 voxels (1.59%) WM (97.0): 97.6 +- 7.9 [70.0 --> 110.0] GM (75.0) : 73.5 +- 10.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.7 (was 70) setting MAX_BORDER_WHITE to 108.9 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 49.3 (was 40) setting MAX_GRAY to 93.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 59.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.0 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-5.2, GM=70+-8.7 mean inside = 93.6, mean outside = 77.6 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 0.90 +- 0.26 (0.03-->7.83) (max @ vno 46682 --> 47728) face area 0.34 +- 0.16 (0.00-->9.78) mean absolute distance = 0.63 +- 0.85 3160 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 165 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown mean border=80.8, 152 (152) missing vertices, mean dist 0.4 [0.7 (%16.5)->0.6 (%83.5))] %64 local maxima, %31 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 +- 0.26 (0.09-->7.93) (max @ vno 46682 --> 47728) face area 0.34 +- 0.17 (0.00-->9.20) mean absolute distance = 0.39 +- 0.62 3880 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1807746.6, rms=7.301 001: dt: 0.5000, sse=1066233.8, rms=4.580 (37.265%) 002: dt: 0.5000, sse=818003.1, rms=3.218 (29.745%) 003: dt: 0.5000, sse=761274.4, rms=2.819 (12.383%) 004: dt: 0.5000, sse=735714.6, rms=2.605 (7.598%) rms = 2.67, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=673792.6, rms=1.992 (23.554%) 006: dt: 0.2500, sse=650773.1, rms=1.689 (15.186%) 007: dt: 0.2500, sse=645030.1, rms=1.610 (4.707%) 008: dt: 0.2500, sse=643867.4, rms=1.556 (3.300%) rms = 1.53, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=642473.4, rms=1.529 (1.766%) 010: dt: 0.1250, sse=635012.4, rms=1.466 (4.102%) rms = 1.44, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=634952.6, rms=1.443 (1.558%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 2 with 75 points - only 0.00% unknown mean border=83.8, 117 (40) missing vertices, mean dist -0.3 [0.5 (%71.4)->0.2 (%28.6))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.06-->8.12) (max @ vno 46682 --> 47728) face area 0.36 +- 0.18 (0.00-->10.93) mean absolute distance = 0.29 +- 0.43 2943 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1067343.9, rms=4.387 012: dt: 0.5000, sse=803273.6, rms=2.773 (36.776%) 013: dt: 0.5000, sse=756263.0, rms=2.365 (14.739%) 014: dt: 0.5000, sse=742896.2, rms=2.308 (2.383%) rms = 2.41, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=701202.3, rms=1.710 (25.936%) 016: dt: 0.2500, sse=671960.1, rms=1.388 (18.806%) 017: dt: 0.2500, sse=665020.5, rms=1.313 (5.383%) rms = 1.28, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=667913.8, rms=1.280 (2.577%) 019: dt: 0.1250, sse=660522.6, rms=1.223 (4.440%) rms = 1.21, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=659820.6, rms=1.213 (0.817%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 2 with 96 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown mean border=85.6, 134 (18) missing vertices, mean dist -0.1 [0.3 (%64.9)->0.2 (%35.1))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.26 (0.06-->8.19) (max @ vno 46682 --> 47728) face area 0.35 +- 0.17 (0.00-->10.84) mean absolute distance = 0.27 +- 0.38 2969 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=769914.9, rms=2.701 021: dt: 0.5000, sse=699001.4, rms=1.965 (27.259%) rms = 1.95, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=694048.2, rms=1.952 (0.642%) 023: dt: 0.2500, sse=644179.5, rms=1.275 (34.709%) 024: dt: 0.2500, sse=636775.1, rms=1.173 (7.944%) rms = 1.18, time step reduction 2 of 3 to 0.125... rms = 1.15, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=633585.6, rms=1.145 (2.395%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 16 points - only 0.00% unknown deleting segment 2 with 100 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown mean border=86.3, 159 (10) missing vertices, mean dist -0.0 [0.3 (%55.5)->0.2 (%44.5))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=653294.9, rms=1.592 026: dt: 0.5000, sse=656641.4, rms=1.500 (5.760%) rms = 1.85, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=622819.6, rms=1.077 (28.198%) rms = 1.04, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=620004.1, rms=1.037 (3.763%) 029: dt: 0.1250, sse=618372.4, rms=0.917 (11.494%) rms = 0.89, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=612092.9, rms=0.888 (3.216%) positioning took 0.5 minutes generating cortex label... 9 non-cortical segments detected only using segment with 6487 vertices erasing segment 0 (vno[0] = 26406) erasing segment 2 (vno[0] = 71077) erasing segment 3 (vno[0] = 87194) erasing segment 4 (vno[0] = 87252) erasing segment 5 (vno[0] = 88984) erasing segment 6 (vno[0] = 89863) erasing segment 7 (vno[0] = 91509) erasing segment 8 (vno[0] = 95241) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.area vertex spacing 0.90 +- 0.27 (0.03-->8.13) (max @ vno 46682 --> 47728) face area 0.34 +- 0.17 (0.00-->10.56) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=57.6, 131 (131) missing vertices, mean dist 1.8 [2.2 (%0.0)->2.9 (%100.0))] %15 local maxima, %44 large gradients and %36 min vals, 591 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=20408548.0, rms=29.413 001: dt: 0.0500, sse=18309564.0, rms=27.813 (5.441%) 002: dt: 0.0500, sse=16789010.0, rms=26.593 (4.385%) 003: dt: 0.0500, sse=15610624.0, rms=25.608 (3.705%) 004: dt: 0.0500, sse=14646511.0, rms=24.772 (3.262%) 005: dt: 0.0500, sse=13824793.0, rms=24.037 (2.967%) 006: dt: 0.0500, sse=13104972.0, rms=23.375 (2.758%) 007: dt: 0.0500, sse=12461850.0, rms=22.766 (2.604%) 008: dt: 0.0500, sse=11878083.0, rms=22.199 (2.490%) 009: dt: 0.0500, sse=11342533.0, rms=21.666 (2.402%) 010: dt: 0.0500, sse=10847932.0, rms=21.161 (2.328%) positioning took 0.8 minutes mean border=57.4, 128 (78) missing vertices, mean dist 1.5 [0.1 (%0.1)->2.4 (%99.9))] %16 local maxima, %44 large gradients and %36 min vals, 541 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=11513734.0, rms=21.837 011: dt: 0.0500, sse=11049723.0, rms=21.368 (2.148%) 012: dt: 0.0500, sse=10617016.0, rms=20.921 (2.091%) 013: dt: 0.0500, sse=10211636.0, rms=20.493 (2.044%) 014: dt: 0.0500, sse=9831656.0, rms=20.084 (1.996%) 015: dt: 0.0500, sse=9475515.0, rms=19.693 (1.948%) 016: dt: 0.0500, sse=9140648.0, rms=19.318 (1.905%) 017: dt: 0.0500, sse=8826024.0, rms=18.958 (1.860%) 018: dt: 0.0500, sse=8530604.0, rms=18.614 (1.813%) 019: dt: 0.0500, sse=8252879.5, rms=18.285 (1.768%) 020: dt: 0.0500, sse=7991695.5, rms=17.970 (1.724%) positioning took 0.8 minutes mean border=57.3, 151 (63) missing vertices, mean dist 1.3 [0.1 (%1.1)->2.1 (%98.9))] %16 local maxima, %44 large gradients and %35 min vals, 547 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=8077674.5, rms=18.079 021: dt: 0.0500, sse=7826690.0, rms=17.773 (1.694%) 022: dt: 0.0500, sse=7591056.5, rms=17.480 (1.646%) 023: dt: 0.0500, sse=7368005.0, rms=17.199 (1.611%) 024: dt: 0.0500, sse=7158465.5, rms=16.930 (1.563%) 025: dt: 0.0500, sse=6961092.0, rms=16.672 (1.520%) 026: dt: 0.0500, sse=6775065.0, rms=16.426 (1.477%) 027: dt: 0.0500, sse=6598864.5, rms=16.189 (1.442%) 028: dt: 0.0500, sse=6430541.0, rms=15.960 (1.419%) 029: dt: 0.0500, sse=6269295.0, rms=15.736 (1.399%) 030: dt: 0.0500, sse=6115394.0, rms=15.520 (1.373%) positioning took 0.8 minutes mean border=57.2, 168 (46) missing vertices, mean dist 1.1 [0.1 (%8.5)->1.9 (%91.5))] %16 local maxima, %45 large gradients and %35 min vals, 495 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=6182341.5, rms=15.613 031: dt: 0.5000, sse=5104997.5, rms=14.018 (10.217%) 032: dt: 0.5000, sse=4330064.5, rms=12.740 (9.115%) 033: dt: 0.5000, sse=3712054.8, rms=11.622 (8.776%) 034: dt: 0.5000, sse=3205165.0, rms=10.611 (8.701%) 035: dt: 0.5000, sse=2788919.0, rms=9.704 (8.548%) 036: dt: 0.5000, sse=2442450.0, rms=8.875 (8.541%) 037: dt: 0.5000, sse=2149780.0, rms=8.113 (8.588%) 038: dt: 0.5000, sse=1908280.9, rms=7.422 (8.513%) 039: dt: 0.5000, sse=1705555.5, rms=6.795 (8.457%) 040: dt: 0.5000, sse=1550840.9, rms=6.270 (7.726%) 041: dt: 0.5000, sse=1434894.1, rms=5.849 (6.702%) 042: dt: 0.5000, sse=1362893.0, rms=5.568 (4.805%) 043: dt: 0.5000, sse=1311564.2, rms=5.363 (3.683%) 044: dt: 0.5000, sse=1280024.9, rms=5.229 (2.505%) 045: dt: 0.5000, sse=1256800.1, rms=5.131 (1.868%) 046: dt: 0.5000, sse=1241845.2, rms=5.064 (1.311%) 047: dt: 0.5000, sse=1227281.8, rms=5.003 (1.197%) rms = 4.98, time step reduction 1 of 3 to 0.250... 