Sat Oct 7 17:01:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0051348 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_c/0051348/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0051348 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-553 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: 65993860 50258380 15735480 1756068 0 47564700 -/+ buffers/cache: 2693680 63300180 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:48-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-15:01:49-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-553 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-6.0.0/0051348 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_c/0051348/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_c/0051348/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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/MaxMun_c/0051348/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-6.0.0/0051348/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 17:01:51 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/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-6.0.0/0051348/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 17:02:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/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-553 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 17:02:01 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.10063 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10063/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10063/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.10063/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 17:02:03 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10063/nu0.mnc ./tmp.mri_nu_correct.mni.10063/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10063/0/ -iterations 1000 -distance 50 [ntraut@tars-553:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/] [2017-10-07 17:02:03] 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.10063/0/ ./tmp.mri_nu_correct.mni.10063/nu0.mnc ./tmp.mri_nu_correct.mni.10063/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 39 CV of field change: 0.000982278 mri_convert ./tmp.mri_nu_correct.mni.10063/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.10063/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.10063/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sat Oct 7 17:03:06 CEST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Oct 7 17:03:06 CEST 2017 Ended at Sat Oct 7 17:03:37 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 17:03:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4171, pval=0.0643 >= 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-6.0.0/0051348/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/transforms/talairach_avi.log TalAviQA: 0.97879 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 17:03:40 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-6.0.0/0051348/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-553 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 17:03:40 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.10873 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10873/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10873/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.10873/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 17:03:42 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10873/nu0.mnc ./tmp.mri_nu_correct.mni.10873/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10873/0/ [ntraut@tars-553:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/] [2017-10-07 17:03:42] 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.10873/0/ ./tmp.mri_nu_correct.mni.10873/nu0.mnc ./tmp.mri_nu_correct.mni.10873/nu1.imp Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 39 CV of field change: 0.000972007 -------------------------------------------------------- Iteration 2 Sat Oct 7 17:04:28 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10873/nu1.mnc ./tmp.mri_nu_correct.mni.10873/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.10873/1/ [ntraut@tars-553:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/] [2017-10-07 17:04:28] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.10873/1/ ./tmp.mri_nu_correct.mni.10873/nu1.mnc ./tmp.mri_nu_correct.mni.10873/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 14 CV of field change: 0.000995407 mri_binarize --i ./tmp.mri_nu_correct.mni.10873/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10873/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-6.0.0/0051348/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.10873/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10873/ones.mgz sysname Linux hostname tars-553 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.10873/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.10873/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.10873/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10873/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10873/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.10873/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10873/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10873/input.mean.dat sysname Linux hostname tars-553 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10873/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.10873/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10873/ones.mgz --i ./tmp.mri_nu_correct.mni.10873/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10873/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10873/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.10873/ones.mgz --i ./tmp.mri_nu_correct.mni.10873/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10873/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10873/output.mean.dat sysname Linux hostname tars-553 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10873/ones.mgz Loading ./tmp.mri_nu_correct.mni.10873/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.10873/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.10873/nu2.mnc ./tmp.mri_nu_correct.mni.10873/nu2.mnc mul .96167811818778809197 Saving result to './tmp.mri_nu_correct.mni.10873/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.10873/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.10873/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.10873/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 (18, 147) to ( 3, 110) Sat Oct 7 17:05:36 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 17:05:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 1.15435 0.02161 -0.16422 7.60110; -0.09427 1.02657 -0.08129 11.33200; 0.15816 0.17914 1.03470 -68.80373; 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 = 15 Starting OpenSpline(): npoints = 15 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 106 gm peak at 73 (73), valley at 39 (39) csf peak at 37, setting threshold to 61 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 72 (72), valley at 37 (37) csf peak at 36, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 12 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 17:07:50 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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=6.0 skull bounding box = (56, 21, 28) --> (197, 171, 221) using (103, 71, 125) as brain centroid... mean wm in atlas = 108, using box (86,53,101) --> (120, 89,148) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 6.1 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -4.709 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.495207 @ (9.091, 27.273, -9.091) max log p = -4.466466 @ (-4.545, 4.545, -4.545) max log p = -4.418298 @ (-6.818, -6.818, 6.818) max log p = -4.413081 @ (3.409, -1.136, -7.955) max log p = -4.408009 @ (0.568, 2.841, 5.114) max log p = -4.400772 @ (-1.989, -1.989, 2.557) Found translation: (-0.3, 24.7, -7.1): log p = -4.401 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.166, old_max_log_p =-4.401 (thresh=-4.4) 1.22567 -0.15998 0.02106 -19.72387; 0.16136 1.21519 -0.15998 5.62621; 0.00000 0.15011 1.14016 -41.27601; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.157, old_max_log_p =-4.166 (thresh=-4.2) 1.13375 -0.14798 0.01948 -8.87893; 0.14926 1.12405 -0.14798 8.36730; 0.00000 0.15011 1.14016 -48.77601; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.157, old_max_log_p =-4.157 (thresh=-4.2) 1.13375 -0.14798 0.01948 -8.87893; 0.14926 1.12405 -0.14798 8.36730; 0.00000 0.15011 1.14016 -48.77601; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.097, old_max_log_p =-4.157 (thresh=-4.2) 1.19064 -0.20039 -0.05621 -0.60923; 0.19287 1.16808 -0.07768 -7.55813; 0.06316 0.06513 1.12392 -41.19419; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.097, old_max_log_p =-4.097 (thresh=-4.1) 1.19064 -0.20039 -0.05621 -0.60923; 0.19287 1.16808 -0.07768 -7.55813; 0.06316 0.06513 1.12392 -41.19419; 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=-4.085, old_max_log_p =-4.097 (thresh=-4.1) 1.19087 -0.19667 -0.01949 -4.58742; 0.19092 1.16669 -0.11455 -2.67036; 0.03044 0.10982 1.12201 -43.22834; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.085, old_max_log_p =-4.085 (thresh=-4.1) 1.19087 -0.19667 -0.01949 -4.58742; 0.19092 1.16669 -0.11455 -2.67036; 0.03044 0.10982 1.12201 -43.22834; 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 1.19087 -0.19667 -0.01949 -4.58742; 0.19092 1.16669 -0.11455 -2.67036; 0.03044 0.10982 1.12201 -43.22834; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.19087 -0.19667 -0.01949 -4.58742; 0.19092 1.16669 -0.11455 -2.67036; 0.03044 0.10982 1.12201 -43.22834; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.19087 -0.19667 -0.01949 -4.58742; 0.19092 1.16669 -0.11455 -2.67036; 0.03044 0.10982 1.12201 -43.22834; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.085 (old=-4.709) transform before final EM align: 1.19087 -0.19667 -0.01949 -4.58742; 0.19092 1.16669 -0.11455 -2.67036; 0.03044 0.10982 1.12201 -43.22834; 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 1.19087 -0.19667 -0.01949 -4.58742; 0.19092 1.16669 -0.11455 -2.67036; 0.03044 0.10982 1.12201 -43.22834; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.19087 -0.19667 -0.01949 -4.58742; 0.19092 1.16669 -0.11455 -2.67036; 0.03044 0.10982 1.12201 -43.22834; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.5 tol 0.000000 final transform: 1.19087 -0.19667 -0.01949 -4.58742; 0.19092 1.16669 -0.11455 -2.67036; 0.03044 0.10982 1.12201 -43.22834; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 2018.600126 mri_em_register stimesec 2.287652 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 157588 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 193060 mri_em_register ru_nivcsw 7776 registration took 20 minutes and 58 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=86 z=124 r=65 first estimation of the main basin volume: 1155728 voxels Looking for seedpoints 2 found in the cerebellum 12 found in the rest of the brain global maximum in x=143, y=73, z=93, Imax=255 CSF=16, 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=6854126761 voxels, voxel volume =1.000 = 6854126761 mmm3 = 6854126.592 cm3 done. PostAnalyze...Basin Prior 34 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=126,y=96, z=119, r=9556 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=52 , nb = 43226 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1104425715 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=10 , nb = -1041375197 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = 1088343356 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=64 , nb = 1057488526 OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=82 , nb = 1078804540 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 52, 47, 45, 66 after analyzing : 31, 47, 47, 51 RIGHT_CER before analyzing : 5, 10, 47, 69 after analyzing : 5, 34, 47, 42 LEFT_CER before analyzing : 10, 19, 44, 66 after analyzing : 10, 35, 44, 42 RIGHT_BRAIN before analyzing : 56, 48, 45, 66 after analyzing : 33, 48, 48, 52 LEFT_BRAIN before analyzing : 64, 49, 44, 66 after analyzing : 37, 49, 49, 53 OTHER before analyzing : 82, 88, 89, 95 after analyzing : 82, 88, 89, 89 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...78 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.013 curvature mean = 68.877, std = 9.407 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 7.87, sigma = 12.16 after rotation: sse = 7.87, sigma = 12.16 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 8.66, its var is 10.83 before Erosion-Dilatation 8.49% of inacurate vertices after Erosion-Dilatation 13.27% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1602451 voxels, voxel volume = 1.000 mm3 = 1602451 mmm3 = 1602.451 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 29.319542 mri_watershed stimesec 0.447931 mri_watershed ru_maxrss 818064 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 211392 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 4544 mri_watershed ru_oublock 2728 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1846 mri_watershed ru_nivcsw 1143 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Oct 7 17:29:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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=21.9 skull bounding box = (62, 29, 37) --> (189, 146, 211) using (104, 68, 124) as brain centroid... mean wm in atlas = 107, using box (88,54,103) --> (119, 82,145) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 5.8 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.512 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.172519 @ (-9.091, 27.273, -9.091) max log p = -4.016878 @ (13.636, -4.545, -4.545) max log p = -3.914818 @ (-2.273, 2.273, 2.273) max log p = -3.914818 @ (0.000, 0.000, 0.000) max log p = -3.912988 @ (-0.568, -3.977, -0.568) max log p = -3.912988 @ (0.000, 0.000, 0.000) Found translation: (1.7, 21.0, -11.9): log p = -3.913 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.747, old_max_log_p =-3.913 (thresh=-3.9) 1.06549 -0.14148 -0.01831 9.56794; 0.13796 1.05700 -0.13912 14.50175; 0.03125 0.11662 0.91709 -17.56709; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.747, old_max_log_p =-3.747 (thresh=-3.7) 1.06549 -0.14148 -0.01831 9.56794; 0.13796 1.05700 -0.13912 14.50175; 0.03125 0.11662 0.91709 -17.56709; 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=-3.606, old_max_log_p =-3.747 (thresh=-3.7) 1.12398 -0.15605 -0.05065 5.54722; 0.13548 1.05776 -0.13706 16.61471; 0.06947 0.11593 0.96848 -30.30967; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.592, old_max_log_p =-3.606 (thresh=-3.6) 1.10004 -0.18067 -0.01250 6.38888; 0.16741 1.04245 -0.20063 21.64808; 0.04214 0.19343 0.97656 -35.28300; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.584, old_max_log_p =-3.592 (thresh=-3.6) 1.10694 -0.11683 -0.05557 4.51488; 0.09651 1.05813 -0.16529 24.88750; 0.07125 0.15034 0.96326 -33.22721; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.584, old_max_log_p =-3.584 (thresh=-3.6) 1.10694 -0.11683 -0.05557 4.51488; 0.09651 1.05813 -0.16529 24.88750; 0.07125 0.15034 0.96326 -33.22721; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.584, old_max_log_p =-3.584 (thresh=-3.6) 1.10694 -0.11683 -0.05557 4.51488; 0.09651 1.05813 -0.16529 24.88750; 0.07125 0.15034 0.96326 -33.22721; 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 1.10694 -0.11683 -0.05557 4.51488; 0.09651 1.05813 -0.16529 24.88750; 0.07125 0.15034 0.96326 -33.22721; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.10694 -0.11683 -0.05557 4.51488; 0.09651 1.05813 -0.16529 24.88750; 0.07125 0.15034 0.96326 -33.22721; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.10694 -0.11683 -0.05557 4.51488; 0.09651 1.05813 -0.16529 24.88750; 0.07125 0.15034 0.96326 -33.22721; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.584 (old=-4.512) transform before final EM align: 1.10694 -0.11683 -0.05557 4.51488; 0.09651 1.05813 -0.16529 24.88750; 0.07125 0.15034 0.96326 -33.22721; 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 1.10694 -0.11683 -0.05557 4.51488; 0.09651 1.05813 -0.16529 24.88750; 0.07125 0.15034 0.96326 -33.22721; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.10694 -0.11683 -0.05557 4.51488; 0.09651 1.05813 -0.16529 24.88750; 0.07125 0.15034 0.96326 -33.22721; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 1.10694 -0.11683 -0.05557 4.51488; 0.09651 1.05813 -0.16529 24.88750; 0.07125 0.15034 0.96326 -33.22721; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1523.550385 mri_em_register stimesec 2.091682 mri_em_register ru_maxrss 599052 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158952 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 13415 mri_em_register ru_nivcsw 5596 registration took 13 minutes and 15 seconds. #-------------------------------------- #@# CA Normalize Sat Oct 7 17:42:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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=21.9 skull bounding box = (62, 29, 37) --> (189, 146, 211) using (104, 68, 124) as brain centroid... mean wm in atlas = 107, using box (88,54,103) --> (119, 82,145) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 5.8 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246344 sample points... INFO: compute sample coordinates transform 1.10694 -0.11683 -0.05557 4.51488; 0.09651 1.05813 -0.16529 24.88750; 0.07125 0.15034 0.96326 -33.22721; 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 (121, 31, 36) --> (187, 145, 208) Left_Cerebral_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 14 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 33, 39) --> (131, 151, 211) Right_Cerebral_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 12 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 108, 53) --> (173, 146, 110) Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 7 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 109, 53) --> (128, 150, 113) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 2 of 18 (11.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 105, 85) --> (146, 168, 124) Brain_Stem: limiting intensities to 104.0 --> 132.0 9 of 10 (90.0%) samples deleted using 61 total control points for intensity normalization... bias field = 0.854 +- 0.081 0 of 50 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (121, 31, 36) --> (187, 145, 208) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 128 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 33, 39) --> (131, 151, 211) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 108 (0.9%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 108, 53) --> (173, 146, 110) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 18 of 59 (30.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 109, 53) --> (128, 150, 113) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 36 of 53 (67.9%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 105, 85) --> (146, 168, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 41 of 104 (39.4%) samples deleted using 452 total control points for intensity normalization... bias field = 0.998 +- 0.103 0 of 348 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (121, 31, 36) --> (187, 145, 208) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 252 (0.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 33, 39) --> (131, 151, 211) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 255 (3.9%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 108, 53) --> (173, 146, 110) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 38 of 68 (55.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 109, 53) --> (128, 150, 113) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 74 of 96 (77.