048: dt: 0.5000, sse=1222123.1, rms=4.978 (0.515%) 049: dt: 0.2500, sse=1137956.1, rms=4.546 (8.661%) 050: dt: 0.2500, sse=1114729.9, rms=4.430 (2.551%) rms = 4.42, time step reduction 2 of 3 to 0.125... 051: dt: 0.2500, sse=1112668.5, rms=4.418 (0.285%) 052: dt: 0.1250, sse=1096986.9, rms=4.333 (1.911%) rms = 4.31, time step reduction 3 of 3 to 0.062... 053: dt: 0.1250, sse=1093048.5, rms=4.313 (0.462%) positioning took 2.5 minutes mean border=55.9, 1844 (19) missing vertices, mean dist 0.2 [0.2 (%44.3)->0.6 (%55.7))] %29 local maxima, %35 large gradients and %30 min vals, 197 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=1417579.2, rms=4.968 054: dt: 0.5000, sse=1314785.0, rms=4.500 (9.422%) 055: dt: 0.5000, sse=1253552.2, rms=4.217 (6.283%) rms = 4.34, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=1169453.6, rms=3.710 (12.026%) 057: dt: 0.2500, sse=1146950.6, rms=3.558 (4.109%) rms = 3.54, time step reduction 2 of 3 to 0.125... 058: dt: 0.2500, sse=1144232.9, rms=3.542 (0.439%) 059: dt: 0.1250, sse=1121915.8, rms=3.391 (4.271%) rms = 3.36, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1117015.8, rms=3.360 (0.918%) positioning took 1.0 minutes mean border=55.2, 2057 (12) missing vertices, mean dist 0.1 [0.2 (%46.4)->0.4 (%53.6))] %36 local maxima, %28 large gradients and %30 min vals, 218 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=1161311.2, rms=3.624 rms = 3.95, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1134411.9, rms=3.450 (4.783%) 062: dt: 0.2500, sse=1123789.9, rms=3.386 (1.863%) rms = 3.39, time step reduction 2 of 3 to 0.125... rms = 3.36, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1119671.1, rms=3.357 (0.856%) positioning took 0.6 minutes mean border=54.7, 4182 (11) missing vertices, mean dist 0.1 [0.2 (%47.3)->0.3 (%52.7))] %41 local maxima, %23 large gradients and %28 min vals, 231 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-6.0.0/0050340/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1135882.9, rms=3.456 rms = 3.72, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1117968.0, rms=3.338 (3.429%) 065: dt: 0.2500, sse=1104542.8, rms=3.267 (2.135%) rms = 3.26, time step reduction 2 of 3 to 0.125... 066: dt: 0.2500, sse=1102385.4, rms=3.263 (0.113%) 067: dt: 0.1250, sse=1086868.2, rms=3.153 (3.369%) rms = 3.12, time step reduction 3 of 3 to 0.062... 068: dt: 0.1250, sse=1081908.5, rms=3.124 (0.919%) positioning took 0.8 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.area.pial vertex spacing 1.04 +- 0.47 (0.08-->7.38) (max @ vno 80091 --> 79091) face area 0.43 +- 0.35 (0.00-->9.74) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 119917 vertices processed 25000 of 119917 vertices processed 50000 of 119917 vertices processed 75000 of 119917 vertices processed 100000 of 119917 vertices processed 0 of 119917 vertices processed 25000 of 119917 vertices processed 50000 of 119917 vertices processed 75000 of 119917 vertices processed 100000 of 119917 vertices processed thickness calculation complete, 426:1456 truncations. 25286 vertices at 0 distance 79460 vertices at 1 distance 73130 vertices at 2 distance 34050 vertices at 3 distance 11585 vertices at 4 distance 3689 vertices at 5 distance 1270 vertices at 6 distance 478 vertices at 7 distance 212 vertices at 8 distance 77 vertices at 9 distance 55 vertices at 10 distance 22 vertices at 11 distance 19 vertices at 12 distance 14 vertices at 13 distance 14 vertices at 14 distance 16 vertices at 15 distance 13 vertices at 16 distance 10 vertices at 17 distance 5 vertices at 18 distance 8 vertices at 19 distance 13 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.thickness positioning took 13.6 minutes PIDs (1380 1383) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 06:07:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label Total face volume 245242 Total vertex volume 242494 (mask=0) #@# 0050340 lh 242494 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 06:07:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label Total face volume 240534 Total vertex volume 237315 (mask=0) #@# 0050340 rh 237315 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 06:07:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 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 = 431 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/ribbon.mgz mris_volmask took 8.55 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 06:15:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 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 0050340 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 06:15:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 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 0050340 rh pial Waiting for PID 2870 of (2870 2873 2876 2879) to complete... Waiting for PID 2873 of (2870 2873 2876 2879) to complete... Waiting for PID 2876 of (2870 2873 2876 2879) to complete... Waiting for PID 2879 of (2870 2873 2876 2879) 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 0050340 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 245242 Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 1314 917 2464 2.810 0.518 0.100 0.018 9 1.0 bankssts 793 503 1459 2.816 0.638 0.131 0.026 10 0.7 caudalanteriorcingulate 2728 1842 6109 2.946 0.565 0.108 0.020 22 2.1 caudalmiddlefrontal 2049 1337 3139 2.098 0.583 0.153 0.042 32 3.5 cuneus 556 381 1327 2.923 0.979 0.141 0.050 9 1.2 entorhinal 3691 2576 8351 2.816 0.687 0.137 0.039 50 5.5 fusiform 5662 3898 11987 2.695 0.613 0.127 0.030 67 7.1 inferiorparietal 4630 3109 10021 2.735 0.866 0.135 0.043 72 8.6 inferiortemporal 1344 858 2584 2.675 0.915 0.126 0.034 18 1.5 isthmuscingulate 7386 5003 13650 2.328 0.668 0.144 0.040 99 12.0 lateraloccipital 4041 2700 7892 2.728 0.754 0.143 0.044 64 7.6 lateralorbitofrontal 4547 3200 7431 2.095 0.673 0.151 0.040 64 7.6 lingual 3018 2057 5467 2.397 0.787 0.128 0.042 40 5.2 medialorbitofrontal 4210 2970 12304 3.138 0.763 0.128 0.034 54 5.8 middletemporal 865 553 1908 2.737 0.915 0.081 0.017 4 0.5 parahippocampal 2026 1340 3945 2.753 0.672 0.108 0.024 15 2.2 paracentral 2223 1505 5498 3.047 0.524 0.113 0.024 22 2.1 parsopercularis 1023 674 2856 3.134 0.656 0.139 0.037 16 1.7 parsorbitalis 1881 1268 4323 2.776 0.722 0.137 0.037 28 2.7 parstriangularis 1908 1312 2105 1.704 0.461 0.130 0.037 20 3.0 pericalcarine 5423 3528 8965 2.255 0.721 0.112 0.025 53 5.3 postcentral 1545 1072 3243 2.760 0.774 0.150 0.037 24 2.2 posteriorcingulate 7139 4402 14254 2.926 0.643 0.110 0.028 68 8.5 precentral 4594 3155 9283 2.512 0.676 0.134 0.031 56 5.8 precuneus 1121 755 2759 2.960 0.719 0.131 0.034 15 1.5 rostralanteriorcingulate 7435 5281 17130 2.711 0.692 0.150 0.042 111 13.4 rostralmiddlefrontal 9620 6566 24949 3.201 0.738 0.129 0.031 116 12.3 superiorfrontal 6646 4481 12027 2.466 0.581 0.127 0.030 74 8.1 superiorparietal 5131 3519 12405 2.862 0.740 0.109 0.024 41 5.4 superiortemporal 4625 3236 10587 2.889 0.585 0.139 0.030 60 5.8 supramarginal 400 269 1300 2.960 0.648 0.183 0.074 12 0.9 frontalpole 566 460 3053 4.182 0.626 0.161 0.048 10 1.1 temporalpole 664 410 1100 2.418 0.448 0.108 0.029 6 0.7 transversetemporal 3441 2303 6603 2.947 0.764 0.126 0.035 39 4.7 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 0050340 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 245242 Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 1314 839 2464 2.810 0.518 0.132 0.035 20 2.1 bankssts 793 615 1459 2.816 0.638 0.214 0.061 77 1.8 caudalanteriorcingulate 2728 2211 6109 2.946 0.565 0.122 0.028 30 3.5 caudalmiddlefrontal 2049 1692 3139 2.098 0.583 0.149 0.037 31 3.3 cuneus 556 528 1327 2.923 0.979 0.232 0.074 20 2.0 entorhinal 3691 3345 8351 2.816 0.687 0.168 0.044 53 7.5 fusiform 5662 4922 11987 2.695 0.613 0.153 0.036 76 9.6 inferiorparietal 4630 4047 10021 2.735 0.866 0.162 0.042 73 9.6 inferiortemporal 1344 1053 2584 2.675 0.915 0.153 0.039 19 2.3 isthmuscingulate 7386 6432 13650 2.328 0.668 0.155 0.038 98 12.9 lateraloccipital 4041 2985 7892 2.728 0.754 0.140 0.037 69 6.8 lateralorbitofrontal 4547 4019 7431 2.095 0.673 0.163 0.041 82 8.2 lingual 3018 2578 5467 2.397 0.787 0.153 0.041 46 5.5 medialorbitofrontal 4210 4553 12304 3.138 0.763 0.167 0.035 48 7.1 middletemporal 865 877 1908 2.737 0.915 0.166 0.039 8 1.6 parahippocampal 2026 1607 3945 2.753 0.672 0.126 0.027 20 2.5 paracentral 2223 2054 5498 3.047 0.524 0.151 0.032 22 3.2 parsopercularis 1023 1085 2856 3.134 0.656 0.157 0.029 11 1.5 parsorbitalis 1881 1740 4323 2.776 0.722 0.162 0.037 39 3.5 parstriangularis 1908 1209 2105 1.704 0.461 0.134 0.036 27 2.9 pericalcarine 5423 4438 8965 2.255 0.721 0.127 0.028 51 7.1 postcentral 1545 1268 3243 2.760 0.774 0.165 0.042 30 2.8 posteriorcingulate 7139 5191 14254 2.926 0.643 0.106 0.023 76 6.9 precentral 4594 4002 9283 2.512 0.676 0.156 0.037 62 7.7 precuneus 1121 1081 2759 2.960 0.719 0.157 0.040 15 1.9 rostralanteriorcingulate 7435 7004 17130 2.711 0.692 0.179 0.040 120 14.6 rostralmiddlefrontal 9620 8749 24949 3.201 0.738 0.155 0.037 134 16.0 superiorfrontal 6646 5237 12027 2.466 0.581 0.132 0.029 74 8.7 superiorparietal 5131 4750 12405 2.862 0.740 0.148 0.030 55 7.3 superiortemporal 4625 4063 10587 2.889 0.585 0.152 0.034 75 6.9 supramarginal 400 552 1300 2.960 0.648 0.264 0.066 10 1.6 frontalpole 566 958 3053 4.182 0.626 0.232 0.041 6 1.1 temporalpole 664 529 1100 2.418 0.448 0.123 0.030 4 0.9 transversetemporal 3441 2123 6603 2.947 0.764 0.123 0.035 59 5.0 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 0050340 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 240534 Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 1269 889 2356 2.931 0.569 0.121 0.023 10 1.2 bankssts 1019 673 2032 2.780 0.630 0.126 0.021 12 0.8 caudalanteriorcingulate 2671 1751 6021 3.060 0.540 0.108 0.023 22 2.4 caudalmiddlefrontal 1864 1270 2889 2.069 0.544 0.164 0.050 31 4.1 cuneus 606 388 1405 2.967 1.018 0.134 0.077 11 2.2 entorhinal 3824 2594 8522 2.773 0.733 0.138 0.040 55 6.5 fusiform 6912 4850 14443 2.484 0.661 0.128 0.031 86 9.1 inferiorparietal 4297 2825 8980 2.640 0.804 0.138 0.055 88 12.2 inferiortemporal 1427 927 3062 2.659 0.878 0.125 0.035 17 1.8 isthmuscingulate 6487 4435 12330 2.298 0.659 0.149 0.040 91 10.2 lateraloccipital 3947 2655 7608 2.578 0.748 0.146 0.053 65 9.1 lateralorbitofrontal 4350 2993 6866 2.056 0.619 0.142 0.038 54 6.8 lingual 2716 1857 5955 2.717 0.879 0.129 0.037 40 4.4 medialorbitofrontal 4604 3223 12027 3.050 0.764 0.130 0.035 64 6.9 middletemporal 1070 654 2008 2.534 0.860 0.108 0.037 13 1.6 parahippocampal 2173 1388 3996 2.681 0.679 0.098 0.021 12 1.9 paracentral 1895 1252 4828 3.122 0.681 0.114 0.023 16 1.9 parsopercularis 1116 784 3263 3.121 0.719 0.153 0.037 17 1.7 parsorbitalis 2166 1488 4811 2.778 0.684 0.120 0.025 22 2.3 parstriangularis 1612 1184 1940 1.766 0.521 0.123 0.033 13 2.1 pericalcarine 4970 3294 8059 2.169 0.710 0.109 0.026 46 5.0 postcentral 1700 1183 3295 2.413 0.906 0.150 0.033 28 2.2 posteriorcingulate 7050 4441 14631 2.935 0.597 0.109 0.029 62 8.8 precentral 5090 3492 9180 2.477 0.663 0.126 0.027 57 5.4 precuneus 753 503 1803 3.244 0.626 0.136 0.037 9 1.1 rostralanteriorcingulate 7675 5391 17447 2.637 0.690 0.146 0.039 108 12.5 rostralmiddlefrontal 9422 6257 23712 3.137 0.711 0.125 0.036 110 14.6 superiorfrontal 7185 4768 12707 2.327 0.572 0.123 0.029 80 8.4 superiorparietal 4860 3324 11522 2.856 0.730 0.111 0.028 52 6.0 superiortemporal 3877 2619 8795 2.871 0.602 0.129 0.031 44 4.6 supramarginal 418 292 1338 2.946 0.877 0.178 0.053 9 1.0 frontalpole 568 403 2480 3.737 0.774 0.144 0.039 10 0.9 temporalpole 519 316 928 2.569 0.574 0.110 0.029 6 0.5 transversetemporal 2915 2016 6038 3.038 0.670 0.129 0.036 30 4.0 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 0050340 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 240534 Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 1269 709 2356 2.931 0.569 0.121 0.030 17 1.5 bankssts 1019 829 2032 2.780 0.630 0.169 0.040 27 1.8 caudalanteriorcingulate 2671 2140 6021 3.060 0.540 0.118 0.026 29 3.0 caudalmiddlefrontal 1864 1592 2889 2.069 0.544 0.156 0.040 25 3.2 cuneus 606 486 1405 2.967 1.018 0.160 0.051 14 1.3 entorhinal 3824 3344 8522 2.773 0.733 0.153 0.041 48 6.7 fusiform 6912 6454 14443 2.484 0.661 0.157 0.034 85 10.6 inferiorparietal 4297 3656 8980 2.640 0.804 0.162 0.043 71 8.6 inferiortemporal 1427 1230 3062 2.659 0.878 0.160 0.042 25 2.7 isthmuscingulate 6487 5930 12330 2.298 0.659 0.164 0.039 98 11.9 lateraloccipital 3947 3160 7608 2.578 0.748 0.160 0.050 78 10.6 lateralorbitofrontal 4350 3782 6866 2.056 0.619 0.154 0.038 57 7.4 lingual 2716 2492 5955 2.717 0.879 0.161 0.041 43 5.1 medialorbitofrontal 4604 4538 12027 3.050 0.764 0.165 0.039 53 8.7 middletemporal 1070 876 2008 2.534 0.860 0.154 0.042 14 2.2 parahippocampal 2173 1570 3996 2.681 0.679 0.114 0.024 17 2.3 paracentral 1895 1675 4828 3.122 0.681 0.140 0.033 17 2.7 parsopercularis 1116 1270 3263 3.121 0.719 0.167 0.030 11 1.5 parsorbitalis 2166 1918 4811 2.778 0.684 0.162 0.033 30 3.3 parstriangularis 1612 1103 1940 1.766 0.521 0.132 0.034 21 2.3 pericalcarine 4970 4090 8059 2.169 0.710 0.123 0.024 47 5.3 postcentral 1700 1459 3295 2.413 0.906 0.160 0.038 31 2.9 posteriorcingulate 7050 5244 14631 2.935 0.597 0.109 0.024 73 7.6 precentral 5090 3942 9180 2.477 0.663 0.141 0.038 78 8.5 precuneus 753 646 1803 3.244 0.626 0.151 0.044 14 1.4 rostralanteriorcingulate 7675 7386 17447 2.637 0.690 0.177 0.041 115 14.8 rostralmiddlefrontal 9422 8322 23712 3.137 0.711 0.150 0.037 126 15.8 superiorfrontal 7185 5858 12707 2.327 0.572 0.139 0.030 85 9.8 superiorparietal 4860 4584 11522 2.856 0.730 0.159 0.039 76 9.5 superiortemporal 3877 3283 8795 2.871 0.602 0.143 0.032 44 5.8 supramarginal 418 593 1338 2.946 0.877 0.248 0.046 7 1.0 frontalpole 568 810 2480 3.737 0.774 0.205 0.040 6 1.1 temporalpole 519 429 928 2.569 0.574 0.131 0.033 4 0.8 transversetemporal 2915 1831 6038 3.038 0.670 0.128 0.046 51 6.6 insula PIDs (2870 2873 2876 2879) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 06:16:55 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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 06:16:55 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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 3003 of (3003 3006) to complete... Waiting for PID 3006 of (3003 3006) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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... 15 labels changed using aseg relabeling using gibbs priors... 000: 8033 changed, 121622 examined... 001: 1932 changed, 31209 examined... 002: 529 changed, 10129 examined... 003: 237 changed, 3043 examined... 004: 104 changed, 1359 examined... 005: 53 changed, 602 examined... 006: 23 changed, 294 examined... 007: 16 changed, 138 examined... 008: 11 changed, 90 examined... 009: 6 changed, 59 examined... 010: 2 changed, 34 examined... 011: 2 changed, 10 examined... 012: 3 changed, 16 examined... 013: 4 changed, 18 examined... 014: 2 changed, 19 examined... 015: 1 changed, 15 examined... 016: 0 changed, 7 examined... 3 labels changed using aseg 000: 253 total segments, 166 labels (2019 vertices) changed 001: 94 total segments, 7 labels (9 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 41 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1361 vertices marked for relabeling... 1361 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 16 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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... 13 labels changed using aseg relabeling using gibbs priors... 000: 7923 changed, 119917 examined... 001: 1863 changed, 31124 examined... 002: 521 changed, 9925 examined... 003: 259 changed, 2964 examined... 004: 109 changed, 1439 examined... 005: 40 changed, 615 examined... 006: 22 changed, 216 examined... 007: 16 changed, 118 examined... 008: 12 changed, 86 examined... 009: 5 changed, 68 examined... 010: 4 changed, 26 examined... 011: 2 changed, 21 examined... 012: 3 changed, 16 examined... 013: 0 changed, 17 examined... 15 labels changed using aseg 000: 219 total segments, 135 labels (1684 vertices) changed 001: 87 total segments, 4 labels (9 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1217 vertices marked for relabeling... 