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 105, 85) --> (146, 168, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 111 of 169 (65.7%) samples deleted using 840 total control points for intensity normalization... bias field = 1.012 +- 0.070 0 of 604 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 51 seconds. #-------------------------------------- #@# CA Reg Sat Oct 7 17:44:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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) = 1.17 (predicted orig area = 6.8) 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=0.814, neg=0, invalid=762 0001: dt=221.952000, rms=0.738 (9.411%), neg=0, invalid=762 0002: dt=156.505747, rms=0.721 (2.269%), neg=0, invalid=762 0003: dt=226.513089, rms=0.711 (1.410%), neg=0, invalid=762 0004: dt=129.472000, rms=0.706 (0.618%), neg=0, invalid=762 0005: dt=295.936000, rms=0.703 (0.507%), neg=0, invalid=762 0006: dt=129.472000, rms=0.700 (0.333%), neg=0, invalid=762 0007: dt=129.472000, rms=0.699 (0.156%), neg=0, invalid=762 0008: dt=129.472000, rms=0.698 (0.133%), neg=0, invalid=762 0009: dt=129.472000, rms=0.697 (0.208%), neg=0, invalid=762 0010: dt=129.472000, rms=0.695 (0.265%), neg=0, invalid=762 0011: dt=129.472000, rms=0.694 (0.214%), neg=0, invalid=762 0012: dt=129.472000, rms=0.692 (0.216%), neg=0, invalid=762 0013: dt=129.472000, rms=0.691 (0.206%), neg=0, invalid=762 0014: dt=129.472000, rms=0.689 (0.187%), neg=0, invalid=762 0015: dt=129.472000, rms=0.688 (0.181%), neg=0, invalid=762 0016: dt=129.472000, rms=0.687 (0.167%), neg=0, invalid=762 0017: dt=129.472000, rms=0.686 (0.176%), neg=0, invalid=762 0018: dt=129.472000, rms=0.685 (0.158%), neg=0, invalid=762 0019: dt=129.472000, rms=0.684 (0.148%), neg=0, invalid=762 0020: dt=129.472000, rms=0.683 (0.135%), neg=0, invalid=762 0021: dt=129.472000, rms=0.682 (0.108%), neg=0, invalid=762 0022: dt=129.472000, rms=0.681 (0.095%), neg=0, invalid=762 0023: dt=517.888000, rms=0.681 (0.051%), neg=0, invalid=762 0024: dt=517.888000, rms=0.680 (0.101%), neg=0, invalid=762 0025: dt=517.888000, rms=0.680 (-1.591%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.681, neg=0, invalid=762 0026: dt=110.976000, rms=0.679 (0.222%), neg=0, invalid=762 0027: dt=92.480000, rms=0.679 (0.016%), neg=0, invalid=762 0028: dt=92.480000, rms=0.679 (0.022%), neg=0, invalid=762 0029: dt=92.480000, rms=0.679 (0.026%), neg=0, invalid=762 0030: dt=92.480000, rms=0.678 (0.043%), neg=0, invalid=762 0031: dt=92.480000, rms=0.678 (0.069%), neg=0, invalid=762 0032: dt=92.480000, rms=0.677 (0.090%), neg=0, invalid=762 0033: dt=92.480000, rms=0.677 (0.092%), neg=0, invalid=762 0034: dt=92.480000, rms=0.676 (0.080%), neg=0, invalid=762 0035: dt=92.480000, rms=0.676 (0.063%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.680, neg=0, invalid=762 0036: dt=92.307692, rms=0.675 (0.775%), neg=0, invalid=762 0037: dt=267.310751, rms=0.661 (1.974%), neg=0, invalid=762 0038: dt=48.905660, rms=0.658 (0.538%), neg=0, invalid=762 0039: dt=497.664000, rms=0.651 (1.078%), neg=0, invalid=762 0040: dt=77.913043, rms=0.644 (1.103%), neg=0, invalid=762 0041: dt=31.104000, rms=0.643 (0.042%), neg=0, invalid=762 0042: dt=31.104000, rms=0.643 (0.031%), neg=0, invalid=762 0043: dt=31.104000, rms=0.643 (0.066%), neg=0, invalid=762 0044: dt=31.104000, rms=0.642 (0.116%), neg=0, invalid=762 0045: dt=31.104000, rms=0.641 (0.189%), neg=0, invalid=762 0046: dt=31.104000, rms=0.639 (0.240%), neg=0, invalid=762 0047: dt=31.104000, rms=0.638 (0.255%), neg=0, invalid=762 0048: dt=31.104000, rms=0.636 (0.263%), neg=0, invalid=762 0049: dt=31.104000, rms=0.634 (0.256%), neg=0, invalid=762 0050: dt=31.104000, rms=0.633 (0.245%), neg=0, invalid=762 0051: dt=31.104000, rms=0.631 (0.235%), neg=0, invalid=762 0052: dt=31.104000, rms=0.630 (0.229%), neg=0, invalid=762 0053: dt=31.104000, rms=0.628 (0.220%), neg=0, invalid=762 0054: dt=31.104000, rms=0.627 (0.197%), neg=0, invalid=762 0055: dt=31.104000, rms=0.626 (0.184%), neg=0, invalid=762 0056: dt=31.104000, rms=0.625 (0.167%), neg=0, invalid=762 0057: dt=31.104000, rms=0.624 (0.159%), neg=0, invalid=762 0058: dt=31.104000, rms=0.623 (0.157%), neg=0, invalid=762 0059: dt=31.104000, rms=0.622 (0.141%), neg=0, invalid=762 0060: dt=31.104000, rms=0.621 (0.123%), neg=0, invalid=762 0061: dt=31.104000, rms=0.621 (0.116%), neg=0, invalid=762 0062: dt=145.152000, rms=0.620 (0.042%), neg=0, invalid=762 0063: dt=145.152000, rms=0.620 (-0.158%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.621, neg=0, invalid=762 0064: dt=66.237762, rms=0.619 (0.324%), neg=0, invalid=762 0065: dt=82.944000, rms=0.619 (0.085%), neg=0, invalid=762 0066: dt=82.944000, rms=0.618 (0.054%), neg=0, invalid=762 0067: dt=82.944000, rms=0.618 (0.076%), neg=0, invalid=762 0068: dt=82.944000, rms=0.618 (0.017%), neg=0, invalid=762 0069: dt=82.944000, rms=0.617 (0.036%), neg=0, invalid=762 0070: dt=82.944000, rms=0.617 (0.040%), neg=0, invalid=762 0071: dt=82.944000, rms=0.617 (0.051%), neg=0, invalid=762 0072: dt=82.944000, rms=0.617 (0.009%), neg=0, invalid=762 0073: dt=82.944000, rms=0.616 (0.057%), neg=0, invalid=762 0074: dt=62.208000, rms=0.616 (0.027%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.635, neg=0, invalid=762 0075: dt=4.800000, rms=0.634 (0.107%), neg=0, invalid=762 0076: dt=2.000000, rms=0.634 (0.003%), neg=0, invalid=762 0077: dt=2.000000, rms=0.634 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.634, neg=0, invalid=762 0078: dt=0.000000, rms=0.634 (0.080%), neg=0, invalid=762 0079: dt=0.000000, rms=0.634 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.686, neg=0, invalid=762 0080: dt=5.775862, rms=0.670 (2.228%), neg=0, invalid=762 0081: dt=2.880000, rms=0.670 (0.085%), neg=0, invalid=762 0082: dt=2.880000, rms=0.670 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.670, neg=0, invalid=762 0083: dt=0.000000, rms=0.670 (0.064%), neg=0, invalid=762 0084: dt=0.000000, rms=0.670 (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=0.722, neg=0, invalid=762 0085: dt=0.448000, rms=0.720 (0.208%), neg=0, invalid=762 0086: dt=1.024000, rms=0.719 (0.189%), neg=0, invalid=762 0087: dt=1.024000, rms=0.717 (0.299%), neg=0, invalid=762 0088: dt=1.024000, rms=0.716 (0.161%), neg=0, invalid=762 0089: dt=1.024000, rms=0.716 (-0.259%), neg=0, invalid=762 0090: dt=1.792000, rms=0.715 (0.130%), neg=0, invalid=762 0091: dt=1.792000, rms=0.713 (0.188%), neg=0, invalid=762 0092: dt=0.000000, rms=0.713 (0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.714, neg=0, invalid=762 0093: dt=0.448000, rms=0.713 (0.103%), neg=0, invalid=762 0094: dt=1.024000, rms=0.713 (0.030%), neg=0, invalid=762 0095: dt=1.024000, rms=0.713 (0.030%), neg=0, invalid=762 0096: dt=1.024000, rms=0.713 (-0.001%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.680, neg=0, invalid=762 0097: dt=0.804555, rms=0.664 (2.366%), neg=0, invalid=762 0098: dt=0.080000, rms=0.663 (0.142%), neg=0, invalid=762 0099: dt=0.080000, rms=0.663 (-0.075%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.663, neg=0, invalid=762 0100: dt=0.028000, rms=0.663 (0.092%), neg=0, invalid=762 0101: dt=0.020000, rms=0.663 (0.005%), neg=0, invalid=762 0102: dt=0.020000, rms=0.663 (-0.004%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.12091 (24) Left_Lateral_Ventricle (4): linear fit = 1.14 x + 0.0 (1031 voxels, overlap=0.812) Left_Lateral_Ventricle (4): linear fit = 1.14 x + 0.0 (1031 voxels, peak = 23), gca=22.9 gca peak = 0.15565 (16) mri peak = 0.11057 (25) Right_Lateral_Ventricle (43): linear fit = 1.48 x + 0.0 (1180 voxels, overlap=0.471) Right_Lateral_Ventricle (43): linear fit = 1.48 x + 0.0 (1180 voxels, peak = 24), gca=23.6 gca peak = 0.26829 (96) mri peak = 0.07828 (93) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (622 voxels, overlap=0.740) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (622 voxels, peak = 92), gca=91.7 gca peak = 0.20183 (93) mri peak = 0.07371 (92) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (526 voxels, overlap=0.679) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (526 voxels, peak = 89), gca=88.8 gca peak = 0.21683 (55) mri peak = 0.09206 (71) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (641 voxels, overlap=0.141) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (641 voxels, peak = 66), gca=66.3 gca peak = 0.30730 (58) mri peak = 0.07674 (67) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (625 voxels, overlap=0.284) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (625 voxels, peak = 68), gca=67.6 gca peak = 0.11430 (101) mri peak = 0.06924 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52326 voxels, overlap=0.809) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52326 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.07337 (105) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (50225 voxels, overlap=0.779) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (50225 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.04646 (70) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (18533 voxels, overlap=0.157) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (18533 voxels, peak = 71), gca=70.5 gca peak = 0.15082 (58) mri peak = 0.04856 (70) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (19732 voxels, overlap=0.245) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (19732 voxels, peak = 69), gca=69.3 gca peak = 0.14161 (67) mri peak = 0.08449 (76) Right_Caudate (50): linear fit = 1.12 x + 0.0 (721 voxels, overlap=0.562) Right_Caudate (50): linear fit = 1.12 x + 0.0 (721 voxels, peak = 75), gca=74.7 gca peak = 0.15243 (71) mri peak = 0.08067 (76) Left_Caudate (11): linear fit = 1.03 x + 0.0 (721 voxels, overlap=0.963) Left_Caudate (11): linear fit = 1.03 x + 0.0 (721 voxels, peak = 73), gca=73.5 gca peak = 0.13336 (57) mri peak = 0.05754 (63) Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (22326 voxels, overlap=0.442) Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (22326 voxels, peak = 66), gca=66.4 gca peak = 0.13252 (56) mri peak = 0.05292 (64) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (23979 voxels, overlap=0.670) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (23979 voxels, peak = 64), gca=63.6 gca peak = 0.18181 (84) mri peak = 0.05431 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7501 voxels, overlap=0.929) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7501 voxels, peak = 86), gca=86.1 gca peak = 0.20573 (83) mri peak = 0.05678 (83) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7261 voxels, overlap=0.978) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7261 voxels, peak = 82), gca=81.8 gca peak = 0.21969 (57) mri peak = 0.08513 (62) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (321 voxels, overlap=0.484) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (321 voxels, peak = 64), gca=63.6 gca peak = 0.39313 (56) mri peak = 0.07977 (63) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (345 voxels, overlap=0.648) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (345 voxels, peak = 64), gca=63.6 gca peak = 0.14181 (85) mri peak = 0.05426 (89) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4628 voxels, overlap=0.923) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4628 voxels, peak = 87), gca=87.1 gca peak = 0.11978 (83) mri peak = 0.05723 (89) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4097 voxels, overlap=0.852) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4097 voxels, peak = 88), gca=87.6 gca peak = 0.13399 (79) mri peak = 0.07389 (79) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1637 voxels, overlap=0.864) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1637 voxels, peak = 83), gca=83.3 gca peak = 0.14159 (79) mri peak = 0.06844 (79) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1878 voxels, overlap=0.913) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1878 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.09480 (82) Brain_Stem (16): linear fit = 1.10 x + 0.0 (8537 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (8537 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07640 (89) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (753 voxels, overlap=0.728) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (753 voxels, peak = 90), gca=89.9 gca peak = 0.12801 (89) mri peak = 0.07967 (89) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (810 voxels, overlap=0.850) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (810 voxels, peak = 91), gca=91.2 gca peak = 0.20494 (23) mri peak = 1.00000 (40) gca peak = 0.15061 (21) mri peak = 0.08803 (25) Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (395 voxels, overlap=0.654) Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (395 voxels, peak = 24), gca=24.5 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 1.17 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.26 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.655, neg=0, invalid=762 0103: dt=92.480000, rms=0.647 (1.195%), neg=0, invalid=762 0104: dt=129.472000, rms=0.645 (0.307%), neg=0, invalid=762 0105: dt=369.920000, rms=0.643 (0.370%), neg=0, invalid=762 0106: dt=295.936000, rms=0.642 (0.203%), neg=0, invalid=762 0107: dt=73.984000, rms=0.641 (0.110%), neg=0, invalid=762 0108: dt=1479.680000, rms=0.638 (0.530%), neg=0, invalid=762 0109: dt=92.480000, rms=0.637 (0.082%), neg=0, invalid=762 0110: dt=369.920000, rms=0.637 (0.078%), neg=0, invalid=762 0111: dt=369.920000, rms=0.635 (0.227%), neg=0, invalid=762 0112: dt=32.368000, rms=0.635 (0.014%), neg=0, invalid=762 0113: dt=32.368000, rms=0.635 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=762 0114: dt=55.488000, rms=0.635 (0.074%), neg=0, invalid=762 0115: dt=92.480000, rms=0.635 (0.017%), neg=0, invalid=762 0116: dt=92.480000, rms=0.635 (0.032%), neg=0, invalid=762 0117: dt=92.480000, rms=0.634 (0.043%), neg=0, invalid=762 0118: dt=92.480000, rms=0.634 (0.052%), neg=0, invalid=762 0119: dt=92.480000, rms=0.634 (0.058%), neg=0, invalid=762 0120: dt=92.480000, rms=0.633 (0.068%), neg=0, invalid=762 0121: dt=92.480000, rms=0.633 (0.063%), neg=0, invalid=762 0122: dt=92.480000, rms=0.633 (0.053%), neg=0, invalid=762 0123: dt=92.480000, rms=0.632 (0.046%), neg=0, invalid=762 0124: dt=92.480000, rms=0.632 (0.055%), neg=0, invalid=762 0125: dt=92.480000, rms=0.631 (0.070%), neg=0, invalid=762 0126: dt=92.480000, rms=0.631 (0.090%), neg=0, invalid=762 0127: dt=92.480000, rms=0.630 (0.096%), neg=0, invalid=762 0128: dt=92.480000, rms=0.630 (0.083%), neg=0, invalid=762 0129: dt=92.480000, rms=0.629 (0.066%), neg=0, invalid=762 0130: dt=92.480000, rms=0.629 (0.047%), neg=0, invalid=762 0131: dt=92.480000, rms=0.629 (0.039%), neg=0, invalid=762 0132: dt=92.480000, rms=0.628 (0.044%), neg=0, invalid=762 0133: dt=92.480000, rms=0.628 (0.049%), neg=0, invalid=762 0134: dt=92.480000, rms=0.628 (0.050%), neg=0, invalid=762 0135: dt=92.480000, rms=0.628 (0.050%), neg=0, invalid=762 0136: dt=92.480000, rms=0.627 (0.045%), neg=0, invalid=762 0137: dt=92.480000, rms=0.627 (0.043%), neg=0, invalid=762 0138: dt=92.480000, rms=0.627 (0.046%), neg=0, invalid=762 0139: dt=92.480000, rms=0.626 (0.053%), neg=0, invalid=762 0140: dt=92.480000, rms=0.626 (0.056%), neg=0, invalid=762 0141: dt=92.480000, rms=0.626 (0.055%), neg=0, invalid=762 0142: dt=92.480000, rms=0.625 (0.044%), neg=0, invalid=762 0143: dt=92.480000, rms=0.625 (0.040%), neg=0, invalid=762 0144: dt=92.480000, rms=0.625 (0.038%), neg=0, invalid=762 0145: dt=92.480000, rms=0.625 (0.037%), neg=0, invalid=762 0146: dt=92.480000, rms=0.624 (0.037%), neg=0, invalid=762 0147: dt=92.480000, rms=0.624 (0.037%), neg=0, invalid=762 0148: dt=92.480000, rms=0.624 (0.036%), neg=0, invalid=762 0149: dt=92.480000, rms=0.624 (0.033%), neg=0, invalid=762 0150: dt=92.480000, rms=0.624 (0.034%), neg=0, invalid=762 0151: dt=92.480000, rms=0.623 (0.038%), neg=0, invalid=762 0152: dt=92.480000, rms=0.623 (0.037%), neg=0, invalid=762 0153: dt=92.480000, rms=0.623 (0.032%), neg=0, invalid=762 0154: dt=92.480000, rms=0.623 (0.030%), neg=0, invalid=762 0155: dt=92.480000, rms=0.623 (0.029%), neg=0, invalid=762 0156: dt=92.480000, rms=0.622 (0.032%), neg=0, invalid=762 0157: dt=92.480000, rms=0.622 (0.033%), neg=0, invalid=762 0158: dt=92.480000, rms=0.622 (0.031%), neg=0, invalid=762 0159: dt=92.480000, rms=0.622 (0.026%), neg=0, invalid=762 0160: dt=92.480000, rms=0.622 (0.024%), neg=0, invalid=762 0161: dt=92.480000, rms=0.622 (0.020%), neg=0, invalid=762 0162: dt=2071.552000, rms=0.621 (0.044%), neg=0, invalid=762 0163: dt=23.120000, rms=0.621 (-0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.622, neg=0, invalid=762 0164: dt=160.603774, rms=0.616 (0.939%), neg=0, invalid=762 0165: dt=129.665944, rms=0.609 (1.128%), neg=0, invalid=762 0166: dt=76.000000, rms=0.606 (0.464%), neg=0, invalid=762 0167: dt=92.790831, rms=0.603 (0.504%), neg=0, invalid=762 0168: dt=68.491228, rms=0.601 (0.356%), neg=0, invalid=762 0169: dt=124.416000, rms=0.599 (0.414%), neg=0, invalid=762 0170: dt=36.288000, rms=0.597 (0.276%), neg=0, invalid=762 0171: dt=580.608000, rms=0.591 (1.069%), neg=0, invalid=762 0172: dt=55.560440, rms=0.587 (0.658%), neg=0, invalid=762 0173: dt=103.680000, rms=0.586 (0.178%), neg=0, invalid=762 0174: dt=69.019608, rms=0.585 (0.176%), neg=0, invalid=762 0175: dt=103.680000, rms=0.584 (0.147%), neg=0, invalid=762 0176: dt=72.186047, rms=0.583 (0.158%), neg=0, invalid=762 0177: dt=103.680000, rms=0.582 (0.127%), neg=0, invalid=762 0178: dt=65.422222, rms=0.581 (0.152%), neg=0, invalid=762 0179: dt=103.680000, rms=0.581 (0.116%), neg=0, invalid=762 0180: dt=82.944000, rms=0.580 (0.131%), neg=0, invalid=762 0181: dt=62.208000, rms=0.579 (0.100%), neg=0, invalid=762 0182: dt=145.152000, rms=0.578 (0.158%), neg=0, invalid=762 0183: dt=36.288000, rms=0.578 (0.087%), neg=0, invalid=762 0184: dt=580.608000, rms=0.575 (0.530%), neg=0, invalid=762 0185: dt=36.288000, rms=0.574 (0.181%), neg=0, invalid=762 0186: dt=331.776000, rms=0.573 (0.163%), neg=0, invalid=762 0187: dt=36.288000, rms=0.572 (0.147%), neg=0, invalid=762 0188: dt=145.152000, rms=0.571 (0.095%), neg=0, invalid=762 0189: dt=82.944000, rms=0.571 (0.080%), neg=0, invalid=762 0190: dt=62.208000, rms=0.571 (0.046%), neg=0, invalid=762 0191: dt=62.208000, rms=0.570 (0.052%), neg=0, invalid=762 0192: dt=62.208000, rms=0.570 (0.078%), neg=0, invalid=762 0193: dt=62.208000, rms=0.569 (0.110%), neg=0, invalid=762 0194: dt=62.208000, rms=0.569 (0.138%), neg=0, invalid=762 0195: dt=62.208000, rms=0.568 (0.168%), neg=0, invalid=762 0196: dt=62.208000, rms=0.567 (0.176%), neg=0, invalid=762 0197: dt=62.208000, rms=0.566 (0.186%), neg=0, invalid=762 0198: dt=62.208000, rms=0.565 (0.186%), neg=0, invalid=762 0199: dt=62.208000, rms=0.564 (0.166%), neg=0, invalid=762 0200: dt=62.208000, rms=0.563 (0.162%), neg=0, invalid=762 0201: dt=62.208000, rms=0.562 (0.165%), neg=0, invalid=762 0202: dt=62.208000, rms=0.561 (0.173%), neg=0, invalid=762 0203: dt=62.208000, rms=0.560 (0.156%), neg=0, invalid=762 0204: dt=62.208000, rms=0.560 (0.021%), neg=0, invalid=762 0205: dt=62.208000, rms=0.560 (0.028%), neg=0, invalid=762 0206: dt=62.208000, rms=0.559 (0.044%), neg=0, invalid=762 0207: dt=62.208000, rms=0.559 (0.051%), neg=0, invalid=762 0208: dt=62.208000, rms=0.559 (0.059%), neg=0, invalid=762 0209: dt=62.208000, rms=0.558 (0.061%), neg=0, invalid=762 0210: dt=62.208000, rms=0.558 (0.076%), neg=0, invalid=762 0211: dt=62.208000, rms=0.558 (0.080%), neg=0, invalid=762 0212: dt=62.208000, rms=0.557 (0.091%), neg=0, invalid=762 0213: dt=31.104000, rms=0.557 (0.008%), neg=0, invalid=762 0214: dt=31.104000, rms=0.557 (0.008%), neg=0, invalid=762 0215: dt=1.944000, rms=0.557 (0.000%), neg=0, invalid=762 0216: dt=0.015187, rms=0.557 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.557, neg=0, invalid=762 0217: dt=103.680000, rms=0.556 (0.317%), neg=0, invalid=762 0218: dt=145.152000, rms=0.554 (0.236%), neg=0, invalid=762 0219: dt=36.288000, rms=0.554 (0.074%), neg=0, invalid=762 0220: dt=103.680000, rms=0.554 (0.034%), neg=0, invalid=762 0221: dt=103.680000, rms=0.553 (0.117%), neg=0, invalid=762 0222: dt=103.680000, rms=0.553 (0.111%), neg=0, invalid=762 0223: dt=103.680000, rms=0.552 (0.076%), neg=0, invalid=762 0224: dt=103.680000, rms=0.551 (0.143%), neg=0, invalid=762 0225: dt=103.680000, rms=0.551 (0.136%), neg=0, invalid=762 0226: dt=103.680000, rms=0.550 (0.103%), neg=0, invalid=762 0227: dt=103.680000, rms=0.549 (0.109%), neg=0, invalid=762 0228: dt=103.680000, rms=0.549 (0.133%), neg=0, invalid=762 0229: dt=103.680000, rms=0.548 (0.142%), neg=0, invalid=762 0230: dt=103.680000, rms=0.547 (0.121%), neg=0, invalid=762 0231: dt=103.680000, rms=0.547 (0.127%), neg=0, invalid=762 0232: dt=103.680000, rms=0.546 (0.129%), neg=0, invalid=762 0233: dt=103.680000, rms=0.545 (0.109%), neg=0, invalid=762 0234: dt=103.680000, rms=0.545 (0.105%), neg=0, invalid=762 0235: dt=103.680000, rms=0.544 (0.097%), neg=0, invalid=762 0236: dt=103.680000, rms=0.544 (0.096%), neg=0, invalid=762 0237: dt=103.680000, rms=0.543 (0.087%), neg=0, invalid=762 0238: dt=103.680000, rms=0.543 (0.071%), neg=0, invalid=762 0239: dt=103.680000, rms=0.542 (0.089%), neg=0, invalid=762 0240: dt=103.680000, rms=0.542 (0.085%), neg=0, invalid=762 0241: dt=103.680000, rms=0.541 (0.085%), neg=0, invalid=762 0242: dt=103.680000, rms=0.541 (0.092%), neg=0, invalid=762 0243: dt=103.680000, rms=0.540 (0.108%), neg=0, invalid=762 0244: dt=103.680000, rms=0.540 (0.102%), neg=0, invalid=762 0245: dt=103.680000, rms=0.539 (0.081%), neg=0, invalid=762 0246: dt=103.680000, rms=0.539 (0.083%), neg=0, invalid=762 0247: dt=103.680000, rms=0.538 (0.074%), neg=0, invalid=762 0248: dt=103.680000, rms=0.538 (0.072%), neg=0, invalid=762 0249: dt=103.680000, rms=0.538 (0.068%), neg=0, invalid=762 0250: dt=103.680000, rms=0.537 (0.068%), neg=0, invalid=762 0251: dt=103.680000, rms=0.537 (0.057%), neg=0, invalid=762 0252: dt=103.680000, rms=0.537 (0.046%), neg=0, invalid=762 0253: dt=103.680000, rms=0.537 (0.036%), neg=0, invalid=762 0254: dt=103.680000, rms=0.536 (0.049%), neg=0, invalid=762 0255: dt=103.680000, rms=0.536 (0.065%), neg=0, invalid=762 0256: dt=103.680000, rms=0.536 (0.046%), neg=0, invalid=762 0257: dt=103.680000, rms=0.535 (0.042%), neg=0, invalid=762 0258: dt=103.680000, rms=0.535 (0.006%), neg=0, invalid=762 0259: dt=103.680000, rms=0.535 (0.001%), neg=0, invalid=762 0260: dt=36.288000, rms=0.535 (0.010%), neg=0, invalid=762 0261: dt=36.288000, rms=0.535 (0.002%), neg=0, invalid=762 0262: dt=36.288000, rms=0.535 (0.001%), neg=0, invalid=762 0263: dt=18.144000, rms=0.535 (0.004%), neg=0, invalid=762 0264: dt=18.144000, rms=0.535 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.545, neg=0, invalid=762 0265: dt=32.000000, rms=0.543 (0.362%), neg=0, invalid=762 0266: dt=90.612245, rms=0.539 (0.620%), neg=0, invalid=762 0267: dt=44.800000, rms=0.537 (0.392%), neg=0, invalid=762 0268: dt=32.000000, rms=0.535 (0.374%), neg=0, invalid=762 0269: dt=32.000000, rms=0.534 (0.197%), neg=0, invalid=762 0270: dt=38.400000, rms=0.533 (0.241%), neg=0, invalid=762 0271: dt=25.600000, rms=0.532 (0.161%), neg=0, invalid=762 0272: dt=44.800000, rms=0.531 (0.225%), neg=0, invalid=762 0273: dt=25.600000, rms=0.530 (0.141%), neg=0, invalid=762 0274: dt=44.800000, rms=0.529 (0.205%), neg=0, invalid=762 0275: dt=25.600000, rms=0.528 (0.118%), neg=0, invalid=762 0276: dt=32.000000, rms=0.527 (0.149%), neg=0, invalid=762 0277: dt=8.000000, rms=0.527 (0.037%), neg=0, invalid=762 0278: dt=0.125000, rms=0.527 (0.002%), neg=0, invalid=762 0279: dt=0.031250, rms=0.527 (0.000%), neg=0, invalid=762 0280: dt=0.000977, rms=0.527 (0.000%), neg=0, invalid=762 0281: dt=0.000684, rms=0.527 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.528, neg=0, invalid=762 0282: dt=44.800000, rms=0.525 (0.519%), neg=0, invalid=762 0283: dt=44.800000, rms=0.523 (0.292%), neg=0, invalid=762 0284: dt=38.400000, rms=0.523 (0.104%), neg=0, invalid=762 0285: dt=44.800000, rms=0.522 (0.183%), neg=0, invalid=762 0286: dt=25.600000, rms=0.521 (0.087%), neg=0, invalid=762 0287: dt=76.800000, rms=0.521 (0.182%), neg=0, invalid=762 0288: dt=24.436364, rms=0.520 (0.109%), neg=0, invalid=762 0289: dt=44.800000, rms=0.519 (0.133%), neg=0, invalid=762 0290: dt=32.000000, rms=0.519 (0.077%), neg=0, invalid=762 0291: dt=38.400000, rms=0.518 (0.092%), neg=0, invalid=762 0292: dt=25.600000, rms=0.518 (0.058%), neg=0, invalid=762 0293: dt=44.800000, rms=0.518 (0.102%), neg=0, invalid=762 0294: dt=25.600000, rms=0.517 (0.043%), neg=0, invalid=762 0295: dt=25.600000, rms=0.517 (0.078%), neg=0, invalid=762 0296: dt=25.600000, rms=0.516 (0.095%), neg=0, invalid=762 0297: dt=25.600000, rms=0.516 (0.134%), neg=0, invalid=762 0298: dt=25.600000, rms=0.515 (0.152%), neg=0, invalid=762 0299: dt=25.600000, rms=0.514 (0.184%), neg=0, invalid=762 0300: dt=25.600000, rms=0.513 (0.187%), neg=0, invalid=762 0301: dt=25.600000, rms=0.512 (0.187%), neg=0, invalid=762 0302: dt=25.600000, rms=0.511 (0.184%), neg=0, invalid=762 