1217 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 16 seconds. PIDs (3003 3006) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 06:17:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 06:17:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 rh white Waiting for PID 3053 of (3053 3056) to complete... Waiting for PID 3056 of (3053 3056) 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 0050340 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 245242 Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 1195 845 2528 2.523 0.659 0.144 0.037 16 1.9 G&S_frontomargin 1436 976 3687 2.815 0.652 0.145 0.037 19 2.0 G&S_occipital_inf 1680 1031 3138 2.573 0.709 0.111 0.028 15 2.0 G&S_paracentral 1209 797 2828 2.959 0.532 0.133 0.027 15 1.3 G&S_subcentral 744 545 2456 2.944 0.775 0.198 0.066 23 2.1 G&S_transv_frontopol 2135 1469 4555 2.942 0.683 0.123 0.030 20 2.5 G&S_cingul-Ant 1023 738 2232 2.998 0.686 0.117 0.021 7 0.8 G&S_cingul-Mid-Ant 1201 840 2571 2.827 0.667 0.123 0.026 12 1.2 G&S_cingul-Mid-Post 548 379 1622 3.112 0.787 0.183 0.054 13 1.3 G_cingul-Post-dorsal 362 202 798 3.066 0.871 0.138 0.053 7 0.5 G_cingul-Post-ventral 1902 1229 3102 2.066 0.633 0.154 0.050 34 4.1 G_cuneus 1388 904 3938 3.178 0.518 0.133 0.031 20 1.7 G_front_inf-Opercular 491 304 1345 3.236 0.710 0.141 0.052 8 1.0 G_front_inf-Orbital 1120 741 3367 3.213 0.583 0.140 0.040 20 1.5 G_front_inf-Triangul 3824 2653 11427 3.074 0.663 0.153 0.043 66 7.0 G_front_middle 6843 4515 19956 3.336 0.726 0.137 0.036 99 10.1 G_front_sup 698 448 1376 3.021 0.788 0.147 0.043 11 1.2 G_Ins_lg&S_cent_ins 753 499 2246 3.224 0.720 0.145 0.048 15 1.3 G_insular_short 2099 1410 5112 2.655 0.618 0.141 0.045 31 3.6 G_occipital_middle 1236 843 1977 2.074 0.518 0.152 0.039 18 1.8 G_occipital_sup 1590 1077 4037 2.935 0.646 0.162 0.049 30 3.0 G_oc-temp_lat-fusifor 3302 2314 5565 1.996 0.696 0.164 0.047 55 6.6 G_oc-temp_med-Lingual 1078 690 2606 2.819 0.932 0.121 0.044 15 1.7 G_oc-temp_med-Parahip 2530 1654 6175 2.768 0.871 0.165 0.065 58 7.1 G_orbital 2154 1482 5737 2.826 0.635 0.150 0.042 38 3.8 G_pariet_inf-Angular 2308 1618 6248 3.032 0.583 0.146 0.031 36 3.1 G_pariet_inf-Supramar 2865 1919 6070 2.540 0.619 0.132 0.033 37 4.2 G_parietal_sup 2113 1272 3888 2.341 0.721 0.126 0.034 30 2.8 G_postcentral 2680 1486 6563 3.238 0.621 0.114 0.038 33 4.2 G_precentral 2265 1544 6127 2.839 0.606 0.158 0.042 40 3.8 G_precuneus 956 657 2277 2.507 0.742 0.153 0.065 18 2.4 G_rectus 900 589 941 1.865 0.813 0.104 0.045 10 1.6 G_subcallosal 529 317 982 2.394 0.542 0.113 0.037 6 0.8 G_temp_sup-G_T_transv 1743 1222 6279 3.408 0.717 0.150 0.041 26 3.0 G_temp_sup-Lateral 600 421 1670 3.235 0.998 0.100 0.024 3 0.5 G_temp_sup-Plan_polar 744 513 1449 2.555 0.571 0.080 0.012 2 0.4 G_temp_sup-Plan_tempo 2374 1558 6267 2.766 0.981 0.151 0.062 54 6.4 G_temporal_inf 2269 1612 8418 3.408 0.704 0.152 0.048 43 4.4 G_temporal_middle 204 143 349 2.513 0.395 0.097 0.012 1 0.1 Lat_Fis-ant-Horizont 166 118 281 2.628 0.497 0.103 0.017 1 0.1 Lat_Fis-ant-Vertical 939 641 1255 2.659 0.597 0.116 0.023 7 0.8 Lat_Fis-post 2177 1454 3839 2.189 0.711 0.151 0.047 33 4.4 Pole_occipital 1379 1039 5267 3.517 0.767 0.150 0.041 22 2.4 Pole_temporal 2296 1599 2636 1.853 0.534 0.122 0.028 17 2.6 S_calcarine 2993 2021 3885 2.192 0.750 0.104 0.023 21 2.8 S_central 1141 789 1724 2.515 0.608 0.104 0.018 7 0.8 S_cingul-Marginalis 538 355 932 3.179 0.552 0.106 0.019 3 0.4 S_circular_insula_ant 1500 1015 2301 2.699 0.625 0.083 0.015 5 1.0 S_circular_insula_inf 1576 1065 2260 2.611 0.525 0.098 0.020 7 1.3 S_circular_insula_sup 645 448 1300 3.243 0.837 0.109 0.021 4 0.6 S_collat_transv_ant 582 406 717 2.164 0.603 0.117 0.021 4 0.5 S_collat_transv_post 2112 1504 3822 2.648 0.455 0.125 0.028 19 2.4 S_front_inf 1167 843 2000 2.464 0.624 0.131 0.031 11 1.6 S_front_middle 2235 1575 3996 2.700 0.521 0.107 0.022 17 2.0 S_front_sup 165 122 392 2.965 0.847 0.133 0.034 2 0.2 S_interm_prim-Jensen 2669 1850 3829 2.452 0.497 0.119 0.022 23 2.2 S_intrapariet&P_trans 1080 756 1419 2.066 0.436 0.135 0.030 9 1.5 S_oc_middle&Lunatus 976 675 1306 2.117 0.386 0.117 0.032 10 1.0 S_oc_sup&transversal 749 516 1211 2.443 0.516 0.130 0.031 9 0.8 S_occipital_ant 928 643 1452 2.495 0.483 0.105 0.021 5 0.8 S_oc-temp_lat 1837 1301 3005 2.517 0.553 0.106 0.018 12 1.3 S_oc-temp_med&Lingual 425 286 555 2.110 0.422 0.107 0.019 2 0.3 S_orbital_lateral 646 468 926 2.202 0.613 0.129 0.028 6 0.6 S_orbital_med-olfact 1660 1127 3189 2.816 0.621 0.132 0.032 21 2.2 S_orbital-H_Shaped 1439 1001 2035 2.116 0.625 0.128 0.025 15 1.4 S_parieto_occipital 1268 757 1277 2.293 0.834 0.124 0.022 17 0.9 S_pericallosal 2440 1656 3952 2.611 0.507 0.112 0.021 18 2.2 S_postcentral 1456 1015 2616 2.838 0.489 0.091 0.013 6 0.8 S_precentral-inf-part 1290 903 2140 2.745 0.463 0.100 0.018 6 1.0 S_precentral-sup-part 667 477 1167 2.789 0.711 0.123 0.019 5 0.6 S_suborbital 793 551 1294 2.499 0.612 0.118 0.022 5 0.7 S_subparietal 1537 1077 2346 2.455 0.602 0.114 0.020 11 1.3 S_temporal_inf 5405 3729 9877 2.752 0.581 0.102 0.018 33 4.2 S_temporal_sup 282 201 384 2.231 0.404 0.129 0.017 2 0.2 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 0050340 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 240534 Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 850 596 1703 2.309 0.759 0.148 0.040 12 1.6 G&S_frontomargin 1171 818 2897 2.699 0.685 0.151 0.044 17 1.9 G&S_occipital_inf 1371 791 2366 2.500 0.675 0.110 0.037 12 2.3 G&S_paracentral 1109 718 2680 3.067 0.565 0.133 0.035 14 1.4 G&S_subcentral 1026 767 3515 3.181 0.793 0.170 0.050 18 2.1 G&S_transv_frontopol 2566 1791 5526 2.924 0.668 0.120 0.028 23 3.0 G&S_cingul-Ant 1265 894 2717 3.096 0.532 0.118 0.023 11 1.1 G&S_cingul-Mid-Ant 1343 953 2655 2.715 0.683 0.139 0.030 16 1.5 G&S_cingul-Mid-Post 568 392 1708 3.105 0.845 0.180 0.047 12 1.2 G_cingul-Post-dorsal 344 209 932 2.919 0.804 0.126 0.042 5 0.5 G_cingul-Post-ventral 1841 1247 2944 2.022 0.593 0.164 0.051 33 4.1 G_cuneus 1256 808 3984 3.371 0.636 0.132 0.030 16 1.5 G_front_inf-Opercular 360 241 1282 3.387 0.526 0.162 0.045 7 0.7 G_front_inf-Orbital 981 665 2854 3.161 0.609 0.140 0.032 16 1.2 G_front_inf-Triangul 3009 1991 9164 3.083 0.690 0.148 0.044 54 5.3 G_front_middle 6492 4108 18458 3.287 0.684 0.137 0.045 102 12.8 G_front_sup 498 358 1332 3.383 0.685 0.130 0.036 7 0.5 G_Ins_lg&S_cent_ins 612 388 1650 3.197 0.671 0.140 0.049 10 1.1 G_insular_short 1785 1200 3795 2.351 0.660 0.152 0.043 30 3.1 G_occipital_middle 1432 932 2556 2.244 0.580 0.145 0.039 20 2.3 G_occipital_sup 1699 1076 4105 2.806 0.766 0.156 0.059 37 4.3 G_oc-temp_lat-fusifor 2758 1873 4656 2.040 0.651 0.154 0.043 41 4.8 G_oc-temp_med-Lingual 1157 679 2568 2.797 0.979 0.134 0.073 23 3.7 G_oc-temp_med-Parahip 2528 1736 6949 2.932 0.780 0.161 0.058 48 6.8 G_orbital 2530 1802 7455 2.849 0.674 0.164 0.046 54 4.8 G_pariet_inf-Angular 1900 1277 5009 3.057 0.638 0.147 0.040 30 2.7 G_pariet_inf-Supramar 2099 1408 5013 2.614 0.566 0.135 0.036 33 3.0 G_parietal_sup 1706 1119 3097 2.137 0.572 0.121 0.032 22 2.3 G_postcentral 2693 1554 7249 3.238 0.552 0.114 0.038 33 4.4 G_precentral 2615 1758 5239 2.402 0.638 0.135 0.033 38 3.2 G_precuneus 779 535 2363 2.868 0.924 0.152 0.057 18 2.0 G_rectus 652 392 804 2.219 1.077 0.102 0.047 10 0.9 G_subcallosal 402 245 800 2.582 0.647 0.122 0.038 5 0.5 G_temp_sup-G_T_transv 1663 1124 5477 3.248 0.688 0.144 0.039 29 2.8 G_temp_sup-Lateral 878 585 1757 2.621 0.763 0.109 0.048 10 2.0 G_temp_sup-Plan_polar 721 507 1431 2.641 0.503 0.090 0.018 6 0.5 G_temp_sup-Plan_tempo 2185 1348 5335 2.701 0.921 0.156 0.089 68 10.2 G_temporal_inf 2739 1925 8728 3.291 0.717 0.157 0.049 55 5.7 G_temporal_middle 373 256 458 2.095 0.433 0.094 0.013 2 0.2 Lat_Fis-ant-Horizont 271 178 467 2.908 0.454 0.097 0.017 1 0.2 Lat_Fis-ant-Vertical 1164 804 1648 2.453 0.519 0.111 0.023 7 1.1 Lat_Fis-post 2844 1939 5024 2.117 0.628 0.149 0.045 42 5.1 Pole_occipital 1420 1046 5706 3.619 0.786 0.147 0.039 22 2.3 Pole_temporal 1807 1307 2386 2.102 0.635 0.122 0.028 16 2.1 S_calcarine 2867 1959 3689 2.195 0.744 0.098 0.020 14 2.3 S_central 1111 785 1606 2.167 0.511 0.098 0.017 6 0.7 S_cingul-Marginalis 483 335 902 3.315 0.467 0.115 0.024 3 0.5 S_circular_insula_ant 1117 776 1729 2.768 0.642 0.100 0.019 6 0.9 S_circular_insula_inf 1302 897 2075 2.834 0.474 0.113 0.022 7 1.4 S_circular_insula_sup 733 535 1500 2.834 0.557 0.108 0.020 5 0.6 S_collat_transv_ant 630 433 872 2.034 0.542 0.142 0.040 7 1.0 S_collat_transv_post 2293 1610 3963 2.441 0.502 0.109 0.020 16 1.9 S_front_inf 1757 1248 3140 2.419 0.556 0.143 0.038 21 2.6 S_front_middle 2388 1651 4557 2.771 0.584 0.113 0.024 16 2.4 S_front_sup 175 131 403 2.798 0.313 0.122 0.021 1 0.2 S_interm_prim-Jensen 3220 2122 4238 2.142 0.496 0.102 0.017 20 2.2 S_intrapariet&P_trans 705 479 962 2.138 0.504 0.132 0.027 6 0.8 S_oc_middle&Lunatus 1104 767 1292 1.842 0.398 0.124 0.029 8 1.3 S_oc_sup&transversal 664 468 1308 2.377 0.553 0.126 0.025 8 0.7 S_occipital_ant 1085 746 1587 2.375 0.538 0.111 0.021 6 1.0 S_oc-temp_lat 2232 1549 3410 2.396 0.585 0.105 0.017 14 1.5 S_oc-temp_med&Lingual 421 287 661 2.707 0.547 0.119 0.031 3 0.5 S_orbital_lateral 713 509 1023 2.116 0.479 0.144 0.039 7 1.3 S_orbital_med-olfact 1328 914 2374 2.549 0.573 0.138 0.044 19 2.2 S_orbital-H_Shaped 1665 1182 2523 2.404 0.677 0.106 0.020 11 1.4 S_parieto_occipital 1607 985 1605 2.115 0.792 0.116 0.021 20 1.1 S_pericallosal 2023 1359 2963 2.292 0.520 0.101 0.018 13 1.4 S_postcentral 1654 1145 2820 2.747 0.444 0.101 0.017 9 1.1 S_precentral-inf-part 1320 903 2149 2.791 0.484 0.085 0.013 4 0.8 S_precentral-sup-part 402 283 640 2.776 0.884 0.099 0.016 2 0.2 S_suborbital 1058 721 2029 2.795 0.576 0.131 0.029 10 1.2 S_subparietal 1243 894 1978 2.496 0.655 0.126 0.021 13 1.2 S_temporal_inf 6039 4197 10542 2.658 0.601 0.099 0.018 35 4.7 S_temporal_sup 228 159 333 2.528 0.454 0.118 0.020 1 0.2 S_temporal_transverse PIDs (3053 3056) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 06:17:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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 06:17:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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 3126 of (3126 3129) to complete... Waiting for PID 3129 of (3126 3129) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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... 