0303: dt=25.600000, rms=0.510 (0.189%), neg=0, invalid=762 0304: dt=25.600000, rms=0.509 (0.183%), neg=0, invalid=762 0305: dt=25.600000, rms=0.508 (0.180%), neg=0, invalid=762 0306: dt=25.600000, rms=0.508 (0.037%), neg=0, invalid=762 0307: dt=25.600000, rms=0.508 (0.034%), neg=0, invalid=762 0308: dt=25.600000, rms=0.508 (0.040%), neg=0, invalid=762 0309: dt=25.600000, rms=0.508 (0.043%), neg=0, invalid=762 0310: dt=12.800000, rms=0.507 (0.011%), neg=0, invalid=762 0311: dt=3.200000, rms=0.507 (0.002%), neg=0, invalid=762 0312: dt=2.800000, rms=0.507 (0.002%), neg=0, invalid=762 0313: dt=0.350000, rms=0.507 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.526, neg=0, invalid=762 0314: dt=0.000000, rms=0.525 (0.084%), neg=0, invalid=762 0315: dt=0.000000, rms=0.525 (0.000%), neg=0, invalid=762 0316: dt=0.150000, rms=0.525 (-0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.526, neg=0, invalid=762 0317: dt=0.000000, rms=0.525 (0.084%), neg=0, invalid=762 0318: dt=0.000000, rms=0.525 (0.000%), neg=0, invalid=762 0319: dt=0.150000, rms=0.525 (-0.016%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.562, neg=0, invalid=762 0320: dt=1.024000, rms=0.560 (0.367%), neg=0, invalid=762 0321: dt=0.112000, rms=0.560 (0.007%), neg=0, invalid=762 0322: dt=0.112000, rms=0.560 (0.002%), neg=0, invalid=762 0323: dt=0.112000, rms=0.560 (-0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.560, neg=0, invalid=762 0324: dt=0.448000, rms=0.559 (0.145%), neg=0, invalid=762 0325: dt=0.384000, rms=0.559 (0.021%), neg=0, invalid=762 0326: dt=0.384000, rms=0.559 (-0.009%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.515, neg=0, invalid=762 0327: dt=0.448000, rms=0.501 (2.543%), neg=0, invalid=762 0328: dt=0.448000, rms=0.499 (0.557%), neg=0, invalid=762 0329: dt=0.448000, rms=0.497 (0.336%), neg=0, invalid=762 0330: dt=0.448000, rms=0.496 (0.203%), neg=0, invalid=762 0331: dt=0.458333, rms=0.495 (0.153%), neg=0, invalid=762 0332: dt=0.448000, rms=0.495 (0.109%), neg=0, invalid=762 0333: dt=0.448000, rms=0.494 (0.088%), neg=0, invalid=762 0334: dt=0.448000, rms=0.494 (0.070%), neg=0, invalid=762 0335: dt=0.448000, rms=0.494 (0.057%), neg=0, invalid=762 0336: dt=0.448000, rms=0.493 (0.046%), neg=0, invalid=762 0337: dt=0.448000, rms=0.493 (0.040%), neg=0, invalid=762 0338: dt=0.448000, rms=0.493 (0.068%), neg=0, invalid=762 0339: dt=0.448000, rms=0.493 (0.026%), neg=0, invalid=762 0340: dt=0.448000, rms=0.492 (0.043%), neg=0, invalid=762 0341: dt=0.448000, rms=0.492 (0.018%), neg=0, invalid=762 0342: dt=0.448000, rms=0.492 (0.026%), neg=0, invalid=762 0343: dt=0.448000, rms=0.492 (0.038%), neg=0, invalid=762 0344: dt=0.448000, rms=0.492 (0.042%), neg=0, invalid=762 0345: dt=0.448000, rms=0.492 (-0.001%), neg=0, invalid=762 0346: dt=0.256000, rms=0.492 (0.003%), neg=0, invalid=762 0347: dt=0.448000, rms=0.492 (0.008%), neg=0, invalid=762 0348: dt=0.256000, rms=0.492 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.492, neg=0, invalid=762 0349: dt=0.384000, rms=0.487 (1.051%), neg=0, invalid=762 0350: dt=0.448000, rms=0.486 (0.292%), neg=0, invalid=762 0351: dt=0.448000, rms=0.485 (0.054%), neg=0, invalid=762 0352: dt=0.448000, rms=0.485 (0.022%), neg=0, invalid=762 0353: dt=0.448000, rms=0.485 (0.005%), neg=0, invalid=762 0354: dt=0.448000, rms=0.485 (0.007%), neg=0, invalid=762 0355: dt=0.448000, rms=0.485 (-0.009%), 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 0356: dt=-0.009615, rms=0.483 (0.098%), neg=0, invalid=762 0357: 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 0358: dt=0.000000, rms=0.483 (0.098%), neg=0, invalid=762 0359: dt=0.000000, rms=0.483 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.484, neg=0, invalid=762 0360: dt=31.104000, rms=0.483 (0.154%), neg=0, invalid=762 0361: dt=20.736000, rms=0.483 (0.010%), neg=0, invalid=762 0362: dt=20.736000, rms=0.483 (0.004%), neg=0, invalid=762 0363: dt=20.736000, rms=0.483 (-0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0364: dt=75.392670, rms=0.482 (0.333%), neg=0, invalid=762 0365: dt=80.372093, rms=0.481 (0.232%), neg=0, invalid=762 0366: dt=80.372093, rms=0.481 (-0.179%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.481, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0367: dt=30.997389, rms=0.478 (0.669%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0368: dt=38.400000, rms=0.476 (0.314%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0369: dt=23.787611, rms=0.476 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0370: dt=23.787611, rms=0.475 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0371: dt=23.787611, rms=0.475 (0.071%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0372: dt=23.787611, rms=0.475 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0373: dt=44.800000, rms=0.474 (0.088%), neg=0, invalid=762 0374: dt=11.200000, rms=0.474 (0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0375: dt=53.807407, rms=0.469 (1.206%), neg=0, invalid=762 0376: dt=30.537143, rms=0.467 (0.488%), neg=0, invalid=762 0377: dt=25.600000, rms=0.466 (0.206%), neg=0, invalid=762 0378: dt=25.600000, rms=0.465 (0.183%), neg=0, invalid=762 0379: dt=25.600000, rms=0.464 (0.216%), neg=0, invalid=762 0380: dt=25.600000, rms=0.463 (0.203%), neg=0, invalid=762 0381: dt=25.600000, rms=0.462 (0.177%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0382: dt=25.600000, rms=0.461 (0.180%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0383: dt=25.600000, rms=0.460 (0.153%), neg=0, invalid=762 0384: dt=25.600000, rms=0.460 (0.138%), neg=0, invalid=762 0385: dt=25.600000, rms=0.459 (0.165%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0386: dt=25.600000, rms=0.458 (0.162%), neg=0, invalid=762 0387: dt=25.600000, rms=0.458 (0.171%), neg=0, invalid=762 0388: dt=25.600000, rms=0.457 (0.139%), neg=0, invalid=762 0389: dt=25.600000, rms=0.456 (0.136%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0390: dt=25.600000, rms=0.456 (0.117%), neg=0, invalid=762 0391: dt=25.600000, rms=0.455 (0.092%), neg=0, invalid=762 0392: dt=19.200000, rms=0.455 (0.031%), neg=0, invalid=762 0393: dt=19.200000, rms=0.455 (0.014%), neg=0, invalid=762 0394: dt=19.200000, rms=0.455 (0.013%), neg=0, invalid=762 0395: dt=19.200000, rms=0.455 (0.015%), neg=0, invalid=762 0396: dt=19.200000, rms=0.455 (0.009%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.460, neg=0, invalid=762 0397: dt=0.000141, rms=0.459 (0.104%), neg=0, invalid=762 0398: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.460, neg=0, invalid=762 0399: dt=1.008000, rms=0.459 (0.107%), neg=0, invalid=762 0400: dt=0.576000, rms=0.459 (0.002%), neg=0, invalid=762 0401: dt=0.576000, rms=0.459 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.468, neg=0, invalid=762 0402: dt=0.448000, rms=0.467 (0.158%), neg=0, invalid=762 0403: dt=0.384000, rms=0.467 (0.015%), neg=0, invalid=762 0404: dt=0.384000, rms=0.467 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=762 0405: dt=1.536000, rms=0.466 (0.315%), neg=0, invalid=762 0406: dt=0.768000, rms=0.466 (0.024%), neg=0, invalid=762 0407: dt=0.768000, rms=0.466 (-0.003%), 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=0.459, neg=0, invalid=762 iter 0, gcam->neg = 521 after 12 iterations, nbhd size=1, neg = 0 0408: dt=2.000000, rms=0.434 (5.363%), neg=0, invalid=762 0409: dt=0.028000, rms=0.434 (0.026%), neg=0, invalid=762 0410: dt=0.028000, rms=0.434 (0.001%), neg=0, invalid=762 0411: dt=0.028000, rms=0.434 (-0.030%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.435, neg=0, invalid=762 0412: dt=0.096000, rms=0.434 (0.198%), neg=0, invalid=762 0413: dt=0.006000, rms=0.434 (-0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 0414: dt=2.023000, rms=0.422 (0.000%), neg=0, invalid=762 0415: dt=0.090313, rms=0.422 (0.000%), neg=0, invalid=762 0416: dt=0.090313, rms=0.422 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 0417: dt=23.120000, rms=0.422 (0.001%), neg=0, invalid=762 0418: dt=6.936000, rms=0.422 (0.000%), neg=0, invalid=762 0419: dt=6.936000, rms=0.422 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 0420: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 0421: dt=36.288000, rms=0.422 (0.020%), neg=0, invalid=762 0422: dt=82.944000, rms=0.422 (0.017%), neg=0, invalid=762 0423: dt=82.944000, rms=0.422 (0.024%), neg=0, invalid=762 0424: dt=82.944000, rms=0.422 (0.021%), neg=0, invalid=762 0425: dt=82.944000, rms=0.422 (0.007%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.423, neg=0, invalid=762 0426: dt=2.800000, rms=0.422 (0.013%), neg=0, invalid=762 0427: dt=2.400000, rms=0.422 (0.004%), neg=0, invalid=762 0428: dt=2.400000, rms=0.422 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0429: dt=102.400000, rms=0.420 (0.601%), neg=0, invalid=762 0430: dt=20.817204, rms=0.419 (0.165%), neg=0, invalid=762 0431: dt=20.817204, rms=0.419 (0.055%), neg=0, invalid=762 0432: dt=20.817204, rms=0.419 (0.062%), neg=0, invalid=762 0433: dt=20.817204, rms=0.418 (0.091%), neg=0, invalid=762 0434: dt=20.817204, rms=0.418 (0.109%), neg=0, invalid=762 0435: dt=20.817204, rms=0.417 (0.136%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0436: dt=20.817204, rms=0.417 (0.128%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0437: dt=20.817204, rms=0.416 (0.104%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0438: dt=20.817204, rms=0.416 (0.094%), neg=0, invalid=762 0439: dt=44.800000, rms=0.416 (0.017%), neg=0, invalid=762 0440: dt=44.800000, rms=0.416 (0.020%), neg=0, invalid=762 0441: dt=44.800000, rms=0.416 (0.037%), neg=0, invalid=762 0442: dt=44.800000, rms=0.415 (0.048%), neg=0, invalid=762 0443: dt=44.800000, rms=0.415 (0.046%), neg=0, invalid=762 0444: dt=44.800000, rms=0.415 (0.060%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0445: dt=44.800000, rms=0.415 (0.068%), neg=0, invalid=762 0446: dt=44.800000, rms=0.414 (0.068%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0447: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0448: dt=6.800000, rms=0.417 (0.056%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0449: dt=12.750000, rms=0.417 (0.064%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 11 iterations, nbhd size=1, neg = 0 0450: dt=49.116279, rms=0.416 (0.257%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0451: dt=20.645161, rms=0.415 (0.178%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 11 iterations, nbhd size=1, neg = 0 0452: dt=20.645161, rms=0.415 (-0.124%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0453: dt=0.000050, rms=0.420 (0.000%), neg=0, invalid=762 0454: dt=0.000000, rms=0.420 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0455: dt=0.000000, rms=0.420 (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=0.412, neg=0, invalid=762 iter 0, gcam->neg = 402 after 15 iterations, nbhd size=1, neg = 0 0456: dt=1.280000, rms=0.404 (2.032%), neg=0, invalid=762 0457: dt=0.000023, rms=0.404 (0.000%), neg=0, invalid=762 0458: dt=0.000023, rms=0.404 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0459: dt=0.112000, rms=0.403 (0.126%), neg=0, invalid=762 0460: dt=0.112000, rms=0.403 (0.066%), neg=0, invalid=762 0461: dt=0.112000, rms=0.403 (0.047%), neg=0, invalid=762 0462: dt=0.112000, rms=0.403 (0.017%), neg=0, invalid=762 0463: dt=0.112000, rms=0.403 (-0.063%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 17 minutes and 4 seconds. mri_ca_register utimesec 9062.624271 mri_ca_register stimesec 10.716370 mri_ca_register ru_maxrss 1348772 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4691929 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63720 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 8322 mri_ca_register ru_nivcsw 35807 FSRUNTIME@ mri_ca_register 2.2843 hours 2 threads #-------------------------------------- #@# SubCort Seg Sat Oct 7 20:01:28 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-553 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-6.0.0/0051348/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 6.83 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 = 0.09618 (23) Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (2614 voxels, overlap=0.944) Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (2614 voxels, peak = 24), gca=24.5 gca peak = 0.17677 (13) mri peak = 0.11519 (25) Right_Lateral_Ventricle (43): linear fit = 1.74 x + 0.0 (2414 voxels, overlap=0.414) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2414 voxels, peak = 23), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.09058 (93) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (543 voxels, overlap=1.013) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (543 voxels, peak = 92), gca=91.7 gca peak = 0.16930 (96) mri peak = 0.10084 (92) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (476 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (476 voxels, peak = 93), gca=92.6 gca peak = 0.24553 (55) mri peak = 0.09346 (67) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (687 voxels, overlap=0.164) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (687 voxels, peak = 66), gca=66.3 gca peak = 0.30264 (59) mri peak = 0.08206 (67) Left_Hippocampus (17): linear fit = 1.17 x + 0.0 (715 voxels, overlap=0.437) Left_Hippocampus (17): linear fit = 1.17 x + 0.0 (715 voxels, peak = 69), gca=69.3 gca peak = 0.07580 (103) mri peak = 0.07576 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (27031 voxels, overlap=0.784) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (27031 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.08048 (106) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (28977 voxels, overlap=0.704) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (28977 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.05035 (69) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (27068 voxels, overlap=0.357) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (27068 voxels, peak = 69), gca=68.7 gca peak = 0.11620 (58) mri peak = 0.04936 (69) Right_Cerebral_Cortex (42): linear fit = 1.18 x + 0.0 (27048 voxels, overlap=0.321) Right_Cerebral_Cortex (42): linear fit = 1.18 x + 0.0 (27048 voxels, peak = 69), gca=68.7 gca peak = 0.30970 (66) mri peak = 0.07407 (80) Right_Caudate (50): linear fit = 1.14 x + 0.0 (982 voxels, overlap=0.380) Right_Caudate (50): linear fit = 1.14 x + 0.0 (982 voxels, peak = 76), gca=75.6 gca peak = 0.15280 (69) mri peak = 0.07643 (76) Left_Caudate (11): linear fit = 1.02 x + 0.0 (942 voxels, overlap=1.006) Left_Caudate (11): linear fit = 1.02 x + 0.0 (942 voxels, peak = 71), gca=70.7 gca peak = 0.13902 (56) mri peak = 0.06089 (63) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (27656 voxels, overlap=0.608) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (27656 voxels, peak = 65), gca=64.7 gca peak = 0.14777 (55) mri peak = 0.05835 (64) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (30163 voxels, overlap=0.721) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (30163 voxels, peak = 64), gca=63.5 gca peak = 0.16765 (84) mri peak = 0.07768 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4480 voxels, overlap=0.960) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4480 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.08056 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4864 voxels, overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4864 voxels, peak = 84), gca=83.6 gca peak = 0.29869 (57) mri peak = 0.10170 (70) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (349 voxels, overlap=0.216) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (349 voxels, peak = 68), gca=67.5 gca peak = 0.33601 (57) mri peak = 0.07832 (67) Right_Amygdala (54): linear fit = 1.16 x + 0.0 (357 voxels, overlap=0.561) Right_Amygdala (54): linear fit = 1.16 x + 0.0 (357 voxels, peak = 66), gca=66.4 gca peak = 0.11131 (90) mri peak = 0.06315 (84) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4166 voxels, overlap=0.997) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4166 voxels, peak = 88), gca=87.8 gca peak = 0.11793 (83) mri peak = 0.05907 (83) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4116 voxels, overlap=0.921) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4116 voxels, peak = 88), gca=87.6 gca peak = 0.08324 (81) mri peak = 0.07483 (80) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1522 voxels, overlap=0.758) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1522 voxels, peak = 85), gca=84.6 gca peak = 0.10360 (77) mri peak = 0.06543 (82) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1821 voxels, overlap=0.810) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1821 voxels, peak = 81), gca=81.2 gca peak = 0.08424 (78) mri peak = 0.08595 (84) Brain_Stem (16): linear fit = 1.07 x + 0.0 (8165 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.07 x + 0.0 (8165 voxels, peak = 83), gca=83.1 gca peak = 0.12631 (89) mri peak = 0.07374 (89) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (881 voxels, overlap=0.807) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (881 voxels, peak = 91), gca=91.2 gca peak = 0.14500 (87) mri peak = 0.07743 (89) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (928 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (928 voxels, peak = 88), gca=88.3 gca peak = 0.14975 (24) mri peak = 0.07166 (19) gca peak = 0.19357 (14) mri peak = 0.09845 (22) Fourth_Ventricle (15): linear fit = 1.52 x + 0.0 (578 voxels, overlap=0.735) Fourth_Ventricle (15): linear fit = 1.52 x + 0.0 (578 voxels, peak = 21), gca=21.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.18 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.36 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.13931 (25) mri peak = 0.09618 (23) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (2614 voxels, overlap=0.862) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (2614 voxels, peak = 25), gca=25.4 gca peak = 0.13758 (19) mri peak = 0.11519 (25) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (2414 voxels, overlap=0.742) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (2414 voxels, peak = 22), gca=21.6 gca peak = 0.26757 (90) mri peak = 0.09058 (93) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (543 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (543 voxels, peak = 91), gca=91.3 gca peak = 0.18617 (93) mri peak = 0.10084 (92) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (476 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (476 voxels, peak = 93), gca=92.5 gca peak = 0.27943 (67) mri peak = 0.09346 (67) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (687 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (687 voxels, peak = 66), gca=66.0 gca peak = 0.29154 (66) mri peak = 0.08206 (67) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (715 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (715 voxels, peak = 66), gca=66.0 gca peak = 0.07614 (105) mri peak = 0.07576 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27031 voxels, overlap=0.864) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27031 voxels, peak = 104), gca=104.5 gca peak = 0.07686 (107) mri peak = 0.08048 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28977 voxels, overlap=0.807) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28977 voxels, peak = 106), gca=106.5 gca peak = 0.08206 (69) mri peak = 0.05035 (69) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (27068 voxels, overlap=0.962) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (27068 voxels, peak = 69), gca=69.0 gca peak = 0.09961 (69) mri peak = 0.04936 (69) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (27048 voxels, overlap=0.956) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (27048 voxels, peak = 69), gca=69.0 gca peak = 0.24442 (76) mri peak = 0.07407 (80) Right_Caudate (50): linear fit = 1.00 x + 0.0 (982 voxels, overlap=1.005) Right_Caudate (50): linear fit = 1.00 x + 0.0 (982 voxels, peak = 76), gca=76.0 gca peak = 0.15167 (70) mri peak = 0.07643 (76) Left_Caudate (11): linear fit = 0.99 x + 0.0 (942 voxels, overlap=1.005) Left_Caudate (11): linear fit = 0.99 x + 0.0 (942 voxels, peak = 69), gca=69.0 gca peak = 0.12579 (65) mri peak = 0.06089 (63) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (27656 voxels, overlap=0.995) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (27656 voxels, peak = 65), gca=65.0 gca peak = 0.13049 (63) mri peak = 0.05835 (64) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (30163 voxels, overlap=0.990) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (30163 voxels, peak = 62), gca=62.1 gca peak = 0.15819 (86) mri peak = 0.07768 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4480 voxels, overlap=0.985) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4480 voxels, peak = 86), gca=85.6 gca peak = 0.15632 (83) mri peak = 0.08056 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4864 voxels, overlap=0.980) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4864 voxels, peak = 83), gca=82.6 gca peak = 0.29148 (69) mri peak = 0.10170 (70) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (349 voxels, overlap=1.016) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (349 voxels, peak = 69), gca=69.0 gca peak = 0.34643 (66) mri peak = 0.07832 (67) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (357 voxels, overlap=1.015) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (357 voxels, peak = 66), gca=66.0 gca peak = 0.11483 (86) mri peak = 0.06315 (84) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4166 voxels, overlap=0.973) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4166 voxels, peak = 87), gca=87.3 gca peak = 0.10619 (85) mri peak = 0.05907 (83) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (4116 voxels, overlap=0.978) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (4116 voxels, peak = 83), gca=82.9 gca peak = 0.07460 (79) mri peak = 0.07483 (80) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1522 voxels, overlap=0.884) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1522 voxels, peak = 79), gca=78.6 gca peak = 0.08162 (81) mri peak = 0.06543 (82) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1821 voxels, overlap=0.957) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1821 voxels, peak = 81), gca=80.6 gca peak = 0.07275 (83) mri peak = 0.08595 (84) Brain_Stem (16): linear fit = 1.01 x + 0.0 (8165 voxels, overlap=0.726) Brain_Stem (16): linear fit = 1.01 x + 0.0 (8165 voxels, peak = 84), gca=84.2 gca peak = 0.11391 (86) mri peak = 0.07374 (89) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (881 voxels, overlap=0.831) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (881 voxels, peak = 84), gca=83.8 gca peak = 0.16107 (87) mri peak = 0.07743 (89) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (928 voxels, overlap=0.933) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (928 voxels, peak = 87), gca=86.6 gca peak = 0.12335 (35) mri peak = 0.07166 (19) gca peak = 0.14598 (22) mri peak = 0.09845 (22) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (578 voxels, overlap=0.835) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (578 voxels, peak = 25), gca=24.