1369 labels changed using aseg relabeling using gibbs priors... 000: 1854 changed, 121622 examined... 001: 428 changed, 8446 examined... 002: 105 changed, 2472 examined... 003: 46 changed, 614 examined... 004: 23 changed, 279 examined... 005: 21 changed, 128 examined... 006: 20 changed, 103 examined... 007: 8 changed, 92 examined... 008: 8 changed, 45 examined... 009: 8 changed, 40 examined... 010: 4 changed, 39 examined... 011: 5 changed, 23 examined... 012: 3 changed, 31 examined... 013: 3 changed, 15 examined... 014: 2 changed, 18 examined... 015: 1 changed, 7 examined... 016: 1 changed, 7 examined... 017: 3 changed, 10 examined... 018: 2 changed, 11 examined... 019: 1 changed, 13 examined... 020: 1 changed, 7 examined... 021: 1 changed, 7 examined... 022: 1 changed, 7 examined... 023: 3 changed, 9 examined... 024: 2 changed, 13 examined... 025: 5 changed, 14 examined... 026: 4 changed, 26 examined... 027: 2 changed, 26 examined... 028: 3 changed, 13 examined... 029: 1 changed, 17 examined... 030: 0 changed, 7 examined... 265 labels changed using aseg 000: 54 total segments, 21 labels (205 vertices) changed 001: 34 total segments, 1 labels (7 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... 851 vertices marked for relabeling... 851 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 0050340 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... 1174 labels changed using aseg relabeling using gibbs priors... 000: 1715 changed, 119917 examined... 001: 381 changed, 8021 examined... 002: 128 changed, 2190 examined... 003: 34 changed, 735 examined... 004: 23 changed, 201 examined... 005: 21 changed, 151 examined... 006: 19 changed, 121 examined... 007: 8 changed, 76 examined... 008: 12 changed, 55 examined... 009: 14 changed, 61 examined... 010: 15 changed, 71 examined... 011: 15 changed, 65 examined... 012: 10 changed, 66 examined... 013: 7 changed, 45 examined... 014: 4 changed, 29 examined... 015: 2 changed, 19 examined... 016: 0 changed, 14 examined... 219 labels changed using aseg 000: 52 total segments, 19 labels (147 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 924 vertices marked for relabeling... 924 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 13 seconds. PIDs (3126 3129) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 06:18:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 06:18:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 rh white Waiting for PID 3214 of (3214 3217) to complete... Waiting for PID 3217 of (3214 3217) 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 0050340 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 245242 Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 1685 1104 3577 2.994 0.654 0.130 0.028 19 1.9 caudalanteriorcingulate 2981 2006 6577 2.924 0.566 0.108 0.019 24 2.3 caudalmiddlefrontal 2602 1721 4078 2.099 0.620 0.142 0.038 36 4.0 cuneus 456 312 1107 2.815 0.963 0.154 0.057 9 1.1 entorhinal 3445 2414 7401 2.777 0.679 0.136 0.037 45 4.9 fusiform 5658 3909 11955 2.663 0.619 0.127 0.030 67 7.0 inferiorparietal 4542 3054 10479 2.765 0.870 0.137 0.044 72 8.8 inferiortemporal 1308 836 2562 2.737 0.879 0.127 0.034 18 1.4 isthmuscingulate 7430 5012 13800 2.331 0.668 0.145 0.040 101 12.1 lateraloccipital 4634 3133 9104 2.603 0.808 0.151 0.052 82 10.2 lateralorbitofrontal 4601 3241 7469 2.084 0.673 0.152 0.040 64 7.8 lingual 2489 1705 4813 2.403 0.770 0.132 0.046 36 4.5 medialorbitofrontal 5565 3910 14616 3.072 0.723 0.124 0.031 65 7.1 middletemporal 945 599 2097 2.770 0.918 0.083 0.019 5 0.5 parahippocampal 2292 1532 4642 2.814 0.687 0.106 0.023 16 2.3 paracentral 2010 1363 5086 3.074 0.521 0.117 0.025 21 2.0 parsopercularis 1017 662 2462 3.095 0.642 0.117 0.024 9 0.9 parsorbitalis 2370 1616 5208 2.722 0.692 0.140 0.038 36 3.6 parstriangularis 1918 1318 2131 1.707 0.463 0.134 0.040 23 3.4 pericalcarine 6209 4038 10678 2.326 0.735 0.116 0.026 63 6.5 postcentral 1742 1212 3515 2.747 0.799 0.147 0.035 26 2.5 posteriorcingulate 6985 4299 13933 2.930 0.642 0.109 0.029 66 8.3 precentral 4508 3110 9385 2.542 0.667 0.138 0.033 58 6.0 precuneus 1531 1025 3373 2.980 0.736 0.125 0.032 17 1.8 rostralanteriorcingulate 5392 3798 13083 2.816 0.672 0.150 0.040 78 9.1 rostralmiddlefrontal 10192 6997 26137 3.078 0.793 0.133 0.034 136 14.4 superiorfrontal 5390 3632 9450 2.461 0.538 0.123 0.028 55 6.1 superiorparietal 6550 4551 16929 2.955 0.814 0.112 0.025 58 7.0 superiortemporal 4286 3007 9814 2.914 0.576 0.140 0.030 56 5.4 supramarginal 691 425 1116 2.399 0.453 0.110 0.031 7 0.8 transversetemporal 2825 1902 5916 3.118 0.646 0.123 0.032 31 3.5 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 0050340 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 240534 Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 1054 707 2119 2.761 0.679 0.129 0.022 13 0.9 caudalanteriorcingulate 2934 1916 6398 3.031 0.546 0.110 0.024 24 2.8 caudalmiddlefrontal 2263 1542 3620 2.122 0.550 0.154 0.047 35 4.6 cuneus 442 303 1152 3.199 0.784 0.112 0.034 5 0.4 entorhinal 3592 2427 7560 2.696 0.679 0.136 0.040 52 6.0 fusiform 6725 4709 14064 2.469 0.669 0.129 0.032 87 9.0 inferiorparietal 4517 2972 10034 2.724 0.852 0.137 0.054 87 12.3 inferiortemporal 1403 903 2976 2.675 0.859 0.125 0.034 17 1.7 isthmuscingulate 6659 4551 12578 2.291 0.658 0.150 0.041 95 10.8 lateraloccipital 4079 2797 8765 2.627 0.734 0.157 0.054 70 10.2 lateralorbitofrontal 4331 2968 6826 2.059 0.615 0.142 0.038 54 6.8 lingual 2094 1409 4436 2.627 0.974 0.125 0.043 34 3.5 medialorbitofrontal 5687 3990 14131 3.023 0.745 0.129 0.033 76 8.2 middletemporal 1245 739 2198 2.459 0.857 0.120 0.058 21 3.5 parahippocampal 2288 1450 4229 2.665 0.683 0.097 0.021 13 2.0 paracentral 2117 1415 5198 3.070 0.697 0.115 0.024 18 2.2 parsopercularis 1023 707 2668 2.903 0.672 0.135 0.032 13 1.4 parsorbitalis 2168 1479 4815 2.778 0.679 0.125 0.027 23 2.4 parstriangularis 1554 1142 1846 1.756 0.522 0.122 0.032 12 2.0 pericalcarine 5451 3609 8885 2.188 0.721 0.112 0.027 53 5.7 postcentral 1800 1260 3471 2.427 0.892 0.149 0.033 29 2.4 posteriorcingulate 6745 4274 14214 2.940 0.603 0.109 0.029 59 8.4 precentral 5257 3606 9566 2.473 0.659 0.129 0.028 61 5.8 precuneus 1043 698 2271 3.100 0.794 0.122 0.031 10 1.3 rostralanteriorcingulate 5479 3861 12521 2.652 0.697 0.147 0.039 80 8.6 rostralmiddlefrontal 12010 8029 29940 3.057 0.726 0.130 0.037 149 19.1 superiorfrontal 5852 3915 10448 2.331 0.567 0.121 0.028 63 6.5 superiorparietal 6266 4302 15343 2.922 0.764 0.115 0.029 70 7.7 superiortemporal 3759 2533 8442 2.852 0.601 0.125 0.031 40 4.4 supramarginal 516 315 916 2.564 0.570 0.112 0.029 6 0.6 transversetemporal 2676 1846 5685 3.112 0.614 0.123 0.032 26 3.2 insula PIDs (3214 3217) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 06:18:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts pctsurfcon --s 0050340 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 06:18:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts pctsurfcon --s 0050340 --rh-only Waiting for PID 3295 of (3295 3306) to complete... Waiting for PID 3306 of (3295 3306) to complete... pctsurfcon --s 0050340 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts/pctsurfcon.log Sun Oct 8 06:18:33 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-6.0.0/0050340/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-593 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-6.0.0/0050340/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.wm.mgh --regheader 0050340 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 58165 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.wm.mgh Dim: 121622 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.gm.mgh --projfrac 0.3 --regheader 0050340 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 68884 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.gm.mgh Dim: 121622 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.w-g.pct.mgh --annot 0050340 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/lh.w-g.pct.mgh --annot 0050340 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-593 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/lh.w-g.pct.mgh Vertex Area is 0.677322 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 0050340 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts/pctsurfcon.log Sun Oct 8 06:18:33 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-6.0.0/0050340/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-593 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-6.0.0/0050340/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.wm.mgh --regheader 0050340 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 57491 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.wm.mgh Dim: 119917 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.gm.mgh --projfrac 0.3 --regheader 0050340 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 68145 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.gm.mgh Dim: 119917 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.w-g.pct.mgh --annot 0050340 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.w-g.pct.mgh --annot 0050340 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-593 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.w-g.pct.mgh Vertex Area is 0.678036 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 (3295 3306) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 06:18:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1543 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1405 voxels changed to hypointensity... 2921 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 06:18:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340 mri_aparc2aseg --s 0050340 --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 06:18:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340 mri_aparc2aseg --s 0050340 --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 06:18:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340 mri_aparc2aseg --s 0050340 --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 3472 of (3472 3475 3478) to complete... Waiting for PID 3475 of (3472 3475 3478) to complete... Waiting for PID 3478 of (3472 3475 3478) to complete... mri_aparc2aseg --s 0050340 --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 0050340 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/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-6.0.0/0050340/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 6.21 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 64 rescaling Left_Lateral_Ventricle from 13 --> 20 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 62 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 70 rescaling Left_Putamen from 80 --> 81 rescaling Left_Pallidum from 98 --> 93 rescaling Third_Ventricle from 25 --> 34 rescaling Fourth_Ventricle from 22 --> 14 rescaling Brain_Stem from 81 --> 89 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 49 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 63 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 61 rescaling Right_Thalamus_Proper from 85 --> 82 rescaling Right_Caudate from 62 --> 72 rescaling Right_Putamen from 80 --> 77 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 64 rescaling Right_Amygdala from 55 --> 72 rescaling Right_Accumbens_area from 65 --> 70 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 42 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 43 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 = 475832 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 96 changed. pass 2: 7 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aparc+aseg.mgz mri_aparc2aseg --s 0050340 --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 0050340 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/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-6.0.0/0050340/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 6.21 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 64 rescaling Left_Lateral_Ventricle from 13 --> 20 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 62 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 70 rescaling Left_Putamen from 80 --> 81 rescaling Left_Pallidum from 98 --> 93 rescaling Third_Ventricle from 25 --> 34 rescaling Fourth_Ventricle from 22 --> 14 rescaling Brain_Stem from 81 --> 89 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 49 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 63 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 61 rescaling Right_Thalamus_Proper from 85 --> 82 rescaling Right_Caudate from 62 --> 72 rescaling Right_Putamen from 80 --> 77 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 64 rescaling Right_Amygdala from 55 --> 72 rescaling Right_Accumbens_area from 65 --> 70 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 42 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 43 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 = 475868 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 96 changed. pass 2: 7 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0050340 --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 0050340 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/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-6.0.0/0050340/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 6.21 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 64 rescaling Left_Lateral_Ventricle from 13 --> 20 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 62 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 70 rescaling Left_Putamen from 80 --> 81 rescaling Left_Pallidum from 98 --> 93 rescaling Third_Ventricle from 25 --> 34 rescaling Fourth_Ventricle from 22 --> 14 rescaling Brain_Stem from 81 --> 89 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 49 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 63 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 61 rescaling Right_Thalamus_Proper from 85 --> 82 rescaling Right_Caudate from 62 --> 72 rescaling Right_Putamen from 80 --> 77 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 64 rescaling Right_Amygdala from 55 --> 72 rescaling Right_Accumbens_area from 65 --> 70 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 42 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 43 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 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#----------------------------------------- #@# APas-to-ASeg Sun Oct 8 06:25:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 06:25:43 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-593 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-6.0.0/0050340/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-593 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 06:25:43 CEST 2017 Ended at Sun Oct 8 06:25:49 CEST 2017 Apas2aseg-Run-Time-Sec 6 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 06:25:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340 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 0050340 $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 0050340 sysname Linux hostname tars-593 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1444308 mm^3 (det: 1.348816 ) Computing euler number orig.nofix lheno = -92, rheno = -104 orig.nofix lhholes = 47, rhholes = 53 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 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 06:27:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340 mri_aparc2aseg --s 0050340 --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 0050340 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-6.0.0/0050340/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7377 vertices from left hemi Ripped 6890 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-6.0.0/0050340/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 891413 Used brute-force search on 19 voxels Fixing Parahip LH WM Found 13 clusters 0 k 2.000000 1 k 3.000000 2 k 1.000000 3 k 1085.000000 4 k 1.000000 5 k 2.000000 6 k 1.000000 7 k 1.000000 8 k 7.000000 9 k 11.000000 10 k 1.000000 11 k 3.000000 12 k 1.000000 Fixing Parahip RH WM Found 11 clusters 0 k 1.000000 1 k 1.000000 2 k 3.