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.14952 (38) gca peak Left_Thalamus = 0.64095 (104) gca peak Third_Ventricle = 0.12335 (35) gca peak CSF = 0.18746 (49) gca peak Left_Accumbens_area = 0.73514 (64) gca peak Left_undetermined = 0.96707 (28) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12577 (35) gca peak Right_Inf_Lat_Vent = 0.24202 (28) gca peak Right_Accumbens_area = 0.29837 (74) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14507 (37) gca peak Fifth_Ventricle = 0.75707 (42) gca peak WM_hypointensities = 0.07984 (78) gca peak non_WM_hypointensities = 0.07502 (56) gca peak Optic_Chiasm = 0.70948 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.09 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 85735 voxels changed in iteration 0 of unlikely voxel relabeling 369 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 61499 gm and wm labels changed (%34 to gray, %66 to white out of all changed labels) 454 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 85068 changed. image ll: -2.107, PF=0.500 pass 2: 20626 changed. image ll: -2.105, PF=0.500 pass 3: 5426 changed. pass 4: 1722 changed. 48787 voxels changed in iteration 0 of unlikely voxel relabeling 481 voxels changed in iteration 1 of unlikely voxel relabeling 22 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 8522 voxels changed in iteration 0 of unlikely voxel relabeling 177 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6345 voxels changed in iteration 0 of unlikely voxel relabeling 71 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4833 voxels changed in iteration 0 of unlikely voxel relabeling 23 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3762.974940 mri_ca_label stimesec 2.082683 mri_ca_label ru_maxrss 2093732 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 743105 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 63712 mri_ca_label ru_oublock 488 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 351 mri_ca_label ru_nivcsw 7278 auto-labeling took 61 minutes and 56 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/transforms/cc_up.lta 0051348 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-6.0.0/0051348/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/norm.mgz 97373 voxels in left wm, 102901 in right wm, xrange [115, 134] searching rotation angles z=[ 2 16], y=[-9 5] searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.7 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.7 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.2 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.7 searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.4 searching scale 1 Z rot 10.7 searching scale 1 Z rot 10.9 searching scale 1 Z rot 11.2 searching scale 1 Z rot 11.4 searching scale 1 Z rot 11.7 searching scale 1 Z rot 11.9 searching scale 1 Z rot 12.2 searching scale 1 Z rot 12.4 searching scale 1 Z rot 12.7 searching scale 1 Z rot 12.9 searching scale 1 Z rot 13.2 searching scale 1 Z rot 13.4 searching scale 1 Z rot 13.7 searching scale 1 Z rot 13.9 searching scale 1 Z rot 14.2 searching scale 1 Z rot 14.4 searching scale 1 Z rot 14.7 searching scale 1 Z rot 14.9 searching scale 1 Z rot 15.2 searching scale 1 Z rot 15.4 global minimum found at slice 123.2, rotations (-2.01, 8.66) final transformation (x=123.2, yr=-2.008, zr=8.656): 0.98800 -0.15051 -0.03463 21.84634; 0.15042 0.98861 -0.00527 35.97475; 0.03503 -0.00000 0.99939 -0.24051; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 129 cc center is found at 129 75 124 eigenvectors: -0.00218 -0.00035 1.00000; 0.36356 -0.93157 0.00047; 0.93157 0.36356 0.00216; writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/aseg.auto.mgz... corpus callosum segmentation took 2.5 minutes #-------------------------------------- #@# Merge ASeg Sat Oct 7 21:05:56 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Oct 7 21:05:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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... 1791 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 107 gm peak at 73 (73), valley at 29 (29) csf peak at 37, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 71 (71), valley at 31 (31) csf peak at 36, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 31 seconds. #-------------------------------------------- #@# Mask BFS Sat Oct 7 21:09:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1569126 voxels in mask (pct= 9.35) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Oct 7 21:09:30 CEST 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.9 +- 6.9 [79.0 --> 125.0] GM (72.0) : 70.0 +- 9.3 [30.0 --> 95.0] setting bottom of white matter range to 79.3 setting top of gray matter range to 88.5 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 21923 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5506 filled 610 bright non-wm voxels segmented. 9130 diagonally connected voxels added... white matter segmentation took 1.7 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 0.55 minutes reading wm segmentation from wm.seg.mgz... 622 voxels added to wm to prevent paths from MTL structures to cortex 3325 additional wm voxels added 0 additional wm voxels added SEG EDIT: 58961 voxels turned on, 26453 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+): 39 found - 39 modified | TOTAL: 39 pass 2 (xy+): 0 found - 39 modified | TOTAL: 39 pass 1 (xy-): 44 found - 44 modified | TOTAL: 83 pass 2 (xy-): 0 found - 44 modified | TOTAL: 83 pass 1 (yz+): 53 found - 53 modified | TOTAL: 136 pass 2 (yz+): 0 found - 53 modified | TOTAL: 136 pass 1 (yz-): 44 found - 44 modified | TOTAL: 180 pass 2 (yz-): 0 found - 44 modified | TOTAL: 180 pass 1 (xz+): 43 found - 43 modified | TOTAL: 223 pass 2 (xz+): 0 found - 43 modified | TOTAL: 223 pass 1 (xz-): 39 found - 39 modified | TOTAL: 262 pass 2 (xz-): 0 found - 39 modified | TOTAL: 262 Iteration Number : 1 pass 1 (+++): 66 found - 66 modified | TOTAL: 66 pass 2 (+++): 0 found - 66 modified | TOTAL: 66 pass 1 (+++): 104 found - 104 modified | TOTAL: 170 pass 2 (+++): 0 found - 104 modified | TOTAL: 170 pass 1 (+++): 73 found - 73 modified | TOTAL: 243 pass 2 (+++): 0 found - 73 modified | TOTAL: 243 pass 1 (+++): 61 found - 61 modified | TOTAL: 304 pass 2 (+++): 0 found - 61 modified | TOTAL: 304 Iteration Number : 1 pass 1 (++): 365 found - 365 modified | TOTAL: 365 pass 2 (++): 0 found - 365 modified | TOTAL: 365 pass 1 (+-): 349 found - 349 modified | TOTAL: 714 pass 2 (+-): 1 found - 350 modified | TOTAL: 715 pass 3 (+-): 0 found - 350 modified | TOTAL: 715 pass 1 (--): 261 found - 261 modified | TOTAL: 976 pass 2 (--): 0 found - 261 modified | TOTAL: 976 pass 1 (-+): 316 found - 316 modified | TOTAL: 1292 pass 2 (-+): 0 found - 316 modified | TOTAL: 1292 Iteration Number : 2 pass 1 (xy+): 32 found - 32 modified | TOTAL: 32 pass 2 (xy+): 0 found - 32 modified | TOTAL: 32 pass 1 (xy-): 23 found - 23 modified | TOTAL: 55 pass 2 (xy-): 0 found - 23 modified | TOTAL: 55 pass 1 (yz+): 32 found - 32 modified | TOTAL: 87 pass 2 (yz+): 0 found - 32 modified | TOTAL: 87 pass 1 (yz-): 38 found - 38 modified | TOTAL: 125 pass 2 (yz-): 0 found - 38 modified | TOTAL: 125 pass 1 (xz+): 40 found - 40 modified | TOTAL: 165 pass 2 (xz+): 0 found - 40 modified | TOTAL: 165 pass 1 (xz-): 42 found - 42 modified | TOTAL: 207 pass 2 (xz-): 0 found - 42 modified | TOTAL: 207 Iteration Number : 2 pass 1 (+++): 16 found - 16 modified | TOTAL: 16 pass 2 (+++): 0 found - 16 modified | TOTAL: 16 pass 1 (+++): 10 found - 10 modified | TOTAL: 26 pass 2 (+++): 0 found - 10 modified | TOTAL: 26 pass 1 (+++): 10 found - 10 modified | TOTAL: 36 pass 2 (+++): 0 found - 10 modified | TOTAL: 36 pass 1 (+++): 10 found - 10 modified | TOTAL: 46 pass 2 (+++): 0 found - 10 modified | TOTAL: 46 Iteration Number : 2 pass 1 (++): 18 found - 18 modified | TOTAL: 18 pass 2 (++): 0 found - 18 modified | TOTAL: 18 pass 1 (+-): 18 found - 18 modified | TOTAL: 36 pass 2 (+-): 0 found - 18 modified | TOTAL: 36 pass 1 (--): 10 found - 10 modified | TOTAL: 46 pass 2 (--): 0 found - 10 modified | TOTAL: 46 pass 1 (-+): 13 found - 13 modified | TOTAL: 59 pass 2 (-+): 0 found - 13 modified | TOTAL: 59 Iteration Number : 3 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 3 found - 3 modified | TOTAL: 5 pass 2 (xy-): 0 found - 3 modified | TOTAL: 5 pass 1 (yz+): 7 found - 7 modified | TOTAL: 12 pass 2 (yz+): 0 found - 7 modified | TOTAL: 12 pass 1 (yz-): 4 found - 4 modified | TOTAL: 16 pass 2 (yz-): 0 found - 4 modified | TOTAL: 16 pass 1 (xz+): 3 found - 3 modified | TOTAL: 19 pass 2 (xz+): 0 found - 3 modified | TOTAL: 19 pass 1 (xz-): 8 found - 8 modified | TOTAL: 27 pass 2 (xz-): 0 found - 8 modified | TOTAL: 27 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 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 4 found - 4 modified | TOTAL: 8 pass 2 (+-): 0 found - 4 modified | TOTAL: 8 pass 1 (--): 2 found - 2 modified | TOTAL: 10 pass 2 (--): 0 found - 2 modified | TOTAL: 10 pass 1 (-+): 5 found - 5 modified | TOTAL: 15 pass 2 (-+): 0 found - 5 modified | TOTAL: 15 Iteration Number : 4 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 2 found - 2 modified | TOTAL: 5 pass 2 (yz+): 0 found - 2 modified | TOTAL: 5 pass 1 (yz-): 0 found - 0 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2218 (out of 506982: 0.437491) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Oct 7 21:11:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 1.10694 -0.11683 -0.05557 4.51487; 0.09651 1.05813 -0.16529 24.88748; 0.07125 0.15034 0.96326 -33.22720; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.10694 -0.11683 -0.05557 4.51487; 0.09651 1.05813 -0.16529 24.88748; 0.07125 0.15034 0.96326 -33.22720; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1888 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using seed (127, 108, 84), TAL = (1.0, -44.0, 20.0) talairach voxel to voxel transform 0.89135 0.08894 0.06669 -4.02203; -0.08942 0.91365 0.15162 -17.29690; -0.05197 -0.14918 1.00954 37.49169; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 108, 84) --> (1.0, -44.0, 20.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (1.00, -44.00, 20.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, -44.00, 20.00) SRC: (108.34, 84.37, 100.52) search lh wm seed point around talairach space (-17.00, -44.00, 20.00), SRC: (140.43, 81.15, 98.65) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sat Oct 7 21:12:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-): 7 found - 7 modified | TOTAL: 7 pass 2 (xy-): 0 found - 7 modified | TOTAL: 7 pass 1 (yz+): 4 found - 4 modified | TOTAL: 11 pass 2 (yz+): 0 found - 4 modified | TOTAL: 11 pass 1 (yz-): 1 found - 1 modified | TOTAL: 12 pass 2 (yz-): 0 found - 1 modified | TOTAL: 12 pass 1 (xz+): 3 found - 3 modified | TOTAL: 15 pass 2 (xz+): 0 found - 3 modified | TOTAL: 15 pass 1 (xz-): 2 found - 2 modified | TOTAL: 17 pass 2 (xz-): 0 found - 2 modified | TOTAL: 17 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 3 found - 3 modified | TOTAL: 5 pass 2 (+-): 0 found - 3 modified | TOTAL: 5 pass 1 (--): 0 found - 0 modified | TOTAL: 5 pass 1 (-+): 0 found - 0 modified | TOTAL: 5 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 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 : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 23 (out of 249465: 0.009220) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 758 vertices, 835 faces slice 50: 5212 vertices, 5403 faces slice 60: 12128 vertices, 12392 faces slice 70: 20621 vertices, 20953 faces slice 80: 31026 vertices, 31414 faces slice 90: 42561 vertices, 43001 faces slice 100: 54980 vertices, 55528 faces slice 110: 68985 vertices, 69548 faces slice 120: 83680 vertices, 84282 faces slice 130: 97696 vertices, 98335 faces slice 140: 110287 vertices, 110917 faces slice 150: 121039 vertices, 121639 faces slice 160: 130249 vertices, 130870 faces slice 170: 139387 vertices, 139994 faces slice 180: 146447 vertices, 146976 faces slice 190: 152290 vertices, 152829 faces slice 200: 157246 vertices, 157700 faces slice 210: 158764 vertices, 159108 faces slice 220: 158764 vertices, 159108 faces slice 230: 158764 vertices, 159108 faces slice 240: 158764 vertices, 159108 faces slice 250: 158764 vertices, 159108 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... 158764 voxel in cpt #1: X=-344 [v=158764,e=477324,f=318216] located at (-22.184683, -10.576838, 45.570080) For the whole surface: X=-344 [v=158764,e=477324,f=318216] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat Oct 7 21:12:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 3 found - 3 modified | TOTAL: 5 pass 2 (yz+): 0 found - 3 modified | TOTAL: 5 pass 1 (yz-): 1 found - 1 modified | TOTAL: 6 pass 2 (yz-): 0 found - 1 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 2 found - 2 modified | TOTAL: 9 pass 2 (xz-): 0 found - 2 modified | TOTAL: 9 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 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 = 12 (out of 243199: 0.004934) 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: 2070 vertices, 2233 faces slice 60: 7445 vertices, 7668 faces slice 70: 14539 vertices, 14800 faces slice 80: 23078 vertices, 23457 faces slice 90: 33633 vertices, 34067 faces slice 100: 45557 vertices, 45994 faces slice 110: 57848 vertices, 58340 faces slice 120: 71660 vertices, 72211 faces slice 130: 85280 vertices, 85855 faces slice 140: 99795 vertices, 100465 faces slice 150: 112081 vertices, 112657 faces slice 160: 121869 vertices, 122374 faces slice 170: 130685 vertices, 131226 faces slice 180: 139306 vertices, 139795 faces slice 190: 146471 vertices, 146965 faces slice 200: 152245 vertices, 152670 faces slice 210: 154026 vertices, 154320 faces slice 220: 154026 vertices, 154320 faces slice 230: 154026 vertices, 154320 faces slice 240: 154026 vertices, 154320 faces slice 250: 154026 vertices, 154320 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... 154026 voxel in cpt #1: X=-294 [v=154026,e=462960,f=308640] located at (28.407425, -4.730974, 37.019054) For the whole surface: X=-294 [v=154026,e=462960,f=308640] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Oct 7 21:12:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sat Oct 7 21:12:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 28760 of (28760 28763) to complete... Waiting for PID 28763 of (28760 28763) 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 (28760 28763) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sat Oct 7 21:12:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sat Oct 7 21:12:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 28811 of (28811 28814) to complete... Waiting for PID 28814 of (28811 28814) 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 = 47.9 mm, total surface area = 79608 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.179 (target=0.015) step 005: RMS=0.139 (target=0.015) step 010: RMS=0.113 (target=0.015) step 015: RMS=0.101 (target=0.015) step 020: RMS=0.093 (target=0.015) step 025: RMS=0.088 (target=0.015) step 030: RMS=0.083 (target=0.015) step 035: RMS=0.081 (target=0.015) step 040: RMS=0.079 (target=0.015) step 045: RMS=0.078 (target=0.015) step 050: RMS=0.076 (target=0.015) step 055: RMS=0.076 (target=0.015) step 060: RMS=0.075 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 49.802428 mris_inflate stimesec 0.116982 mris_inflate ru_maxrss 233884 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 34391 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11200 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2053 mris_inflate ru_nivcsw 3496 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.7 mm, total surface area = 77385 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.177 (target=0.015) step 005: RMS=0.136 (target=0.015) step 010: RMS=0.111 (target=0.015) step 015: RMS=0.100 (target=0.015) step 020: RMS=0.094 (target=0.015) step 025: RMS=0.090 (target=0.015) step 030: RMS=0.086 (target=0.015) step 035: RMS=0.082 (target=0.015) step 040: RMS=0.078 (target=0.015) step 045: RMS=0.076 (target=0.015) step 050: RMS=0.075 (target=0.015) step 055: RMS=0.073 (target=0.015) step 060: RMS=0.072 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 48.837575 mris_inflate stimesec 0.112982 mris_inflate ru_maxrss 226636 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 33089 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10848 mris_inflate ru_oublock 10864 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2310 mris_inflate ru_nivcsw 3540 PIDs (28811 28814) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sat Oct 7 21:13:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sat Oct 7 21:13:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 28866 of (28866 28870) to complete... Waiting for PID 28870 of (28866 28870) to complete... mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.90 +- 0.60 (0.00-->7.90) (max @ vno 61838 --> 63181) face area 0.02 +- 0.03 (-0.35-->0.53) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.292... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.239, avgs=0 005/300: dt: 0.9000, rms radial error=176.982, avgs=0 010/300: dt: 0.9000, rms radial error=176.432, avgs=0 015/300: dt: 0.9000, rms radial error=175.708, avgs=0 020/300: dt: 0.9000, rms radial error=174.883, avgs=0 025/300: dt: 0.9000, rms radial error=174.001, avgs=0 030/300: dt: 0.9000, rms radial error=173.087, avgs=0 035/300: dt: 0.9000, rms radial error=172.151, avgs=0 040/300: dt: 0.9000, rms radial error=171.207, avgs=0 045/300: dt: 0.9000, rms radial error=170.260, avgs=0 050/300: dt: 0.9000, rms radial error=169.313, avgs=0 055/300: dt: 0.9000, rms radial error=168.369, avgs=0 060/300: dt: 0.9000, rms radial error=167.427, avgs=0 065/300: dt: 0.9000, rms radial error=166.487, avgs=0 070/300: dt: 0.9000, rms radial error=165.551, avgs=0 075/300: dt: 0.9000, rms radial error=164.619, avgs=0 080/300: dt: 0.9000, rms radial error=163.693, avgs=0 085/300: dt: 0.9000, rms radial error=162.773, avgs=0 090/300: dt: 0.9000, rms radial error=161.858, avgs=0 095/300: dt: 0.9000, rms radial error=160.947, avgs=0 100/300: dt: 0.9000, rms radial error=160.042, avgs=0 105/300: dt: 0.9000, rms radial error=159.144, avgs=0 110/300: dt: 0.9000, rms radial error=158.250, avgs=0 115/300: dt: 0.9000, rms radial error=157.361, avgs=0 120/300: dt: 0.9000, rms radial error=156.476, avgs=0 125/300: dt: 0.9000, rms radial error=155.597, avgs=0 130/300: dt: 0.9000, rms radial error=154.722, avgs=0 135/300: dt: 0.9000, rms radial error=153.852, avgs=0 140/300: dt: 0.9000, rms radial error=152.987, avgs=0 145/300: dt: 0.9000, rms radial error=152.126, avgs=0 150/300: dt: 0.9000, rms radial error=151.270, avgs=0 155/300: dt: 0.9000, rms radial error=150.420, avgs=0 160/300: dt: 0.9000, rms radial error=149.574, avgs=0 165/300: dt: 0.9000, rms radial error=148.733, avgs=0 170/300: dt: 0.9000, rms radial error=147.896, avgs=0 175/300: dt: 0.9000, rms radial error=147.064, avgs=0 180/300: dt: 0.9000, rms radial error=146.236, avgs=0 185/300: dt: 0.9000, rms radial error=145.413, avgs=0 190/300: dt: 0.9000, rms radial error=144.595, avgs=0 195/300: dt: 0.9000, rms radial error=143.781, avgs=0 200/300: dt: 0.9000, rms radial error=142.971, avgs=0 205/300: dt: 0.9000, rms radial error=142.166, avgs=0 210/300: dt: 0.9000, rms radial error=141.365, avgs=0 215/300: dt: 0.9000, rms radial error=140.569, avgs=0 220/300: dt: 0.9000, rms radial error=139.777, avgs=0 225/300: dt: 0.9000, rms radial error=138.989, avgs=0 230/300: dt: 0.9000, rms radial error=138.206, avgs=0 235/300: dt: 0.9000, rms radial error=137.427, avgs=0 240/300: dt: 0.9000, rms radial error=136.653, avgs=0 245/300: dt: 0.9000, rms radial error=135.883, avgs=0 250/300: dt: 0.9000, rms radial error=135.118, avgs=0 255/300: dt: 0.9000, rms radial error=134.357, avgs=0 260/300: dt: 0.9000, rms radial error=133.600, avgs=0 265/300: dt: 0.9000, rms radial error=132.848, avgs=0 270/300: dt: 0.9000, rms radial error=132.100, avgs=0 275/300: dt: 0.9000, rms radial error=131.357, avgs=0 280/300: dt: 0.9000, rms radial error=130.617, avgs=0 285/300: dt: 0.9000, rms radial error=129.882, avgs=0 290/300: dt: 0.9000, rms radial error=129.151, avgs=0 295/300: dt: 0.9000, rms radial error=128.423, avgs=0 300/300: dt: 0.9000, rms radial error=127.700, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19177.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 3502.03 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 465.95 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00298 epoch 4 (K=640.0), pass 1, starting sse = 58.39 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00527 final distance error %30.63 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 285.245636 mris_sphere stimesec 0.257960 mris_sphere ru_maxrss 234084 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 33928 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 11184 mris_sphere ru_oublock 11224 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8273 mris_sphere ru_nivcsw 20221 FSRUNTIME@ mris_sphere 0.0789 hours 1 threads mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.92 +- 0.58 (0.00-->8.27) (max @ vno 50224 --> 50233) face area 0.02 +- 0.03 (-0.15-->0.64) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.296... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.101, avgs=0 005/300: dt: 0.9000, rms radial error=176.843, avgs=0 010/300: dt: 0.9000, rms radial error=176.290, avgs=0 015/300: dt: 0.9000, rms radial error=175.562, avgs=0 020/300: dt: 0.9000, rms radial error=174.730, avgs=0 025/300: dt: 0.9000, rms radial error=173.840, avgs=0 030/300: dt: 0.9000, rms radial error=172.918, avgs=0 035/300: dt: 0.9000, rms radial error=171.980, avgs=0 040/300: dt: 0.9000, rms radial error=171.033, avgs=0 045/300: dt: 0.9000, rms radial error=170.084, avgs=0 050/300: dt: 0.9000, rms radial error=169.135, avgs=0 055/300: dt: 0.9000, rms radial error=168.188, avgs=0 060/300: dt: 0.9000, rms radial error=167.249, avgs=0 065/300: dt: 0.9000, rms radial error=166.315, avgs=0 070/300: dt: 0.9000, rms radial error=165.385, avgs=0 075/300: dt: 0.9000, rms radial error=164.459, avgs=0 080/300: dt: 0.9000, rms radial error=163.539, avgs=0 085/300: dt: 0.9000, rms radial error=162.624, avgs=0 090/300: dt: 0.9000, rms radial error=161.714, avgs=0 095/300: dt: 0.9000, rms radial error=160.809, avgs=0 100/300: dt: 0.9000, rms radial error=159.908, avgs=0 105/300: dt: 0.9000, rms radial error=159.013, avgs=0 110/300: dt: 0.9000, rms radial error=158.122, avgs=0 115/300: dt: 0.9000, rms radial error=157.236, avgs=0 120/300: dt: 0.9000, rms radial error=156.355, avgs=0 125/300: dt: 0.9000, rms radial error=155.478, avgs=0 130/300: dt: 0.9000, rms radial error=154.606, avgs=0 135/300: dt: 0.9000, rms radial error=153.739, avgs=0 140/300: dt: 0.9000, rms radial error=152.877, avgs=0 145/300: dt: 0.9000, rms radial error=152.019, avgs=0 150/300: dt: 0.9000, rms radial error=151.166, avgs=0 155/300: dt: 0.9000, rms radial error=150.317, avgs=0 160/300: dt: 0.9000, rms radial error=149.473, avgs=0 165/300: dt: 0.9000, rms radial error=148.634, avgs=0 170/300: dt: 0.9000, rms radial error=147.798, avgs=0 175/300: dt: 0.9000, rms radial error=146.968, avgs=0 180/300: dt: 0.9000, rms radial error=146.142, avgs=0 185/300: dt: 0.9000, rms radial error=145.320, avgs=0 190/300: dt: 0.9000, rms radial error=144.503, avgs=0 195/300: dt: 0.9000, rms radial error=143.691, avgs=0 200/300: dt: 0.9000, rms radial error=142.882, avgs=0 205/300: dt: 0.9000, rms radial error=142.079, avgs=0 210/300: dt: 0.9000, rms radial error=141.280, avgs=0 215/300: dt: 0.9000, rms radial error=140.485, avgs=0 220/300: dt: 0.9000, rms radial error=139.694, avgs=0 225/300: dt: 0.9000, rms radial error=138.908, avgs=0 230/300: dt: 0.9000, rms radial error=138.127, avgs=0 235/300: dt: 0.9000, rms radial error=137.349, avgs=0 240/300: dt: 0.9000, rms radial error=136.576, avgs=0 245/300: dt: 0.9000, rms radial error=135.807, avgs=0 250/300: dt: 0.9000, rms radial error=135.043, avgs=0 255/300: dt: 0.9000, rms radial error=134.283, avgs=0 260/300: dt: 0.9000, rms radial error=133.526, avgs=0 265/300: dt: 0.9000, rms radial error=132.775, avgs=0 270/300: dt: 0.9000, rms radial error=132.027, avgs=0 275/300: dt: 0.9000, rms radial error=131.283, avgs=0 280/300: dt: 0.9000, rms radial error=130.544, avgs=0 285/300: dt: 0.9000, rms radial error=129.809, avgs=0 290/300: dt: 0.9000, rms radial error=129.078, avgs=0 295/300: dt: 0.9000, rms radial error=128.351, avgs=0 300/300: dt: 0.9000, rms radial error=127.628, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18474.20 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 3281.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 410.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00396 epoch 4 (K=640.0), pass 1, starting sse = 44.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/12 = 0.00633 final distance error %28.42 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 280.674331 mris_sphere stimesec 0.157975 mris_sphere ru_maxrss 226836 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 32626 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10888 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8395 mris_sphere ru_nivcsw 19808 FSRUNTIME@ mris_sphere 0.0780 hours 1 threads PIDs (28866 28870) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sat Oct 7 21:18:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat Oct 7 21:18:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat Oct 7 21:18:33 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051348 lh #@# Fix Topology rh Sat Oct 7 21:18:33 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051348 rh Waiting for PID 29128 of (29128 29131) to complete... Waiting for PID 29131 of (29128 29131) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051348 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=-344 (nv=158764, nf=318216, ne=477324, g=173) 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... 28132 ambiguous faces found in tessellation segmenting defects... 126 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 55 into 47 -merging segment 69 into 64 -merging segment 70 into 65 -merging segment 79 into 76 -merging segment 83 into 82 -merging segment 104 into 111 120 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4356 (-4.7178) -vertex loglikelihood: -6.2727 (-3.1363) -normal dot loglikelihood: -3.5893 (-3.5893) -quad curv loglikelihood: -6.1361 (-3.0681) Total Loglikelihood : -25.4338 CORRECTING DEFECT 0 (vertices=183, convex hull=140, v0=280) After retessellation of defect 0 (v0=280), euler #=-114 (142578,422848,280156) : difference with theory (-117) = -3 CORRECTING DEFECT 1 (vertices=13, convex hull=21, v0=2532) After retessellation of defect 1 (v0=2532), euler #=-113 (142579,422860,280168) : difference with theory (-116) = -3 CORRECTING DEFECT 2 (vertices=31, convex hull=63, v0=4193) After retessellation of defect 2 (v0=4193), euler #=-112 (142594,422930,280224) : difference with theory (-115) = -3 CORRECTING DEFECT 3 (vertices=33, convex hull=62, v0=14515) After retessellation of defect 3 (v0=14515), euler #=-111 (142615,423021,280295) : difference with theory (-114) = -3 CORRECTING DEFECT 4 (vertices=37, convex hull=82, v0=14552) After retessellation of defect 4 (v0=14552), euler #=-110 (142633,423110,280367) : difference with theory (-113) = -3 CORRECTING DEFECT 5 (vertices=4678, convex hull=1805, v0=15315) XL defect detected... After retessellation of defect 5 (v0=15315), euler #=-110 (143285,426027,282632) : difference with theory (-112) = -2 CORRECTING DEFECT 6 (vertices=41, convex hull=68, v0=16122) After retessellation of defect 6 (v0=16122), euler #=-109 (143294,426080,282677) : difference with theory (-111) = -2 CORRECTING DEFECT 7 (vertices=23, convex hull=31, v0=16738) After retessellation of defect 7 (v0=16738), euler #=-108 (143297,426096,282691) : difference with theory (-110) = -2 CORRECTING DEFECT 8 (vertices=54, convex hull=31, v0=16906) After retessellation of defect 8 (v0=16906), euler #=-107 (143300,426113,282706) : difference with theory (-109) = -2 CORRECTING DEFECT 9 (vertices=54, convex hull=42, v0=18343) After retessellation of defect 9 (v0=18343), euler #=-106 (143306,426147,282735) : difference with theory (-108) = -2 CORRECTING DEFECT 10 (vertices=24, convex hull=51, v0=22129) After retessellation of defect 10 (v0=22129), euler #=-105 (143316,426193,282772) : difference with theory (-107) = -2 CORRECTING DEFECT 11 (vertices=58, convex hull=55, v0=22488) After retessellation of defect 11 (v0=22488), euler #=-104 (143331,426264,282829) : difference with theory (-106) = -2 CORRECTING DEFECT 12 (vertices=20, convex hull=56, v0=22608) After retessellation of defect 12 (v0=22608), euler #=-103 (143342,426316,282871) : difference with theory (-105) = -2 CORRECTING DEFECT 13 (vertices=64, convex hull=90, v0=23346) After retessellation of defect 13 (v0=23346), euler #=-102 (143383,426480,282995) : difference with theory (-104) = -2 CORRECTING DEFECT 14 (vertices=48, convex hull=72, v0=28181) After retessellation of defect 14 (v0=28181), euler #=-101 (143404,426572,283067) : difference with theory (-103) = -2 CORRECTING DEFECT 15 (vertices=84, convex hull=119, v0=30544) After retessellation of defect 15 (v0=30544), euler #=-100 (143451,426765,283214) : difference with theory (-102) = -2 CORRECTING DEFECT 16 (vertices=10, convex hull=13, v0=32493) After retessellation of defect 16 (v0=32493), euler #=-99 (143453,426773,283221) : difference with theory (-101) = -2 CORRECTING DEFECT 17 (vertices=60, convex hull=100, v0=33251) After retessellation of defect 17 (v0=33251), euler #=-98 (143484,426906,283324) : difference with theory (-100) = -2 CORRECTING DEFECT 18 (vertices=42, convex hull=73, v0=36702) After retessellation of defect 18 (v0=36702), euler #=-97 (143498,426979,283384) : difference with theory (-99) = -2 CORRECTING DEFECT 19 (vertices=17, convex hull=18, v0=40244) After retessellation of defect 19 (v0=40244), euler #=-96 (143500,426990,283394) : difference with theory (-98) = -2 CORRECTING DEFECT 20 (vertices=6, convex hull=20, v0=40606) After retessellation of defect 20 (v0=40606), euler #=-95 (143501,426999,283403) : difference with theory (-97) = -2 CORRECTING DEFECT 21 (vertices=51, convex hull=85, v0=42209) After retessellation of defect 21 (v0=42209), euler #=-94 (143510,427064,283460) : difference with theory (-96) = -2 CORRECTING DEFECT 22 (vertices=41, convex hull=68, v0=43148) After retessellation of defect 22 (v0=43148), euler #=-93 (143530,427149,283526) : difference with theory (-95) = -2 CORRECTING DEFECT 23 (vertices=11, convex hull=21, v0=43808) After retessellation of defect 23 (v0=43808), euler #=-92 (143531,427158,283535) : difference with theory (-94) = -2 CORRECTING DEFECT 24 (vertices=72, convex hull=109, v0=43819) After retessellation of defect 24 (v0=43819), euler #=-91 (143540,427233,283602) : difference with theory (-93) = -2 CORRECTING DEFECT 25 (vertices=35, convex hull=46, v0=46369) After retessellation of defect 25 (v0=46369), euler #=-90 (143546,427270,283634) : difference with theory (-92) = -2 CORRECTING DEFECT 26 (vertices=63, convex hull=31, v0=46734) After retessellation of defect 26 (v0=46734), euler #=-89 (143553,427302,283660) : difference with theory (-91) = -2 CORRECTING DEFECT 27 (vertices=122, convex hull=193, v0=50700) After retessellation of defect 27 (v0=50700), euler #=-88 (143565,427429,283776) : difference with theory (-90) = -2 CORRECTING DEFECT 28 (vertices=156, convex hull=132, v0=50981) After retessellation of defect 28 (v0=50981), euler #=-87 (143627,427667,283953) : difference with theory (-89) = -2 CORRECTING DEFECT 29 (vertices=5, convex hull=21, v0=51623) After retessellation of defect 29 (v0=51623), euler #=-86 (143628,427676,283962) : difference with theory (-88) = -2 CORRECTING DEFECT 30 (vertices=86, convex hull=60, v0=54980) After retessellation of defect 30 (v0=54980), euler #=-85 (143651,427771,284035) : difference with theory (-87) = -2 CORRECTING DEFECT 31 (vertices=87, convex hull=84, v0=57266) After retessellation of defect 31 (v0=57266), euler #=-84 (143670,427863,284109) : difference with theory (-86) = -2 CORRECTING DEFECT 32 (vertices=35, convex hull=53, v0=58363) After retessellation of defect 32 (v0=58363), euler #=-83 (143685,427929,284161) : difference with theory (-85) = -2 CORRECTING DEFECT 33 (vertices=23, convex hull=54, v0=58941) After retessellation of defect 33 (v0=58941), euler #=-82 (143697,427987,284208) : difference with theory (-84) = -2 CORRECTING DEFECT 34 (vertices=154, convex hull=31, v0=59136) After retessellation of defect 34 (v0=59136), euler #=-81 (143704,428017,284232) : difference with theory (-83) = -2 CORRECTING DEFECT 35 (vertices=19, convex hull=34, v0=60479) After retessellation of defect 35 (v0=60479), euler #=-80 (143708,428040,284252) : difference with theory (-82) = -2 CORRECTING DEFECT 36 (vertices=30, convex hull=85, v0=61693) After retessellation of defect 36 (v0=61693), euler #=-79 (143725,428122,284318) : difference with theory (-81) = -2 CORRECTING DEFECT 37 (vertices=23, convex hull=49, v0=63274) After retessellation of defect 37 (v0=63274), euler #=-78 (143734,428168,284356) : difference with theory (-80) = -2 CORRECTING DEFECT 38 (vertices=35, convex hull=43, v0=68767) After retessellation of defect 38 (v0=68767), euler #=-77 (143741,428203,284385) : difference with theory (-79) = -2 CORRECTING DEFECT 39 (vertices=51, convex hull=54, v0=68969) After retessellation of defect 39 (v0=68969), euler #=-76 (143752,428257,284429) : difference with theory (-78) = -2 CORRECTING DEFECT 40 (vertices=132, convex hull=85, v0=69230) After retessellation of defect 40 (v0=69230), euler #=-75 (143789,428405,284541) : difference with theory (-77) = -2 CORRECTING DEFECT 41 (vertices=53, convex hull=82, v0=69774) After retessellation of defect 41 (v0=69774), euler #=-74 (143816,428521,284631) : difference with theory (-76) = -2 CORRECTING DEFECT 42 (vertices=123, convex hull=120, v0=72986) After retessellation of defect 42 (v0=72986), euler #=-73 (143862,428729,284794) : difference with theory (-75) = -2 CORRECTING DEFECT 43 (vertices=17, convex hull=49, v0=73944) After retessellation of defect 43 (v0=73944), euler #=-72 (143871,428775,284832) : difference with theory (-74) = -2 CORRECTING DEFECT 44 (vertices=78, convex hull=135, v0=74123) After retessellation of defect 44 (v0=74123), euler #=-71 (143889,428891,284931) : difference with theory (-73) = -2 CORRECTING DEFECT 45 (vertices=43, convex hull=33, v0=76075) After retessellation of defect 45 (v0=76075), euler #=-70 (143895,428921,284956) : difference with theory (-72) = -2 CORRECTING DEFECT 46 (vertices=27, convex hull=64, v0=76758) After retessellation of defect 46 (v0=76758), euler #=-69 (143907,428978,285002) : difference with theory (-71) = -2 CORRECTING DEFECT 47 (vertices=617, convex hull=231, v0=77766) After retessellation of defect 47 (v0=77766), euler #=-68 (144014,429412,285330) : difference with theory (-70) = -2 CORRECTING DEFECT 48 (vertices=29, convex hull=48, v0=80186) After retessellation of defect 48 (v0=80186), euler #=-67 (144022,429455,285366) : difference with theory (-69) = -2 CORRECTING DEFECT 49 (vertices=46, convex hull=42, v0=81787) After retessellation of defect 49 (v0=81787), euler #=-66 (144028,429487,285393) : difference with theory (-68) = -2 CORRECTING DEFECT 50 (vertices=20, convex hull=58, v0=82150) After retessellation of defect 50 (v0=82150), euler #=-65 (144041,429545,285439) : difference with theory (-67) = -2 CORRECTING DEFECT 51 (vertices=233, convex hull=148, v0=85097) After retessellation of defect 51 (v0=85097), euler #=-64 (144071,429712,285577) : difference with theory (-66) = -2 CORRECTING DEFECT 52 (vertices=61, convex hull=86, v0=86538) After retessellation of defect 52 (v0=86538), euler #=-64 (144085,429792,285643) : difference with theory (-65) = -1 CORRECTING DEFECT 53 (vertices=7, convex hull=19, v0=87374) After retessellation of defect 53 (v0=87374), euler #=-63 (144086,429800,285651) : difference with theory (-64) = -1 CORRECTING DEFECT 54 (vertices=9, convex hull=21, v0=89105) After retessellation of defect 54 (v0=89105), euler #=-62 (144088,429814,285664) : difference with theory (-63) = -1 CORRECTING DEFECT 55 (vertices=63, convex hull=75, v0=89394) After retessellation of defect 55 (v0=89394), euler #=-61 (144103,429895,285731) : difference with theory (-62) = -1 CORRECTING DEFECT 56 (vertices=31, convex hull=58, v0=90341) After retessellation of defect 56 (v0=90341), euler #=-60 (144122,429973,285791) : difference with theory (-61) = -1 CORRECTING DEFECT 57 (vertices=9, convex hull=27, v0=90516) After retessellation of defect 57 (v0=90516), euler #=-59 (144124,429986,285803) : difference with theory (-60) = -1 CORRECTING DEFECT 58 (vertices=39, convex hull=51, v0=90697) After retessellation of defect 58 (v0=90697), euler #=-58 (144135,430039,285846) : difference with theory (-59) = -1 CORRECTING DEFECT 59 (vertices=21, convex hull=53, v0=91464) After retessellation of defect 59 (v0=91464), euler #=-57 (144144,430084,285883) : difference with theory (-58) = -1 CORRECTING DEFECT 60 (vertices=56, convex hull=82, v0=92002) After retessellation of defect 60 (v0=92002), euler #=-56 (144174,430210,285980) : difference with theory (-57) = -1 CORRECTING DEFECT 61 (vertices=31, convex hull=31, v0=92552) After retessellation of defect 61 (v0=92552), euler #=-55 (144177,430231,285999) : difference with theory (-56) = -1 CORRECTING DEFECT 62 (vertices=15, convex hull=26, v0=94755) After retessellation of defect 62 (v0=94755), euler #=-54 (144181,430249,286014) : difference with theory (-55) = -1 CORRECTING DEFECT 63 (vertices=106, convex hull=117, v0=95865) After retessellation of defect 63 (v0=95865), euler #=-52 (144234,430464,286178) : difference with theory (-54) = -2 CORRECTING DEFECT 64 (vertices=151, convex hull=233, v0=96121) After retessellation of defect 64 (v0=96121), euler #=-50 (144272,430681,286359) : difference with theory (-53) = -3 CORRECTING DEFECT 65 (vertices=125, convex hull=110, v0=96322) After retessellation of defect 65 (v0=96322), euler #=-49 (144287,430780,286444) : difference with theory (-52) = -3 CORRECTING DEFECT 66 (vertices=26, convex hull=61, v0=96715) After retessellation of defect 66 (v0=96715), euler #=-48 (144296,430829,286485) : difference with theory (-51) = -3 CORRECTING DEFECT 67 (vertices=242, convex hull=243, v0=97159) After retessellation of defect 67 (v0=97159), euler #=-47 (144381,431203,286775) : difference with theory (-50) = -3 CORRECTING DEFECT 68 (vertices=373, convex hull=55, v0=100083) After retessellation of defect 68 (v0=100083), euler #=-46 (144398,431275,286831) : difference with theory (-49) = -3 CORRECTING DEFECT 69 (vertices=24, convex hull=32, v0=100468) After retessellation of defect 69 (v0=100468), euler #=-45 (144400,431294,286849) : difference with theory (-48) = -3 CORRECTING DEFECT 70 (vertices=17, convex hull=65, v0=102841) After retessellation of defect 70 (v0=102841), euler #=-44 (144411,431351,286896) : difference with theory (-47) = -3 CORRECTING DEFECT 71 (vertices=43, convex hull=26, v0=102920) After retessellation of defect 71 (v0=102920), euler #=-43 (144416,431374,286915) : difference with theory (-46) = -3 CORRECTING DEFECT 72 (vertices=9, convex hull=18, v0=104250) After retessellation of defect 72 (v0=104250), euler #=-42 (144417,431381,286922) : difference with theory (-45) = -3 CORRECTING DEFECT 73 (vertices=145, convex hull=129, v0=107535) After retessellation of defect 73 (v0=107535), euler #=-40 (144454,431563,287069) : difference with theory (-44) = -4 CORRECTING DEFECT 74 (vertices=23, convex hull=60, v0=107824) After retessellation of defect 74 (v0=107824), euler #=-39 (144469,431629,287121) : difference with theory (-43) = -4 CORRECTING DEFECT 75 (vertices=32, convex hull=64, v0=108064) After retessellation of defect 75 (v0=108064), euler #=-38 (144491,431718,287189) : difference with theory (-42) = -4 CORRECTING DEFECT 76 (vertices=1750, convex hull=572, v0=108846) XL defect detected... After retessellation of defect 76 (v0=108846), euler #=-39 (144892,433230,288299) : difference with theory (-41) = -2 CORRECTING DEFECT 77 (vertices=23, convex hull=44, v0=109051) After retessellation of defect 77 (v0=109051), euler #=-38 (144894,433255,288323) : difference with theory (-40) = -2 CORRECTING DEFECT 78 (vertices=163, convex hull=79, v0=111380) After retessellation of defect 78 (v0=111380), euler #=-36 (144918,433363,288409) : difference with theory (-39) = -3 CORRECTING DEFECT 79 (vertices=8, convex hull=23, v0=111649) After retessellation of defect 79 (v0=111649), euler #=-35 (144919,433373,288419) : difference with theory (-38) = -3 CORRECTING DEFECT 80 (vertices=61, convex hull=98, v0=113734) After retessellation of defect 80 (v0=113734), euler #=-34 (144950,433510,288526) : difference with theory (-37) = -3 CORRECTING DEFECT 81 (vertices=188, convex hull=105, v0=115170) After retessellation of defect 81 (v0=115170), euler #=-33 (144963,433595,288599) : difference with theory (-36) = -3 CORRECTING DEFECT 82 (vertices=571, convex hull=163, v0=116032) After retessellation of defect 82 (v0=116032), euler #=-33 (145049,433935,288853) : difference with theory (-35) = -2 CORRECTING DEFECT 83 (vertices=32, convex hull=41, v0=116655) After retessellation of defect 83 (v0=116655), euler #=-32 (145056,433969,288881) : difference with theory (-34) = -2 CORRECTING DEFECT 84 (vertices=20, convex hull=63, v0=116872) After retessellation of defect 84 (v0=116872), euler #=-31 (145070,434029,288928) : difference with theory (-33) = -2 CORRECTING DEFECT 85 (vertices=19, convex hull=49, v0=117148) After retessellation of defect 85 (v0=117148), euler #=-30 (145080,434074,288964) : difference with theory (-32) = -2 CORRECTING DEFECT 86 (vertices=14, convex hull=29, v0=118718) After retessellation of defect 86 (v0=118718), euler #=-29 (145082,434085,288974) : difference with theory (-31) = -2 CORRECTING DEFECT 87 (vertices=7, convex hull=21, v0=118732) After retessellation of defect 87 (v0=118732), euler #=-28 (145083,434093,288982) : difference with theory (-30) = -2 CORRECTING DEFECT 88 (vertices=23, convex hull=56, v0=119551) After retessellation of defect 88 (v0=119551), euler #=-27 (145093,434142,289022) : difference with theory (-29) = -2 CORRECTING DEFECT 89 (vertices=28, convex hull=70, v0=119858) After retessellation of defect 89 (v0=119858), euler #=-26 (145102,434199,289071) : difference with theory (-28) = -2 CORRECTING DEFECT 90 (vertices=7, convex hull=18, v0=120656) After retessellation of defect 90 (v0=120656), euler #=-25 (145103,434207,289079) : difference with theory (-27) = -2 CORRECTING DEFECT 91 (vertices=31, convex hull=24, v0=121984) After retessellation of defect 91 (v0=121984), euler #=-24 (145104,434219,289091) : difference with theory (-26) = -2 CORRECTING DEFECT 92 (vertices=40, convex hull=19, v0=122257) After retessellation of defect 92 (v0=122257), euler #=-23 (145104,434228,289101) : difference with theory (-25) = -2 CORRECTING DEFECT 93 (vertices=45, convex hull=76, v0=124358) After retessellation of defect 93 (v0=124358), euler #=-22 (145113,434289,289154) : difference with theory (-24) = -2 CORRECTING DEFECT 94 (vertices=43, convex hull=43, v0=126648) After retessellation of defect 94 (v0=126648), euler #=-21 (145129,434353,289203) : difference with theory (-23) = -2 CORRECTING DEFECT 95 (vertices=81, convex hull=22, v0=126882) After retessellation of defect 95 (v0=126882), euler #=-20 (145131,434364,289213) : difference with theory (-22) = -2 CORRECTING DEFECT 96 (vertices=142, convex hull=132, v0=131182) After retessellation of defect 96 (v0=131182), euler #=-19 (145164,434522,289339) : difference with theory (-21) = -2 CORRECTING DEFECT 97 (vertices=65, convex hull=36, v0=132358) After retessellation of defect 97 (v0=132358), euler #=-19 (145169,434556,289368) : difference with theory (-20) = -1 CORRECTING DEFECT 98 (vertices=59, convex hull=34, v0=134230) After retessellation of defect 98 (v0=134230), euler #=-18 (145174,434584,289392) : difference with theory (-19) = -1 CORRECTING DEFECT 99 (vertices=30, convex hull=81, v0=137988) After retessellation of defect 99 (v0=137988), euler #=-17 (145189,434664,289458) : difference with theory (-18) = -1 CORRECTING DEFECT 100 (vertices=77, convex hull=112, v0=139495) After retessellation of defect 100 (v0=139495), euler #=-16 (145235,434854,289603) : difference with theory (-17) = -1 CORRECTING DEFECT 101 (vertices=6, convex hull=35, v0=140961) After retessellation of defect 101 (v0=140961), euler #=-15 (145236,434867,289616) : difference with theory (-16) = -1 CORRECTING DEFECT 102 (vertices=62, convex hull=104, v0=142366) After retessellation of defect 102 (v0=142366), euler #=-14 (145257,434978,289707) : difference with theory (-15) = -1 CORRECTING DEFECT 103 (vertices=31, convex hull=68, v0=142836) After retessellation of defect 103 (v0=142836), euler #=-13 (145267,435035,289755) : difference with theory (-14) = -1 CORRECTING DEFECT 104 (vertices=31, convex hull=28, v0=145003) After retessellation of defect 104 (v0=145003), euler #=-12 (145268,435051,289771) : difference with theory (-13) = -1 CORRECTING DEFECT 105 (vertices=1213, convex hull=509, v0=145849) L defect detected... After retessellation of defect 105 (v0=145849), euler #=-12 (145559,436188,290617) : difference with theory (-12) = 0 CORRECTING DEFECT 106 (vertices=59, convex hull=101, v0=147878) After retessellation of defect 106 (v0=147878), euler #=-11 (145593,436334,290730) : difference with theory (-11) = 0 CORRECTING DEFECT 107 (vertices=51, convex hull=79, v0=148682) After retessellation of defect 107 (v0=148682), euler #=-10 (145615,436431,290806) : difference with theory (-10) = 0 CORRECTING DEFECT 108 (vertices=121, convex hull=106, v0=149185) After retessellation of defect 108 (v0=149185), euler #=-9 (145656,436595,290930) : difference with theory (-9) = 0 CORRECTING DEFECT 109 (vertices=597, convex hull=136, v0=150154) After retessellation of defect 109 (v0=150154), euler #=-8 (145722,436856,291126) : difference with theory (-8) = 0 CORRECTING DEFECT 110 (vertices=109, convex hull=121, v0=150331) After retessellation of defect 110 (v0=150331), euler #=-7 (145747,436986,291232) : difference with theory (-7) = 0 CORRECTING DEFECT 111 (vertices=23, convex hull=30, v0=150759) After retessellation of defect 111 (v0=150759), euler #=-6 (145748,437002,291248) : difference with theory (-6) = 0 CORRECTING DEFECT 112 (vertices=188, convex hull=48, v0=152908) After retessellation of defect 112 (v0=152908), euler #=-5 (145756,437045,291284) : difference with theory (-5) = 0 CORRECTING DEFECT 113 (vertices=59, convex hull=109, v0=154521) After retessellation of defect 113 (v0=154521), euler #=-4 (145774,437143,291365) : difference with theory (-4) = 0 CORRECTING DEFECT 114 (vertices=30, convex hull=70, v0=155588) After retessellation of defect 114 (v0=155588), euler #=-3 (145786,437207,291418) : difference with theory (-3) = 0 CORRECTING DEFECT 115 (vertices=28, convex hull=70, v0=156064) After retessellation of defect 115 (v0=156064), euler #=-2 (145795,437257,291460) : difference with theory (-2) = 0 CORRECTING DEFECT 116 (vertices=146, convex hull=95, v0=156326) After retessellation of defect 116 (v0=156326), euler #=-1 (145837,437423,291585) : difference with theory (-1) = 0 CORRECTING DEFECT 117 (vertices=100, convex hull=115, v0=157744) After retessellation of defect 117 (v0=157744), euler #=0 (145854,437523,291669) : difference with theory (0) = 0 CORRECTING DEFECT 118 (vertices=43, convex hull=69, v0=158331) After retessellation of defect 118 (v0=158331), euler #=1 (145873,437606,291734) : difference with theory (1) = 0 CORRECTING DEFECT 119 (vertices=13, convex hull=19, v0=158749) After retessellation of defect 119 (v0=158749), euler #=2 (145874,437616,291744) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.30 (0.04-->11.86) (max @ vno 44778 --> 56635) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.30 (0.04-->11.86) (max @ vno 44778 --> 56635) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 444 mutations (35.0%), 823 crossovers (65.0%), 1501 vertices were eliminated building final representation... 12890 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=145874, nf=291744, ne=437616, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 184.1 minutes 0 defective edges removing intersecting faces 000: 1288 intersecting 001: 113 intersecting 002: 31 intersecting 003: 9 intersecting 004: 6 intersecting 005: 3 intersecting mris_fix_topology utimesec 11050.300099 mris_fix_topology stimesec 1.940704 mris_fix_topology ru_maxrss 640620 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 126325 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 33552 mris_fix_topology ru_oublock 14704 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 732 mris_fix_topology ru_nivcsw 20545 FSRUNTIME@ mris_fix_topology lh 3.0684 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051348 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=-294 (nv=154026, nf=308640, ne=462960, g=148) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 18613 ambiguous faces found in tessellation segmenting defects... 147 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 4 into 3 -merging segment 56 into 62 -merging segment 74 into 66 -merging segment 88 into 71 -merging segment 77 into 76 -merging segment 96 into 92 -merging segment 134 into 133 -merging segment 137 into 133 -merging segment 142 into 141 -merging segment 145 into 141 137 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3764 (-4.6882) -vertex loglikelihood: -6.2514 (-3.1257) -normal dot loglikelihood: -3.5644 (-3.5644) -quad curv loglikelihood: -6.0734 (-3.0367) Total Loglikelihood : -25.2656 CORRECTING DEFECT 0 (vertices=154, convex hull=46, v0=586) After retessellation of defect 0 (v0=586), euler #=-140 (142688,423487,280659) : difference with theory (-134) = 6 CORRECTING DEFECT 1 (vertices=29, convex hull=70, v0=1312) After retessellation of defect 1 (v0=1312), euler #=-139 (142700,423547,280708) : difference with theory (-133) = 6 CORRECTING DEFECT 2 (vertices=27, convex hull=62, v0=7191) After retessellation of defect 2 (v0=7191), euler #=-138 (142710,423598,280750) : difference with theory (-132) = 6 CORRECTING DEFECT 3 (vertices=41, convex hull=64, v0=8063) After retessellation of defect 3 (v0=8063), euler #=-136 (142720,423656,280800) : difference with theory (-131) = 5 CORRECTING DEFECT 4 (vertices=28, convex hull=51, v0=11207) After retessellation of defect 4 (v0=11207), euler #=-135 (142736,423725,280854) : difference with theory (-130) = 5 CORRECTING DEFECT 5 (vertices=63, convex hull=55, v0=16474) After retessellation of defect 5 (v0=16474), euler #=-134 (142745,423773,280894) : difference with theory (-129) = 5 CORRECTING DEFECT 6 (vertices=83, convex hull=74, v0=16739) After retessellation of defect 6 (v0=16739), euler #=-133 (142776,423895,280986) : difference with theory (-128) = 5 CORRECTING DEFECT 7 (vertices=72, convex hull=97, v0=16802) After retessellation of defect 7 (v0=16802), euler #=-132 (142809,424037,281096) : difference with theory (-127) = 5 CORRECTING DEFECT 8 (vertices=36, convex hull=45, v0=19250) After retessellation of defect 8 (v0=19250), euler #=-131 (142822,424096,281143) : difference with theory (-126) = 5 CORRECTING DEFECT 9 (vertices=48, convex hull=46, v0=19759) After retessellation of defect 9 (v0=19759), euler #=-130 (142830,424135,281175) : difference with theory (-125) = 5 CORRECTING DEFECT 10 (vertices=8, convex hull=26, v0=20111) After retessellation of defect 10 (v0=20111), euler #=-129 (142830,424142,281183) : difference with theory (-124) = 5 CORRECTING DEFECT 11 (vertices=59, convex hull=50, v0=24782) After retessellation of defect 11 (v0=24782), euler #=-128 (142839,424190,281223) : difference with theory (-123) = 5 CORRECTING DEFECT 12 (vertices=31, convex hull=19, v0=25066) After retessellation of defect 12 (v0=25066), euler #=-127 (142845,424213,281241) : difference with theory (-122) = 5 CORRECTING DEFECT 13 (vertices=46, convex hull=51, v0=27961) After retessellation of defect 13 (v0=27961), euler #=-126 (142849,424244,281269) : difference with theory (-121) = 5 CORRECTING DEFECT 14 (vertices=40, convex hull=81, v0=28025) After retessellation of defect 14 (v0=28025), euler #=-125 (142877,424361,281359) : difference with theory (-120) = 5 CORRECTING DEFECT 15 (vertices=72, convex hull=87, v0=29203) After retessellation of defect 15 (v0=29203), euler #=-124 (142906,424487,281457) : difference with theory (-119) = 5 CORRECTING DEFECT 16 (vertices=1289, convex hull=771, v0=30574) XL defect detected... After retessellation of defect 16 (v0=30574), euler #=-124 (143310,426145,282711) : difference with theory (-118) = 6 CORRECTING DEFECT 17 (vertices=29, convex hull=25, v0=33155) After retessellation of defect 17 (v0=33155), euler #=-123 (143314,426163,282726) : difference with theory (-117) = 6 CORRECTING DEFECT 18 (vertices=25, convex hull=62, v0=35960) After retessellation of defect 18 (v0=35960), euler #=-122 (143323,426215,282770) : difference with theory (-116) = 6 CORRECTING DEFECT 19 (vertices=26, convex hull=54, v0=36109) After retessellation of defect 19 (v0=36109), euler #=-121 (143340,426287,282826) : difference with theory (-115) = 6 CORRECTING DEFECT 20 (vertices=46, convex hull=91, v0=38390) After retessellation of defect 20 (v0=38390), euler #=-120 (143352,426357,282885) : difference with theory (-114) = 6 CORRECTING DEFECT 21 (vertices=31, convex hull=78, v0=39139) After retessellation of defect 21 (v0=39139), euler #=-119 (143361,426415,282935) : difference with theory (-113) = 6 CORRECTING DEFECT 22 (vertices=32, convex hull=59, v0=42109) After retessellation of defect 22 (v0=42109), euler #=-118 (143378,426486,282990) : difference with theory (-112) = 6 CORRECTING DEFECT 23 (vertices=37, convex hull=96, v0=43262) After retessellation of defect 23 (v0=43262), euler #=-117 (143399,426589,283073) : difference with theory (-111) = 6 CORRECTING DEFECT 24 (vertices=29, convex hull=77, v0=44238) After retessellation of defect 24 (v0=44238), euler #=-116 (143417,426674,283141) : difference with theory (-110) = 6 CORRECTING DEFECT 25 (vertices=12, convex hull=23, v0=44389) After retessellation of defect 25 (v0=44389), euler #=-115 (143418,426685,283152) : difference with theory (-109) = 6 CORRECTING DEFECT 26 (vertices=113, convex hull=137, v0=45118) After retessellation of defect 26 (v0=45118), euler #=-114 (143453,426851,283284) : difference with theory (-108) = 6 CORRECTING DEFECT 27 (vertices=87, convex hull=127, v0=47018) After retessellation of defect 27 (v0=47018), euler #=-113 (143495,427033,283425) : difference with theory (-107) = 6 CORRECTING DEFECT 28 (vertices=25, convex hull=26, v0=47579) After retessellation of defect 28 (v0=47579), euler #=-112 (143501,427057,283444) : difference with theory (-106) = 6 CORRECTING DEFECT 29 (vertices=293, convex hull=214, v0=49064) After retessellation of defect 29 (v0=49064), euler #=-111 (143544,427284,283629) : difference with theory (-105) = 6 CORRECTING DEFECT 30 (vertices=30, convex hull=67, v0=50715) After retessellation of defect 30 (v0=50715), euler #=-110 (143566,427377,283701) : difference with theory (-104) = 6 CORRECTING DEFECT 31 (vertices=20, convex hull=31, v0=52966) After retessellation of defect 31 (v0=52966), euler #=-109 (143567,427391,283715) : difference with theory (-103) = 6 CORRECTING DEFECT 32 (vertices=37, convex hull=104, v0=53534) After retessellation of defect 32 (v0=53534), euler #=-108 (143581,427474,283785) : difference with theory (-102) = 6 CORRECTING DEFECT 33 (vertices=35, convex hull=23, v0=54178) After retessellation of defect 33 (v0=54178), euler #=-107 (143584,427491,283800) : difference with theory (-101) = 6 CORRECTING DEFECT 34 (vertices=44, convex hull=34, v0=58407) After retessellation of defect 34 (v0=58407), euler #=-106 (143592,427525,283827) : difference with theory (-100) = 6 CORRECTING DEFECT 35 (vertices=23, convex hull=18, v0=62220) After retessellation of defect 35 (v0=62220), euler #=-105 (143596,427541,283840) : difference with theory (-99) = 6 CORRECTING DEFECT 36 (vertices=139, convex hull=93, v0=63142) After retessellation of defect 36 (v0=63142), euler #=-104 (143635,427694,283955) : difference with theory (-98) = 6 CORRECTING DEFECT 37 (vertices=49, convex hull=68, v0=64450) After retessellation of defect 37 (v0=64450), euler #=-103 (143670,427826,284053) : difference with theory (-97) = 6 CORRECTING DEFECT 38 (vertices=6, convex hull=17, v0=67531) After retessellation of defect 38 (v0=67531), euler #=-102 (143670,427830,284058) : difference with theory (-96) = 6 CORRECTING DEFECT 39 (vertices=29, convex hull=24, v0=67634) After retessellation of defect 39 (v0=67634), euler #=-101 (143675,427851,284075) : difference with theory (-95) = 6 CORRECTING DEFECT 40 (vertices=57, convex hull=58, v0=67801) After retessellation of defect 40 (v0=67801), euler #=-100 (143694,427932,284138) : difference with theory (-94) = 6 CORRECTING DEFECT 41 (vertices=46, convex hull=71, v0=68776) After retessellation of defect 41 (v0=68776), euler #=-99 (143707,428003,284197) : difference with theory (-93) = 6 CORRECTING DEFECT 42 (vertices=138, convex hull=44, v0=71332) After retessellation of defect 42 (v0=71332), euler #=-98 (143718,428050,284234) : difference with theory (-92) = 6 CORRECTING DEFECT 43 (vertices=47, convex hull=29, v0=72996) After retessellation of defect 43 (v0=72996), euler #=-97 (143723,428076,284256) : difference with theory (-91) = 6 CORRECTING DEFECT 44 (vertices=29, convex hull=58, v0=73159) After retessellation of defect 44 (v0=73159), euler #=-96 (143734,428129,284299) : difference with theory (-90) = 6 CORRECTING DEFECT 45 (vertices=45, convex hull=75, v0=74167) After retessellation of defect 45 (v0=74167), euler #=-95 (143762,428244,284387) : difference with theory (-89) = 6 CORRECTING DEFECT 46 (vertices=30, convex hull=63, v0=74483) After retessellation of defect 46 (v0=74483), euler #=-94 (143771,428296,284431) : difference with theory (-88) = 6 CORRECTING DEFECT 47 (vertices=27, convex hull=66, v0=74829) After retessellation of defect 47 (v0=74829), euler #=-93 (143786,428366,284487) : difference with theory (-87) = 6 CORRECTING DEFECT 48 (vertices=199, convex hull=130, v0=79933) After retessellation of defect 48 (v0=79933), euler #=-92 (143796,428450,284562) : difference with theory (-86) = 6 CORRECTING DEFECT 49 (vertices=66, convex hull=68, v0=79956) After retessellation of defect 49 (v0=79956), euler #=-91 (143805,428504,284608) : difference with theory (-85) = 6 CORRECTING DEFECT 50 (vertices=38, convex hull=48, v0=80972) After retessellation of defect 50 (v0=80972), euler #=-90 (143826,428587,284671) : difference with theory (-84) = 6 CORRECTING DEFECT 51 (vertices=36, convex hull=66, v0=83762) After retessellation of defect 51 (v0=83762), euler #=-89 (143851,428687,284747) : difference with theory (-83) = 6 CORRECTING DEFECT 52 (vertices=105, convex hull=64, v0=85254) After retessellation of defect 52 (v0=85254), euler #=-88 (143860,428741,284793) : difference with theory (-82) = 6 CORRECTING DEFECT 53 (vertices=63, convex hull=60, v0=86364) After retessellation of defect 53 (v0=86364), euler #=-87 (143871,428797,284839) : difference with theory (-81) = 6 CORRECTING DEFECT 54 (vertices=22, convex hull=34, v0=86689) After retessellation of defect 54 (v0=86689), euler #=-86 (143875,428819,284858) : difference with theory (-80) = 6 CORRECTING DEFECT 55 (vertices=44, convex hull=92, v0=88212) After retessellation of defect 55 (v0=88212), euler #=-85 (143884,428886,284917) : difference with theory (-79) = 6 CORRECTING DEFECT 56 (vertices=89, convex hull=138, v0=88578) After retessellation of defect 56 (v0=88578), euler #=-84 (143929,429081,285068) : difference with theory (-78) = 6 CORRECTING DEFECT 57 (vertices=32, convex hull=60, v0=88704) After retessellation of defect 57 (v0=88704), euler #=-83 (143950,429168,285135) : difference with theory (-77) = 6 CORRECTING DEFECT 58 (vertices=23, convex hull=60, v0=89385) After retessellation of defect 58 (v0=89385), euler #=-82 (143962,429226,285182) : difference with theory (-76) = 6 CORRECTING DEFECT 59 (vertices=39, convex hull=59, v0=89521) After retessellation of defect 59 (v0=89521), euler #=-81 (143975,429287,285231) : difference with theory (-75) = 6 CORRECTING DEFECT 60 (vertices=51, convex hull=63, v0=90368) After retessellation of defect 60 (v0=90368), euler #=-79 (143984,429337,285274) : difference with theory (-74) = 5 CORRECTING DEFECT 61 (vertices=42, convex hull=75, v0=91294) After retessellation of defect 61 (v0=91294), euler #=-78 (144009,429446,285359) : difference with theory (-73) = 5 CORRECTING DEFECT 62 (vertices=42, convex hull=20, v0=91925) After retessellation of defect 62 (v0=91925), euler #=-77 (144016,429471,285378) : difference with theory (-72) = 5 CORRECTING DEFECT 63 (vertices=11, convex hull=30, v0=91960) After retessellation of defect 63 (v0=91960), euler #=-76 (144018,429486,285392) : difference with theory (-71) = 5 CORRECTING DEFECT 64 (vertices=429, convex hull=284, v0=92053) After retessellation of defect 64 (v0=92053), euler #=-74 (144123,429946,285749) : difference with theory (-70) = 4 CORRECTING DEFECT 65 (vertices=25, convex hull=47, v0=92055) After retessellation of defect 65 (v0=92055), euler #=-74 (144138,430010,285798) : difference with theory (-69) = 5 CORRECTING DEFECT 66 (vertices=12, convex hull=27, v0=94792) After retessellation of defect 66 (v0=94792), euler #=-73 (144141,430027,285813) : difference with theory (-68) = 5 CORRECTING DEFECT 67 (vertices=30, convex hull=78, v0=95053) After retessellation of defect 67 (v0=95053), euler #=-72 (144152,430093,285869) : difference with theory (-67) = 5 CORRECTING DEFECT 68 (vertices=11, convex hull=13, v0=96319) After retessellation of defect 68 (v0=96319), euler #=-71 (144154,430101,285876) : difference with theory (-66) = 5 CORRECTING DEFECT 69 (vertices=518, convex hull=205, v0=96712) After retessellation of defect 69 (v0=96712), euler #=-69 (144192,430312,286051) : difference with theory (-65) = 4 CORRECTING DEFECT 70 (vertices=104, convex hull=57, v0=98239) After retessellation of defect 70 (v0=98239), euler #=-68 (144215,430402,286119) : difference with theory (-64) = 4 CORRECTING DEFECT 71 (vertices=62, convex hull=103, v0=98631) After retessellation of defect 71 (v0=98631), euler #=-67 (144253,430559,286239) : difference with theory (-63) = 4 CORRECTING DEFECT 72 (vertices=172, convex hull=140, v0=99979) After retessellation of defect 72 (v0=99979), euler #=-66 (144304,430785,286415) : difference with theory (-62) = 4 CORRECTING DEFECT 73 (vertices=84, convex hull=155, v0=100320) After retessellation of defect 73 (v0=100320), euler #=-64 (144334,430947,286549) : difference with theory (-61) = 3 CORRECTING DEFECT 74 (vertices=70, convex hull=111, v0=100489) After retessellation of defect 74 (v0=100489), euler #=-63 (144371,431103,286669) : difference with theory (-60) = 3 CORRECTING DEFECT 75 (vertices=54, convex hull=102, v0=100822) After retessellation of defect 75 (v0=100822), euler #=-62 (144411,431266,286793) : difference with theory (-59) = 3 CORRECTING DEFECT 76 (vertices=111, convex hull=52, v0=101004) After retessellation of defect 76 (v0=101004), euler #=-61 (144420,431315,286834) : difference with theory (-58) = 3 CORRECTING DEFECT 77 (vertices=28, convex hull=51, v0=102487) After retessellation of defect 77 (v0=102487), euler #=-61 (144432,431372,286879) : difference with theory (-57) = 4 CORRECTING DEFECT 78 (vertices=31, convex hull=24, v0=103509) After retessellation of defect 78 (v0=103509), euler #=-60 (144438,431397,286899) : difference with theory (-56) = 4 CORRECTING DEFECT 79 (vertices=61, convex hull=83, v0=104653) After retessellation of defect 79 (v0=104653), euler #=-59 (144459,431495,286977) : difference with theory (-55) = 4 CORRECTING DEFECT 80 (vertices=21, convex hull=52, v0=104745) After retessellation of defect 80 (v0=104745), euler #=-58 (144469,431545,287018) : difference with theory (-54) = 4 CORRECTING DEFECT 81 (vertices=31, convex hull=46, v0=104754) After retessellation of defect 81 (v0=104754), euler #=-57 (144479,431591,287055) : difference with theory (-53) = 4 CORRECTING DEFECT 82 (vertices=32, convex hull=70, v0=105306) After retessellation of defect 82 (v0=105306), euler #=-56 (144491,431655,287108) : difference with theory (-52) = 4 CORRECTING DEFECT 83 (vertices=22, convex hull=50, v0=106005) After retessellation of defect 83 (v0=106005), euler #=-55 (144500,431703,287148) : difference with theory (-51) = 4 CORRECTING DEFECT 84 (vertices=19, convex hull=24, v0=106928) After retessellation of defect 84 (v0=106928), euler #=-54 (144504,431722,287164) : difference with theory (-50) = 4 CORRECTING DEFECT 85 (vertices=86, convex hull=87, v0=108991) After retessellation of defect 85 (v0=108991), euler #=-53 (144537,431855,287265) : difference with theory (-49) = 4 CORRECTING DEFECT 86 (vertices=42, convex hull=61, v0=109890) After retessellation of defect 86 (v0=109890), euler #=-52 (144546,431908,287310) : difference with theory (-48) = 4 CORRECTING DEFECT 87 (vertices=85, convex hull=100, v0=109910) After retessellation of defect 87 (v0=109910), euler #=-50 (144568,432018,287400) : difference with theory (-47) = 3 CORRECTING DEFECT 88 (vertices=39, convex hull=39, v0=110684) After retessellation of defect 88 (v0=110684), euler #=-49 (144575,432050,287426) : difference with theory (-46) = 3 CORRECTING DEFECT 89 (vertices=67, convex hull=67, v0=110802) After retessellation of defect 89 (v0=110802), euler #=-48 (144593,432131,287490) : difference with theory (-45) = 3 CORRECTING DEFECT 90 (vertices=6, convex hull=24, v0=111002) After retessellation of defect 90 (v0=111002), euler #=-47 (144593,432139,287499) : difference with theory (-44) = 3 CORRECTING DEFECT 91 (vertices=110, convex hull=117, v0=111339) After retessellation of defect 91 (v0=111339), euler #=-46 (144636,432320,287638) : difference with theory (-43) = 3 CORRECTING DEFECT 92 (vertices=21, convex hull=27, v0=111848) After