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1441.000000 8 k 1.000000 9 k 1.000000 10 k 1.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050340 --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 0050340 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-593 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1444308 mm^3 (det: 1.348816 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 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-6.0.0/0050340/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 06:35:32 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 5436 of (5436 5442 5448 5454 5457) to complete... Waiting for PID 5442 of (5436 5442 5448 5454 5457) to complete... Waiting for PID 5448 of (5436 5442 5448 5454 5457) to complete... Waiting for PID 5454 of (5436 5442 5448 5454 5457) to complete... Waiting for PID 5457 of (5436 5442 5448 5454 5457) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 190 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4319 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 256 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8165 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4173 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 220 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6203 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 348 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6132 mri_label2label: Done PIDs (5436 5442 5448 5454 5457) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 5517 of (5517 5523 5529 5535) to complete... Waiting for PID 5523 of (5517 5523 5529 5535) to complete... Waiting for PID 5529 of (5517 5523 5529 5535) to complete... Waiting for PID 5535 of (5517 5523 5529 5535) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 224 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4294 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 851 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14440 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4446 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 671 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4093 mri_label2label: Done PIDs (5517 5523 5529 5535) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 5580 of (5580 5586 5592 5597 5603) to complete... Waiting for PID 5586 of (5580 5586 5592 5597 5603) to complete... Waiting for PID 5592 of (5580 5586 5592 5597 5603) to complete... Waiting for PID 5597 of (5580 5586 5592 5597 5603) to complete... Waiting for PID 5603 of (5580 5586 5592 5597 5603) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 1247 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5888 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 2608 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10722 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 446 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2464 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1353 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1220 mri_label2label: Done PIDs (5580 5586 5592 5597 5603) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 5651 of (5651 5657 5663 5669 5674) to complete... Waiting for PID 5657 of (5651 5657 5663 5669 5674) to complete... Waiting for PID 5663 of (5651 5657 5663 5669 5674) to complete... Waiting for PID 5669 of (5651 5657 5663 5669 5674) to complete... Waiting for PID 5674 of (5651 5657 5663 5669 5674) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1090 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2173 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1546 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2051 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 143 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2462 mri_label2label: Done PIDs (5651 5657 5663 5669 5674) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 5729 of (5729 5735 5741 5746) to complete... Waiting for PID 5735 of (5729 5735 5741 5746) to complete... Waiting for PID 5741 of (5729 5735 5741 5746) to complete... Waiting for PID 5746 of (5729 5735 5741 5746) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 84 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1633 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 456 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7491 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2006 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 299 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1450 mri_label2label: Done PIDs (5729 5735 5741 5746) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 5789 of (5789 5795 5801 5807 5811) to complete... Waiting for PID 5795 of (5789 5795 5801 5807 5811) to complete... Waiting for PID 5801 of (5789 5795 5801 5807 5811) to complete... Waiting for PID 5807 of (5789 5795 5801 5807 5811) to complete... Waiting for PID 5811 of (5789 5795 5801 5807 5811) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 818 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4223 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 1240 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4574 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 607 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 523 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 465 mri_label2label: Done PIDs (5789 5795 5801 5807 5811) completed and logs appended. mris_label2annot --s 0050340 --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-6.0.0/0050340/label cmdline mris_label2annot --s 0050340 --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-593 machine x86_64 user ntraut subject 0050340 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-6.0.0/0050340/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 83379 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.BA_exvivo.annot mris_label2annot --s 0050340 --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-6.0.0/0050340/label cmdline mris_label2annot --s 0050340 --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-593 machine x86_64 user ntraut subject 0050340 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-6.0.0/0050340/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 98785 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 245242 Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 1077 612 1991 2.405 0.607 0.127 0.038 15 1.4 BA1_exvivo 3283 2202 6266 2.671 0.586 0.119 0.026 33 3.4 BA2_exvivo 1009 672 1035 1.933 0.489 0.130 0.026 10 1.0 BA3a_exvivo 2002 1375 3099 1.979 0.801 0.119 0.025 20 2.0 BA3b_exvivo 1558 949 3189 2.959 0.622 0.105 0.030 11 2.1 BA4a_exvivo 1330 820 2250 2.811 0.600 0.102 0.031 12 1.8 BA4p_exvivo 8441 5435 21257 3.237 0.679 0.114 0.028 86 9.5 BA6_exvivo 2006 1343 4659 3.016 0.507 0.111 0.022 18 1.7 BA44_exvivo 3016 2058 7163 2.835 0.655 0.139 0.035 44 4.1 BA45_exvivo 3336 2333 4455 1.808 0.608 0.143 0.043 45 6.2 V1_exvivo 8133 5455 13180 2.088 0.646 0.151 0.041 116 13.9 V2_exvivo 2075 1417 4189 2.586 0.583 0.140 0.034 26 3.0 MT_exvivo 490 316 1377 3.025 0.950 0.124 0.050 8 1.0 perirhinal_exvivo 487 359 1209 3.128 0.960 0.135 0.032 6 0.6 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050340 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 245242 Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 700 363 1210 2.396 0.594 0.139 0.041 12 1.1 BA1_exvivo 1338 883 2452 2.540 0.630 0.105 0.024 12 1.3 BA2_exvivo 855 572 839 1.896 0.479 0.137 0.030 9 0.9 BA3a_exvivo 1228 875 1434 1.576 0.426 0.098 0.018 7 1.0 BA3b_exvivo 1588 946 3115 3.021 0.592 0.102 0.031 12 2.1 BA4a_exvivo 1092 695 1744 2.611 0.578 0.108 0.030 10 1.6 BA4p_exvivo 4741 2929 10918 3.137 0.684 0.108 0.030 45 5.6 BA6_exvivo 1250 865 3151 3.110 0.480 0.117 0.026 12 1.1 BA44_exvivo 1278 859 4029 3.246 0.583 0.154 0.041 25 2.1 BA45_exvivo 3585 2486 4929 1.838 0.627 0.144 0.043 48 6.8 V1_exvivo 4133 2807 5934 1.915 0.588 0.159 0.047 64 8.1 V2_exvivo 511 348 978 2.524 0.503 0.130 0.030 6 0.5 MT_exvivo 261 168 718 2.887 1.085 0.134 0.066 5 0.8 perirhinal_exvivo 277 201 695 3.109 0.886 0.139 0.038 3 0.5 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 06:38:12 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 5934 of (5934 5940 5946 5952 5958) to complete... Waiting for PID 5940 of (5934 5940 5946 5952 5958) to complete... Waiting for PID 5946 of (5934 5940 5946 5952 5958) to complete... Waiting for PID 5952 of (5934 5940 5946 5952 5958) to complete... Waiting for PID 5958 of (5934 5940 5946 5952 5958) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 164 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4126 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 177 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6864 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4079 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 127 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4649 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 341 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6088 mri_label2label: Done PIDs (5934 5940 5946 5952 5958) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 6003 of (6003 6009 6015 6021) to complete... Waiting for PID 6009 of (6003 6009 6015 6021) to complete... Waiting for PID 6015 of (6003 6009 6015 6021) to complete... Waiting for PID 6021 of (6003 6009 6015 6021) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 232 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4705 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 877 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13133 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 524 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7436 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 761 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6116 mri_label2label: Done PIDs (6003 6009 6015 6021) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 6075 of (6075 6081 6087 6092 6097) to complete... Waiting for PID 6081 of (6075 6081 6087 6092 6097) to complete... Waiting for PID 6087 of (6075 6081 6087 6092 6097) to complete... Waiting for PID 6092 of (6075 6081 6087 6092 6097) to complete... Waiting for PID 6097 of (6075 6081 6087 6092 6097) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 907 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5634 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 1973 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9989 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 283 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2215 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 173 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1211 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 84 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 836 mri_label2label: Done PIDs (6075 6081 6087 6092 6097) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 6160 of (6160 6166 6172 6177 6183) to complete... Waiting for PID 6166 of (6160 6166 6172 6177 6183) to complete... Waiting for PID 6172 of (6160 6166 6172 6177 6183) to complete... Waiting for PID 6177 of (6160 6166 6172 6177 6183) to complete... Waiting for PID 6183 of (6160 6166 6172 6177 6183) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 922 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2732 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1736 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2239 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1447 mri_label2label: Done PIDs (6160 6166 6172 6177 6183) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 6229 of (6229 6235 6241 6246) to complete... Waiting for PID 6235 of (6229 6235 6241 6246) to complete... Waiting for PID 6241 of (6229 6235 6241 6246) to complete... Waiting for PID 6246 of (6229 6235 6241 6246) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 92 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1581 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 339 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7298 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1081 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 124 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1302 mri_label2label: Done PIDs (6229 6235 6241 6246) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 6298 of (6298 6304 6310 6316 6322) to complete... Waiting for PID 6304 of (6298 6304 6310 6316 6322) to complete... Waiting for PID 6310 of (6298 6304 6310 6316 6322) to complete... Waiting for PID 6316 of (6298 6304 6310 6316 6322) to complete... Waiting for PID 6322 of (6298 6304 6310 6316 6322) 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 514 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3746 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 975 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4412 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 304 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 143 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 837 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 0050340 --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 = 0050340 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-6.0.0/0050340/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 303 mri_label2label: Done PIDs (6298 6304 6310 6316 6322) completed and logs appended. mris_label2annot --s 0050340 --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-6.0.0/0050340/label cmdline mris_label2annot --s 0050340 --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-593 machine x86_64 user ntraut subject 0050340 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-6.0.0/0050340/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 83420 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.BA_exvivo.annot mris_label2annot --s 0050340 --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-6.0.0/0050340/label cmdline mris_label2annot --s 0050340 --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-593 machine x86_64 user ntraut subject 0050340 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-6.0.0/0050340/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 99885 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 240534 Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 844 496 1560 2.233 0.621 0.146 0.048 16 1.8 BA1_exvivo 2478 1685 4164 2.317 0.555 0.104 0.020 19 1.8 BA2_exvivo 1048 687 1002 1.956 0.518 0.119 0.027 8 1.0 BA3a_exvivo 1674 1108 2276 1.830 0.649 0.103 0.022 13 1.4 BA3b_exvivo 1548 896 3206 3.050 0.486 0.093 0.028 11 2.0 BA4a_exvivo 1294 834 2277 2.768 0.549 0.105 0.029 8 1.8 BA4p_exvivo 7369 4631 17464 3.089 0.627 0.111 0.034 78 10.7 BA6_exvivo 3194 2147 7565 3.024 0.599 0.117 0.024 28 3.2 BA44_exvivo 4118 2836 9849 2.817 0.681 0.131 0.029 48 5.1 BA45_exvivo 3022 2198 4627 1.882 0.625 0.144 0.044 39 5.4 V1_exvivo 7166 4799 11441 2.121 0.581 0.149 0.042 100 12.1 V2_exvivo 1781 1256 3213 2.284 0.566 0.130 0.031 19 2.4 MT_exvivo 614 364 1484 2.934 1.088 0.136 0.089 13 2.7 perirhinal_exvivo 347 244 899 3.061 1.075 0.128 0.051 6 0.7 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 0050340 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 240534 Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 ) lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099 rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276 lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286 rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654 SubCortGMVol 57332.000 SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272 SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273 BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209 BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005 BrainSegVolNotVent 1089936.000 CerebellumVol 138078.000 VentChorVol 6338.000 3rd4th5thCSF 3059.000 CSFVol 756.000, OptChiasmVol 205.000 MaskVol 1454196.000 515 320 898 2.012 0.577 0.147 0.052 11 1.1 BA1_exvivo 1352 959 2381 2.276 0.483 0.093 0.017 8 0.9 BA2_exvivo 941 615 821 1.928 0.482 0.124 0.027 7 1.0 BA3a_exvivo 1329 937 1527 1.589 0.386 0.092 0.016 7 0.8 BA3b_exvivo 907 519 1779 3.027 0.518 0.098 0.032 6 1.4 BA4a_exvivo 1084 716 1953 2.833 0.536 0.103 0.030 7 1.5 BA4p_exvivo 4602 2931 10884 3.001 0.612 0.111 0.029 45 5.6 BA6_exvivo 790 522 2464 3.362 0.701 0.116 0.026 7 0.9 BA44_exvivo 960 670 2806 3.170 0.624 0.143 0.035 14 1.4 BA45_exvivo 2873 2076 4282 1.878 0.618 0.138 0.042 34 4.9 V1_exvivo 3794 2574 5826 1.992 0.577 0.160 0.048 60 7.5 V2_exvivo 255 184 567 2.439 0.543 0.124 0.029 3 0.3 MT_exvivo 418 225 844 2.664 1.085 0.166 0.136 15 2.9 perirhinal_exvivo 212 165 459 2.890 0.957 0.124 0.026 1 0.2 entorhinal_exvivo Started at Sat Oct 7 23:40:21 CEST 2017 Ended at Sun Oct 8 06:40:50 CEST 2017 #@#%# recon-all-run-time-hours 7.008 recon-all -s 0050340 finished without error at Sun Oct 8 06:40:50 CEST 2017