retessellation of defect 92 (v0=111848), euler #=-45 (144641,432342,287656) : difference with theory (-42) = 3 CORRECTING DEFECT 93 (vertices=28, convex hull=40, v0=112559) After retessellation of defect 93 (v0=112559), euler #=-44 (144646,432371,287681) : difference with theory (-41) = 3 CORRECTING DEFECT 94 (vertices=537, convex hull=225, v0=113084) normal vector of length zero at vertex 150191 with 3 faces normal vector of length zero at vertex 150191 with 3 faces normal vector of length zero at vertex 150191 with 3 faces normal vector of length zero at vertex 150191 with 3 faces After retessellation of defect 94 (v0=113084), euler #=-43 (144757,432817,288017) : difference with theory (-40) = 3 CORRECTING DEFECT 95 (vertices=73, convex hull=42, v0=114242) After retessellation of defect 95 (v0=114242), euler #=-42 (144774,432886,288070) : difference with theory (-39) = 3 CORRECTING DEFECT 96 (vertices=69, convex hull=133, v0=114895) After retessellation of defect 96 (v0=114895), euler #=-41 (144794,433006,288171) : difference with theory (-38) = 3 CORRECTING DEFECT 97 (vertices=73, convex hull=121, v0=116201) After retessellation of defect 97 (v0=116201), euler #=-40 (144818,433134,288276) : difference with theory (-37) = 3 CORRECTING DEFECT 98 (vertices=33, convex hull=60, v0=116405) After retessellation of defect 98 (v0=116405), euler #=-39 (144836,433218,288343) : difference with theory (-36) = 3 CORRECTING DEFECT 99 (vertices=226, convex hull=139, v0=116445) After retessellation of defect 99 (v0=116445), euler #=-38 (144881,433424,288505) : difference with theory (-35) = 3 CORRECTING DEFECT 100 (vertices=14, convex hull=23, v0=116480) After retessellation of defect 100 (v0=116480), euler #=-37 (144882,433436,288517) : difference with theory (-34) = 3 CORRECTING DEFECT 101 (vertices=137, convex hull=120, v0=118265) After retessellation of defect 101 (v0=118265), euler #=-36 (144901,433561,288624) : difference with theory (-33) = 3 CORRECTING DEFECT 102 (vertices=527, convex hull=179, v0=119213) After retessellation of defect 102 (v0=119213), euler #=-36 (144978,433896,288882) : difference with theory (-32) = 4 CORRECTING DEFECT 103 (vertices=17, convex hull=41, v0=122457) After retessellation of defect 103 (v0=122457), euler #=-35 (144987,433934,288912) : difference with theory (-31) = 4 CORRECTING DEFECT 104 (vertices=40, convex hull=25, v0=126513) After retessellation of defect 104 (v0=126513), euler #=-34 (144994,433961,288933) : difference with theory (-30) = 4 CORRECTING DEFECT 105 (vertices=113, convex hull=93, v0=126817) After retessellation of defect 105 (v0=126817), euler #=-33 (145014,434060,289013) : difference with theory (-29) = 4 CORRECTING DEFECT 106 (vertices=22, convex hull=30, v0=129456) After retessellation of defect 106 (v0=129456), euler #=-32 (145017,434078,289029) : difference with theory (-28) = 4 CORRECTING DEFECT 107 (vertices=108, convex hull=41, v0=132428) After retessellation of defect 107 (v0=132428), euler #=-31 (145025,434121,289065) : difference with theory (-27) = 4 CORRECTING DEFECT 108 (vertices=27, convex hull=30, v0=132484) After retessellation of defect 108 (v0=132484), euler #=-30 (145028,434138,289080) : difference with theory (-26) = 4 CORRECTING DEFECT 109 (vertices=52, convex hull=89, v0=134728) After retessellation of defect 109 (v0=134728), euler #=-29 (145055,434256,289172) : difference with theory (-25) = 4 CORRECTING DEFECT 110 (vertices=65, convex hull=87, v0=134872) After retessellation of defect 110 (v0=134872), euler #=-28 (145081,434373,289264) : difference with theory (-24) = 4 CORRECTING DEFECT 111 (vertices=61, convex hull=97, v0=136600) After retessellation of defect 111 (v0=136600), euler #=-27 (145098,434463,289338) : difference with theory (-23) = 4 CORRECTING DEFECT 112 (vertices=51, convex hull=66, v0=137839) After retessellation of defect 112 (v0=137839), euler #=-26 (145126,434572,289420) : difference with theory (-22) = 4 CORRECTING DEFECT 113 (vertices=19, convex hull=49, v0=139020) After retessellation of defect 113 (v0=139020), euler #=-25 (145136,434622,289461) : difference with theory (-21) = 4 CORRECTING DEFECT 114 (vertices=6, convex hull=29, v0=139209) After retessellation of defect 114 (v0=139209), euler #=-24 (145137,434633,289472) : difference with theory (-20) = 4 CORRECTING DEFECT 115 (vertices=59, convex hull=70, v0=139874) After retessellation of defect 115 (v0=139874), euler #=-23 (145155,434717,289539) : difference with theory (-19) = 4 CORRECTING DEFECT 116 (vertices=119, convex hull=53, v0=141308) After retessellation of defect 116 (v0=141308), euler #=-22 (145164,434769,289583) : difference with theory (-18) = 4 CORRECTING DEFECT 117 (vertices=125, convex hull=43, v0=142100) After retessellation of defect 117 (v0=142100), euler #=-21 (145171,434808,289616) : difference with theory (-17) = 4 CORRECTING DEFECT 118 (vertices=63, convex hull=36, v0=142143) After retessellation of defect 118 (v0=142143), euler #=-20 (145175,434829,289634) : difference with theory (-16) = 4 CORRECTING DEFECT 119 (vertices=41, convex hull=34, v0=142227) After retessellation of defect 119 (v0=142227), euler #=-19 (145175,434840,289646) : difference with theory (-15) = 4 CORRECTING DEFECT 120 (vertices=180, convex hull=84, v0=144328) After retessellation of defect 120 (v0=144328), euler #=-18 (145207,434977,289752) : difference with theory (-14) = 4 CORRECTING DEFECT 121 (vertices=56, convex hull=32, v0=145369) After retessellation of defect 121 (v0=145369), euler #=-17 (145210,434997,289770) : difference with theory (-13) = 4 CORRECTING DEFECT 122 (vertices=115, convex hull=74, v0=146482) After retessellation of defect 122 (v0=146482), euler #=-16 (145219,435052,289817) : difference with theory (-12) = 4 CORRECTING DEFECT 123 (vertices=29, convex hull=37, v0=146612) After retessellation of defect 123 (v0=146612), euler #=-15 (145221,435074,289838) : difference with theory (-11) = 4 CORRECTING DEFECT 124 (vertices=57, convex hull=84, v0=147091) After retessellation of defect 124 (v0=147091), euler #=-14 (145244,435180,289922) : difference with theory (-10) = 4 CORRECTING DEFECT 125 (vertices=6, convex hull=26, v0=147513) After retessellation of defect 125 (v0=147513), euler #=-13 (145244,435188,289931) : difference with theory (-9) = 4 CORRECTING DEFECT 126 (vertices=142, convex hull=98, v0=147692) After retessellation of defect 126 (v0=147692), euler #=-12 (145274,435323,290037) : difference with theory (-8) = 4 CORRECTING DEFECT 127 (vertices=214, convex hull=210, v0=147848) After retessellation of defect 127 (v0=147848), euler #=-9 (145326,435579,290244) : difference with theory (-7) = 2 CORRECTING DEFECT 128 (vertices=147, convex hull=117, v0=148708) After retessellation of defect 128 (v0=148708), euler #=-8 (145359,435732,290365) : difference with theory (-6) = 2 CORRECTING DEFECT 129 (vertices=163, convex hull=126, v0=149039) After retessellation of defect 129 (v0=149039), euler #=-7 (145404,435925,290514) : difference with theory (-5) = 2 CORRECTING DEFECT 130 (vertices=28, convex hull=64, v0=149523) After retessellation of defect 130 (v0=149523), euler #=-6 (145413,435977,290558) : difference with theory (-4) = 2 CORRECTING DEFECT 131 (vertices=8, convex hull=17, v0=150026) After retessellation of defect 131 (v0=150026), euler #=-5 (145414,435986,290567) : difference with theory (-3) = 2 CORRECTING DEFECT 132 (vertices=38, convex hull=88, v0=150190) After retessellation of defect 132 (v0=150190), euler #=-4 (145432,436074,290638) : difference with theory (-2) = 2 CORRECTING DEFECT 133 (vertices=286, convex hull=263, v0=151449) After retessellation of defect 133 (v0=151449), euler #=-1 (145550,436569,291018) : difference with theory (-1) = 0 CORRECTING DEFECT 134 (vertices=39, convex hull=54, v0=152043) After retessellation of defect 134 (v0=152043), euler #=0 (145553,436600,291047) : difference with theory (0) = 0 CORRECTING DEFECT 135 (vertices=67, convex hull=89, v0=152163) After retessellation of defect 135 (v0=152163), euler #=1 (145576,436709,291134) : difference with theory (1) = 0 CORRECTING DEFECT 136 (vertices=31, convex hull=40, v0=153056) After retessellation of defect 136 (v0=153056), euler #=2 (145578,436728,291152) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.28 (0.02-->12.46) (max @ vno 74883 --> 87903) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.28 (0.02-->12.46) (max @ vno 74883 --> 87903) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 446 mutations (34.2%), 857 crossovers (65.8%), 669 vertices were eliminated building final representation... 8448 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=145578, nf=291152, ne=436728, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 87.8 minutes 0 defective edges removing intersecting faces 000: 1107 intersecting 001: 72 intersecting 002: 22 intersecting 003: 17 intersecting 004: 6 intersecting mris_fix_topology utimesec 5268.424077 mris_fix_topology stimesec 0.213967 mris_fix_topology ru_maxrss 496532 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 59963 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 14584 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 746 mris_fix_topology ru_nivcsw 11799 FSRUNTIME@ mris_fix_topology rh 1.4628 hours 1 threads PIDs (29128 29131) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 145874 - 437616 + 291744 = 2 --> 0 holes F =2V-4: 291744 = 291748-4 (0) 2E=3F: 875232 = 875232 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 145578 - 436728 + 291152 = 2 --> 0 holes F =2V-4: 291152 = 291156-4 (0) 2E=3F: 873456 = 873456 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 382 intersecting 001: 66 intersecting 002: 19 intersecting 003: 9 intersecting 004: 6 intersecting 005: 4 intersecting 006: 3 intersecting expanding nbhd size to 2 007: 3 intersecting expanding nbhd size to 3 008: 6 intersecting 009: 3 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 199 intersecting 001: 42 intersecting 002: 3 intersecting expanding nbhd size to 2 003: 3 intersecting 004: 2 intersecting expanding nbhd size to 3 005: 2 intersecting expanding nbhd size to 4 006: 8 intersecting 007: 5 intersecting expanding nbhd size to 5 008: 8 intersecting 009: 2 intersecting expanding nbhd size to 6 010: 2 intersecting expanding nbhd size to 7 011: 2 intersecting expanding nbhd size to 8 012: 2 intersecting expanding nbhd size to 9 013: 6 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Oct 8 00:23:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051348 lh #-------------------------------------------- #@# Make White Surf rh Sun Oct 8 00:23:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051348 rh Waiting for PID 3867 of (3867 3870) to complete... Waiting for PID 3870 of (3867 3870) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051348 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-6.0.0/0051348/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... 34293 bright wm thresholded. 656 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.orig... computing class statistics... border white: 276628 voxels (1.65%) border gray 335243 voxels (2.00%) WM (96.0): 96.6 +- 8.7 [70.0 --> 110.0] GM (73.0) : 72.5 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.9 (was 70) setting MAX_BORDER_WHITE to 110.7 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 51.7 (was 40) setting MAX_GRAY to 93.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.25 (0.03-->5.62) (max @ vno 41855 --> 52144) face area 0.27 +- 0.14 (0.00-->5.85) mean absolute distance = 0.65 +- 0.81 3822 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+-8.7, GM=72+-6.1 mean inside = 93.0, mean outside = 76.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=81.6, 301 (301) missing vertices, mean dist 0.2 [0.6 (%37.9)->0.7 (%62.1))] %72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.27 (0.03-->5.73) (max @ vno 41855 --> 52144) face area 0.27 +- 0.14 (0.00-->5.29) mean absolute distance = 0.37 +- 0.55 3910 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2594127.8, rms=8.379 001: dt: 0.5000, sse=1495255.6, rms=5.770 (31.143%) 002: dt: 0.5000, sse=1111286.5, rms=4.422 (23.361%) 003: dt: 0.5000, sse=965084.5, rms=3.804 (13.980%) 004: dt: 0.5000, sse=902894.1, rms=3.512 (7.663%) 005: dt: 0.5000, sse=878662.6, rms=3.378 (3.817%) 006: dt: 0.5000, sse=863832.9, rms=3.304 (2.192%) rms = 3.27, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=863070.2, rms=3.274 (0.912%) 008: dt: 0.2500, sse=727426.4, rms=2.337 (28.629%) 009: dt: 0.2500, sse=698040.1, rms=2.095 (10.358%) rms = 2.05, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=693159.5, rms=2.050 (2.119%) 011: dt: 0.1250, sse=686558.6, rms=1.996 (2.635%) rms = 1.99, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=686173.8, rms=1.990 (0.318%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.9, 249 (95) missing vertices, mean dist -0.2 [0.4 (%75.1)->0.3 (%24.9))] %83 local maxima, %11 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 0.88 +- 0.27 (0.09-->5.67) (max @ vno 41855 --> 52144) face area 0.33 +- 0.17 (0.00-->6.78) mean absolute distance = 0.26 +- 0.38 3868 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1253677.5, rms=4.461 013: dt: 0.5000, sse=948499.9, rms=2.868 (35.696%) rms = 2.93, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=851385.1, rms=2.290 (20.148%) 015: dt: 0.2500, sse=806170.1, rms=1.914 (16.453%) 016: dt: 0.2500, sse=795726.5, rms=1.766 (7.696%) rms = 1.72, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=788819.3, rms=1.719 (2.674%) rms = 1.67, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=782337.2, rms=1.671 (2.790%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=86.6, 278 (64) missing vertices, mean dist -0.1 [0.3 (%65.3)->0.2 (%34.7))] %88 local maxima, % 7 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 0.88 +- 0.27 (0.09-->5.58) (max @ vno 41855 --> 52144) face area 0.32 +- 0.17 (0.00-->6.75) mean absolute distance = 0.23 +- 0.33 3308 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=897526.2, rms=2.732 019: dt: 0.5000, sse=884461.6, rms=2.518 (7.810%) rms = 2.79, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=794124.9, rms=1.881 (25.296%) 021: dt: 0.2500, sse=768843.8, rms=1.611 (14.349%) 022: dt: 0.2500, sse=774989.6, rms=1.558 (3.311%) rms = 1.55, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=781992.4, rms=1.552 (0.352%) rms = 1.51, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=757646.4, rms=1.510 (2.763%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=87.2, 357 (46) missing vertices, mean dist -0.0 [0.2 (%54.0)->0.2 (%46.0))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=768535.2, rms=1.694 025: dt: 0.5000, sse=770753.4, rms=1.642 (3.048%) rms = 2.41, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=729075.9, rms=1.245 (24.195%) rms = 1.25, time step reduction 2 of 3 to 0.125... rms = 1.21, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=725656.4, rms=1.212 (2.615%) positioning took 0.5 minutes generating cortex label... 12 non-cortical segments detected only using segment with 8271 vertices erasing segment 1 (vno[0] = 55077) erasing segment 2 (vno[0] = 80379) erasing segment 3 (vno[0] = 91230) erasing segment 4 (vno[0] = 95168) erasing segment 5 (vno[0] = 97325) erasing segment 6 (vno[0] = 99430) erasing segment 7 (vno[0] = 100465) erasing segment 8 (vno[0] = 102306) erasing segment 9 (vno[0] = 103750) erasing segment 10 (vno[0] = 105689) erasing segment 11 (vno[0] = 109031) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.area vertex spacing 0.88 +- 0.27 (0.04-->5.57) (max @ vno 41855 --> 52144) face area 0.32 +- 0.17 (0.00-->6.58) refinement took 5.2 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051348 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-6.0.0/0051348/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... 34293 bright wm thresholded. 656 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.orig... computing class statistics... border white: 276628 voxels (1.65%) border gray 335243 voxels (2.00%) WM (96.0): 96.6 +- 8.7 [70.0 --> 110.0] GM (73.0) : 72.5 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.9 (was 70) setting MAX_BORDER_WHITE to 108.7 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 52.7 (was 40) setting MAX_GRAY to 91.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.24 (0.02-->4.80) (max @ vno 74884 --> 86646) face area 0.27 +- 0.14 (0.00-->3.84) mean absolute distance = 0.65 +- 0.83 4031 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=100+-7.8, GM=73+-6.1 mean inside = 92.5, mean outside = 76.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=82.2, 202 (202) missing vertices, mean dist 0.2 [0.6 (%39.9)->0.7 (%60.1))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.26 (0.04-->5.98) (max @ vno 35333 --> 143154) face area 0.27 +- 0.14 (0.00-->3.23) mean absolute distance = 0.37 +- 0.56 4218 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2377997.2, rms=7.900 001: dt: 0.5000, sse=1386108.2, rms=5.430 (31.271%) 002: dt: 0.5000, sse=1047858.4, rms=4.199 (22.677%) 003: dt: 0.5000, sse=933180.9, rms=3.646 (13.165%) 004: dt: 0.5000, sse=882892.8, rms=3.403 (6.654%) 005: dt: 0.5000, sse=869807.1, rms=3.293 (3.237%) 006: dt: 0.5000, sse=853364.4, rms=3.237 (1.697%) rms = 3.19, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=843710.1, rms=3.195 (1.313%) 008: dt: 0.2500, sse=714812.8, rms=2.291 (28.292%) 009: dt: 0.2500, sse=690878.7, rms=2.057 (10.189%) rms = 2.02, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=702278.2, rms=2.016 (2.021%) rms = 1.97, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=680809.0, rms=1.968 (2.364%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=85.2, 241 (46) missing vertices, mean dist -0.2 [0.4 (%73.4)->0.3 (%26.6))] %82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.88 +- 0.26 (0.01-->6.23) (max @ vno 35333 --> 143154) face area 0.33 +- 0.17 (0.00-->3.51) mean absolute distance = 0.27 +- 0.40 3686 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1170159.5, rms=4.138 012: dt: 0.5000, sse=924853.6, rms=2.799 (32.345%) rms = 2.84, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=837667.1, rms=2.256 (19.410%) 014: dt: 0.2500, sse=804004.9, rms=1.906 (15.518%) 015: dt: 0.2500, sse=786238.7, rms=1.779 (6.655%) rms = 1.73, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=783844.8, rms=1.730 (2.753%) rms = 1.68, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=782531.1, rms=1.684 (2.676%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.8, 238 (23) missing vertices, mean dist -0.1 [0.3 (%63.5)->0.2 (%36.5))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.26 (0.04-->6.25) (max @ vno 35333 --> 143154) face area 0.32 +- 0.17 (0.00-->3.64) mean absolute distance = 0.24 +- 0.35 3828 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=878056.4, rms=2.582 018: dt: 0.5000, sse=872984.1, rms=2.436 (5.660%) rms = 2.65, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=794855.9, rms=1.869 (23.274%) 020: dt: 0.2500, sse=771151.7, rms=1.620 (13.316%) rms = 1.57, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=762816.8, rms=1.575 (2.793%) rms = 1.53, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=751332.1, rms=1.532 (2.714%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.4, 325 (18) missing vertices, mean dist -0.0 [0.3 (%53.3)->0.2 (%46.7))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=760450.4, rms=1.685 023: dt: 0.5000, sse=765409.2, rms=1.604 (4.785%) rms = 2.31, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=728589.2, rms=1.253 (21.906%) rms = 1.26, time step reduction 2 of 3 to 0.125... rms = 1.22, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=719645.2, rms=1.223 (2.342%) positioning took 0.5 minutes generating cortex label... 10 non-cortical segments detected only using segment with 7425 vertices erasing segment 1 (vno[0] = 54668) erasing segment 2 (vno[0] = 74790) erasing segment 3 (vno[0] = 78775) erasing segment 4 (vno[0] = 96968) erasing segment 5 (vno[0] = 98092) erasing segment 6 (vno[0] = 100203) erasing segment 7 (vno[0] = 103185) erasing segment 8 (vno[0] = 106167) erasing segment 9 (vno[0] = 106209) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.area vertex spacing 0.88 +- 0.27 (0.04-->6.49) (max @ vno 35333 --> 143154) face area 0.32 +- 0.16 (0.00-->3.43) refinement took 4.8 minutes PIDs (3867 3870) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sun Oct 8 00:28:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sun Oct 8 00:28:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 4165 of (4165 4168) to complete... Waiting for PID 4168 of (4165 4168) 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 (4165 4168) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sun Oct 8 00:28:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sun Oct 8 00:28:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 4209 of (4209 4212) to complete... Waiting for PID 4212 of (4209 4212) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 47.3 mm, total surface area = 84438 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.188 (target=0.015) step 005: RMS=0.132 (target=0.015) step 010: RMS=0.103 (target=0.015) step 015: RMS=0.086 (target=0.015) step 020: RMS=0.074 (target=0.015) step 025: RMS=0.063 (target=0.015) step 030: RMS=0.054 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.041 (target=0.015) step 045: RMS=0.036 (target=0.015) step 050: RMS=0.033 (target=0.015) step 055: RMS=0.031 (target=0.015) step 060: RMS=0.029 (target=0.015) inflation complete. inflation took 0.8 minutes mris_inflate utimesec 47.679751 mris_inflate stimesec 0.120981 mris_inflate ru_maxrss 215248 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31393 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11424 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2066 mris_inflate ru_nivcsw 3590 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 46.3 mm, total surface area = 83700 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.188 (target=0.015) step 005: RMS=0.131 (target=0.015) step 010: RMS=0.103 (target=0.015) step 015: RMS=0.088 (target=0.015) step 020: RMS=0.077 (target=0.015) step 025: RMS=0.066 (target=0.015) step 030: RMS=0.056 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.038 (target=0.015) step 050: RMS=0.035 (target=0.015) step 055: RMS=0.031 (target=0.015) step 060: RMS=0.029 (target=0.015) inflation complete. inflation took 1.0 minutes mris_inflate utimesec 63.951277 mris_inflate stimesec 0.106983 mris_inflate ru_maxrss 214468 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31197 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11408 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2125 mris_inflate ru_nivcsw 3649 PIDs (4209 4212) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sun Oct 8 00:29:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Sun Oct 8 00:29:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 4311 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... Waiting for PID 4314 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... Waiting for PID 4317 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... Waiting for PID 4320 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... Waiting for PID 4323 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... Waiting for PID 4326 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... Waiting for PID 4329 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... Waiting for PID 4332 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... Waiting for PID 4335 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... Waiting for PID 4338 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... Waiting for PID 4341 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... Waiting for PID 4345 of (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 31.185*4pi (391.885) --> -30 handles ICI = 266.7, FI = 2345.5, variation=38079.671 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 168 vertices thresholded to be in k1 ~ [-0.52 0.37], k2 ~ [-0.15 0.10] total integrated curvature = 0.381*4pi (4.787) --> 1 handles ICI = 1.4, FI = 11.2, variation=181.055 158 vertices thresholded to be in [-0.03 0.03] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 126 vertices thresholded to be in [-0.21 0.11] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.024 done. mris_curvature -w rh.white.preaparc total integrated curvature = 23.705*4pi (297.882) --> -23 handles ICI = 266.7, FI = 2247.7, variation=37002.831 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 179 vertices thresholded to be in k1 ~ [-0.38 0.27], k2 ~ [-0.18 0.10] total integrated curvature = 0.294*4pi (3.693) --> 1 handles ICI = 1.4, FI = 11.4, variation=187.106 160 vertices thresholded to be in [-0.02 0.03] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 127 vertices thresholded to be in [-0.18 0.12] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.018, std = 0.025 done. PIDs (4311 4314 4317 4320 4323 4326 4329 4332 4335 4338 4341 4345) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sun Oct 8 00:31:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051348 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 [ 0051348/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 [ 299 ] Gb_filter = 0 WARN: S lookup min: -0.304746 WARN: S explicit min: 0.000000 vertex = 49 #----------------------------------------- #@# Curvature Stats rh Sun Oct 8 00:31:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051348 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 [ 0051348/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 [ 290 ] Gb_filter = 0 WARN: S lookup min: -0.113278 WARN: S explicit min: 0.000000 vertex = 55 #-------------------------------------------- #@# Sphere lh Sun Oct 8 00:31:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sun Oct 8 00:31:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 4702 of (4702 4706) to complete... Waiting for PID 4706 of (4702 4706) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0.276... 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 %19.87 pass 1: epoch 2 of 3 starting distance error %19.84 unfolding complete - removing small folds... starting distance error %19.72 removing remaining folds... final distance error %19.75 MRISunfold() return, current seed 1234 -01: dt=0.0000, 497 negative triangles 200: dt=0.9900, 497 negative triangles 201: dt=0.9900, 249 negative triangles 202: dt=0.9900, 150 negative triangles 203: dt=0.9900, 128 negative triangles 204: dt=0.9900, 105 negative triangles 205: dt=0.9900, 109 negative triangles 206: dt=0.9900, 94 negative triangles 207: dt=0.9900, 109 negative triangles 208: dt=0.9900, 98 negative triangles 209: dt=0.9900, 75 negative triangles 210: dt=0.9900, 77 negative triangles 211: dt=0.9900, 80 negative triangles 212: dt=0.9900, 65 negative triangles 213: dt=0.9900, 58 negative triangles 214: dt=0.9900, 49 negative triangles 215: dt=0.9900, 45 negative triangles 216: dt=0.9900, 36 negative triangles 217: dt=0.9900, 41 negative triangles 218: dt=0.9900, 37 negative triangles 219: dt=0.9900, 33 negative triangles 220: dt=0.9900, 31 negative triangles 221: dt=0.9900, 27 negative triangles 222: dt=0.9900, 24 negative triangles 223: dt=0.9900, 24 negative triangles 224: dt=0.9900, 23 negative triangles 225: dt=0.9900, 16 negative triangles 226: dt=0.9900, 16 negative triangles 227: dt=0.9900, 18 negative triangles 228: dt=0.9900, 19 negative triangles 229: dt=0.9900, 7 negative triangles 230: dt=0.9900, 9 negative triangles 231: dt=0.9900, 4 negative triangles 232: dt=0.9900, 4 negative triangles 233: dt=0.9900, 5 negative triangles 234: dt=0.9900, 3 negative triangles 235: dt=0.9900, 1 negative triangles 236: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.08 hours mris_sphere utimesec 3874.372005 mris_sphere stimesec 1.644749 mris_sphere ru_maxrss 300416 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 52819 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10312 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 135768 mris_sphere ru_nivcsw 318891 FSRUNTIME@ mris_sphere 1.0760 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0.280... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.01 pass 1: epoch 2 of 3 starting distance error %19.95 unfolding complete - removing small folds... starting distance error %19.81 removing remaining folds... final distance error %19.85 MRISunfold() return, current seed 1234 -01: dt=0.0000, 288 negative triangles 293: dt=0.9900, 288 negative triangles 294: dt=0.9900, 111 negative triangles 295: dt=0.9900, 94 negative triangles 296: dt=0.9900, 80 negative triangles 297: dt=0.9900, 63 negative triangles 298: dt=0.9900, 68 negative triangles 299: dt=0.9900, 65 negative triangles 300: dt=0.9900, 64 negative triangles 301: dt=0.9900, 52 negative triangles 302: dt=0.9900, 59 negative triangles 303: dt=0.9900, 48 negative triangles 304: dt=0.9900, 54 negative triangles 305: dt=0.9900, 52 negative triangles 306: dt=0.9900, 46 negative triangles 307: dt=0.9900, 44 negative triangles 308: dt=0.9900, 42 negative triangles 309: dt=0.9900, 41 negative triangles 310: dt=0.9900, 38 negative triangles 311: dt=0.9900, 43 negative triangles 312: dt=0.9900, 39 negative triangles 313: dt=0.9900, 37 negative triangles 314: dt=0.9900, 38 negative triangles 315: dt=0.9900, 31 negative triangles 316: dt=0.9900, 35 negative triangles 317: dt=0.9900, 34 negative triangles 318: dt=0.9900, 26 negative triangles 319: dt=0.9900, 31 negative triangles 320: dt=0.9900, 26 negative triangles 321: dt=0.9900, 22 negative triangles 322: dt=0.9900, 22 negative triangles 323: dt=0.9900, 15 negative triangles 324: dt=0.9900, 17 negative triangles 325: dt=0.9900, 16 negative triangles 326: dt=0.9900, 19 negative triangles 327: dt=0.9900, 12 negative triangles 328: dt=0.9900, 18 negative triangles 329: dt=0.9900, 16 negative triangles 330: dt=0.9900, 16 negative triangles 331: dt=0.9900, 16 negative triangles 332: dt=0.9900, 17 negative triangles 333: dt=0.9900, 16 negative triangles 334: dt=0.9900, 10 negative triangles 335: dt=0.9900, 10 negative triangles 336: dt=0.9900, 11 negative triangles 337: dt=0.9900, 6 negative triangles 338: dt=0.9900, 8 negative triangles 339: dt=0.9900, 10 negative triangles 340: dt=0.9900, 8 negative triangles 341: dt=0.9900, 7 negative triangles 342: dt=0.9900, 9 negative triangles 343: dt=0.9900, 5 negative triangles 344: dt=0.9900, 5 negative triangles 345: dt=0.9900, 2 negative triangles 346: dt=0.9900, 4 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.15 hours mris_sphere utimesec 4302.337945 mris_sphere stimesec 1.346795 mris_sphere ru_maxrss 299540 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 53112 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10288 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 150372 mris_sphere ru_nivcsw 314300 FSRUNTIME@ mris_sphere 1.1499 hours 1 threads PIDs (4702 4706) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sun Oct 8 01:40:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 01:40:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 10574 of (10574 10577) to complete... Waiting for PID 10577 of (10574 10577) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 5.397 curvature mean = 0.042, std = 0.822 curvature mean = 0.024, std = 0.863 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 349481.3, tmin=1.1258 d=32.00 min @ (-8.00, 0.00, 8.00) sse = 255635.6, tmin=2.2899 d=16.00 min @ (4.00, 4.00, -4.00) sse = 230553.5, tmin=3.4594 d=8.00 min @ (-2.00, 0.00, 2.00) sse = 214545.4, tmin=4.6626 d=1.00 min @ (0.25, 0.25, -0.25) sse = 214239.8, tmin=8.2937 d=0.50 min @ (0.00, -0.12, 0.00) sse = 214222.4, tmin=9.4774 tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 9.48 min curvature mean = -0.003, std = 0.836 curvature mean = 0.008, std = 0.948 curvature mean = -0.009, std = 0.845 curvature mean = 0.003, std = 0.979 curvature mean = -0.010, std = 0.847 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.042, std = 0.410 curvature mean = 0.036, std = 0.249 curvature mean = 0.076, std = 0.244 curvature mean = 0.028, std = 0.307 curvature mean = 0.051, std = 0.378 curvature mean = 0.027, std = 0.334 curvature mean = 0.031, std = 0.494 curvature mean = 0.027, std = 0.345 curvature mean = 0.012, std = 0.605 MRISregister() return, current seed 0 -01: dt=0.0000, 162 negative triangles 114: dt=0.9900, 162 negative triangles expanding nbhd size to 1 115: dt=0.9900, 222 negative triangles 116: dt=0.9900, 151 negative triangles 117: dt=0.9900, 139 negative triangles 118: dt=0.9900, 145 negative triangles 119: dt=0.9900, 142 negative triangles 120: dt=0.9900, 132 negative triangles 121: dt=0.9900, 114 negative triangles 122: dt=0.9900, 108 negative triangles 123: dt=0.9900, 89 negative triangles 124: dt=0.9900, 82 negative triangles 125: dt=0.9900, 75 negative triangles 126: dt=0.9900, 72 negative triangles 127: dt=0.9900, 65 negative triangles 128: dt=0.9900, 61 negative triangles 129: dt=0.9900, 55 negative triangles 130: dt=0.9900, 53 negative triangles 131: dt=0.9900, 47 negative triangles 132: dt=0.9900, 42 negative triangles 133: dt=0.9900, 35 negative triangles 134: dt=0.9900, 27 negative triangles 135: dt=0.9900, 29 negative triangles 136: dt=0.9900, 29 negative triangles 137: dt=0.9900, 28 negative triangles 138: dt=0.9900, 25 negative triangles 139: dt=0.9900, 18 negative triangles 140: dt=0.9900, 20 negative triangles 141: dt=0.9900, 21 negative triangles 142: dt=0.9900, 19 negative triangles 143: dt=0.9900, 17 negative triangles 144: dt=0.9900, 15 negative triangles 145: dt=0.9900, 18 negative triangles 146: dt=0.9900, 22 negative triangles 147: dt=0.9900, 16 negative triangles 148: dt=0.9900, 16 negative triangles 149: dt=0.9900, 15 negative triangles 150: dt=0.9900, 11 negative triangles 151: dt=0.9900, 9 negative triangles 152: dt=0.9900, 9 negative triangles 153: dt=0.9900, 7 negative triangles 154: dt=0.9900, 6 negative triangles 155: dt=0.9900, 8 negative triangles 156: dt=0.9900, 5 negative triangles 157: dt=0.9900, 5 negative triangles 158: dt=0.9900, 3 negative triangles 159: dt=0.9900, 3 negative triangles 160: dt=0.9900, 3 negative triangles 161: dt=0.9900, 2 negative triangles 162: dt=0.9900, 1 negative triangles 163: dt=0.9900, 1 negative triangles 164: dt=0.9900, 1 negative triangles 165: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.10 hours mris_register utimesec 3959.446072 mris_register stimesec 2.863564 mris_register ru_maxrss 268916 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 39473 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 10264 mris_register ru_oublock 10352 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 283323 mris_register ru_nivcsw 187665 FSRUNTIME@ mris_register 1.1001 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 5.530 curvature mean = 0.037, std = 0.806 curvature mean = 0.023, std = 0.865 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 32.00) sse = 330577.3, tmin=1.7733 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 325806.0, tmin=3.5554 d=16.00 min @ (4.00, 4.00, -4.00) sse = 283991.1, tmin=5.2201 d=8.00 min @ (0.00, 0.00, 2.00) sse = 283094.7, tmin=6.8810 d=4.00 min @ (0.00, 0.00, -1.00) sse = 282233.6, tmin=8.5878 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 281958.2, tmin=10.2638 d=1.00 min @ (0.25, 0.25, 0.00) sse = 281944.8, tmin=11.9313 d=0.50 min @ (-0.12, -0.12, 0.12) sse = 281916.7, tmin=13.4244 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 13.42 min curvature mean = 0.010, std = 0.830 curvature mean = 0.008, std = 0.950 curvature mean = 0.006, std = 0.841 curvature mean = 0.003, std = 0.979 curvature mean = 0.005, std = 0.843 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.041, std = 0.399 curvature mean = 0.034, std = 0.241 curvature mean = 0.075, std = 0.251 curvature mean = 0.027, std = 0.300 curvature mean = 0.050, std = 0.385 curvature mean = 0.026, std = 0.326 curvature mean = 0.030, std = 0.506 curvature mean = 0.026, std = 0.338 curvature mean = 0.010, std = 0.654 MRISregister() return, current seed 0 -01: dt=0.0000, 182 negative triangles 121: dt=0.9900, 182 negative triangles expanding nbhd size to 1 122: dt=0.9900, 232 negative triangles 123: dt=0.9900, 166 negative triangles 124: dt=0.9900, 170 negative triangles 125: dt=0.9900, 164 negative triangles 126: dt=0.9900, 159 negative triangles 127: dt=0.9900, 156 negative triangles 128: dt=0.9900, 152 negative triangles 129: dt=0.9900, 144 negative triangles 130: dt=0.9900, 130 negative triangles 131: dt=0.9900, 126 negative triangles 132: dt=0.9900, 127 negative triangles 133: dt=0.9900, 133 negative triangles 134: dt=0.9900, 116 negative triangles 135: dt=0.9900, 110 negative triangles 136: dt=0.9900, 112 negative triangles 137: dt=0.9900, 98 negative triangles 138: dt=0.9900, 94 negative triangles 139: dt=0.9900, 97 negative triangles 140: dt=0.9900, 91 negative triangles 141: dt=0.9900, 90 negative triangles 142: dt=0.9900, 85 negative triangles 143: dt=0.9900, 87 negative triangles 144: dt=0.9900, 80 negative triangles 145: dt=0.9900, 75 negative triangles 146: dt=0.9900, 75 negative triangles 147: dt=0.9900, 68 negative triangles 148: dt=0.9900, 70 negative triangles 149: dt=0.9900, 67 negative triangles 150: dt=0.9900, 64 negative triangles 151: dt=0.9900, 61 negative triangles 152: dt=0.9900, 59 negative triangles 153: dt=0.9900, 65 negative triangles 154: dt=0.9900, 59 negative triangles 155: dt=0.9900, 59 negative triangles 156: dt=0.9900, 58 negative triangles 157: dt=0.9900, 53 negative triangles 158: dt=0.9900, 53 negative triangles 159: dt=0.9900, 51 negative triangles 160: dt=0.9900, 51 negative triangles 161: dt=0.9900, 47 negative triangles 162: dt=0.9900, 49 negative triangles 163: dt=0.9900, 41 negative triangles 164: dt=0.9900, 36 negative triangles 165: dt=0.9900, 43 negative triangles 166: dt=0.9900, 37 negative triangles 167: dt=0.9900, 30 negative triangles 168: dt=0.9900, 26 negative triangles 169: dt=0.9900, 28 negative triangles 170: dt=0.9900, 29 negative triangles 171: dt=0.9900, 23 negative triangles 172: dt=0.9900, 21 negative triangles 173: dt=0.9900, 21 negative triangles 174: dt=0.9900, 14 negative triangles 175: dt=0.9900, 11 negative triangles 176: dt=0.9900, 12 negative triangles 177: dt=0.9900, 14 negative triangles 178: dt=0.9900, 10 negative triangles 179: dt=0.9900, 8 negative triangles 180: dt=0.9900, 6 negative triangles 181: dt=0.9900, 9 negative triangles 182: dt=0.9900, 4 negative triangles 183: dt=0.9900, 5 negative triangles 184: dt=0.9900, 4 negative triangles 185: dt=0.9900, 4 negative triangles 186: dt=0.9900, 3 negative triangles 187: dt=0.9900, 6 negative triangles 188: dt=0.9900, 3 negative triangles 189: dt=0.9900, 4 negative triangles 190: dt=0.9900, 2 negative triangles 191: dt=0.9900, 4 negative triangles 192: dt=0.9900, 2 negative triangles 193: dt=0.9900, 1 negative triangles 194: dt=0.9900, 2 negative triangles 195: dt=0.9900, 2 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.88 hours mris_register utimesec 8524.866023 mris_register stimesec 3.690438 mris_register ru_maxrss 269536 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 38253 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10352 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 260532 mris_register ru_nivcsw 239105 FSRUNTIME@ mris_register 1.8789 hours 1 threads PIDs (10574 10577) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 03:33:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 03:33:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 17075 of (17075 17078) to complete... Waiting for PID 17078 of (17075 17078) 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 (17075 17078) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 03:33:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 03:33:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 17119 of (17119 17122) to complete... Waiting for PID 17122 of (17119 17122) 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 (17119 17122) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 03:33:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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 03:33:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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 17165 of (17165 17168) to complete... Waiting for PID 17168 of (17165 17168) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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... 2010 labels changed using aseg relabeling using gibbs priors... 000: 3488 changed, 145874 examined... 001: 774 changed, 14441 examined... 002: 196 changed, 4263 examined... 003: 83 changed, 1167 examined... 004: 22 changed, 511 examined... 005: 6 changed, 142 examined... 006: 1 changed, 35 examined... 007: 1 changed, 7 examined... 008: 1 changed, 5 examined... 009: 0 changed, 8 examined... 302 labels changed using aseg 000: 158 total segments, 115 labels (487 vertices) changed 001: 41 total segments, 1 labels (3 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 17 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2035 vertices marked for relabeling... 2035 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 17 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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... 1297 labels changed using aseg relabeling using gibbs priors... 000: 2958 changed, 145578 examined... 001: 712 changed, 12719 examined... 002: 205 changed, 4034 examined... 003: 72 changed, 1225 examined... 004: 32 changed, 429 examined... 005: 14 changed, 171 examined... 006: 6 changed, 77 examined... 007: 4 changed, 26 examined... 008: 2 changed, 21 examined... 009: 1 changed, 14 examined... 010: 1 changed, 9 examined... 011: 0 changed, 7 examined... 198 labels changed using aseg 000: 117 total segments, 80 labels (361 vertices) changed 001: 40 total segments, 3 labels (6 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1846 vertices marked for relabeling... 1846 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 16 seconds. PIDs (17165 17168) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 03:33:31 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051348 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 03:33:31 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051348 rh Waiting for PID 17210 of (17210 17213) to complete... Waiting for PID 17213 of (17210 17213) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051348 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-6.0.0/0051348/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... 34293 bright wm thresholded. 656 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.orig... computing class statistics... border white: 276628 voxels (1.65%) border gray 335243 voxels (2.00%) WM (96.0): 96.6 +- 8.7 [70.0 --> 110.0] GM (73.0) : 72.5 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.9 (was 70) setting MAX_BORDER_WHITE to 110.7 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 51.7 (was 40) setting MAX_GRAY to 93.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.6 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-8.7, GM=72+-6.1 mean inside = 93.0, mean outside = 76.3 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 0.88 +- 0.27 (0.04-->5.57) (max @ vno 41855 --> 52144) face area 0.32 +- 0.17 (0.00-->6.60) mean absolute distance = 0.61 +- 0.80 3617 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 14 points - only 0.00% unknown deleting segment 4 with 336 points - only 0.00% unknown deleting segment 5 with 47 points - only 0.00% unknown deleting segment 6 with 119 points - only 3.36% unknown deleting segment 7 with 9 points - only 0.00% unknown deleting segment 8 with 77 points - only 0.00% unknown deleting segment 9 with 70 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown deleting segment 11 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown mean border=81.4, 389 (389) missing vertices, mean dist 0.4 [0.9 (%12.3)->0.6 (%87.7))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.28 (0.04-->5.51) (max @ vno 144523 --> 99492) face area 0.32 +- 0.17 (0.00-->6.09) mean absolute distance = 0.36 +- 0.55 3645 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2198188.2, rms=7.356 001: dt: 0.5000, sse=1208734.9, rms=4.308 (41.429%) 002: dt: 0.5000, sse=992092.4, rms=3.339 (22.513%) 003: dt: 0.5000, sse=972265.1, rms=3.236 (3.073%) 004: dt: 0.5000, sse=945914.4, rms=3.096 (4.314%) rms = 3.21, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=846407.2, rms=2.426 (21.663%) 006: dt: 0.2500, sse=812834.5, rms=2.121 (12.566%) 007: dt: 0.2500, sse=806034.5, rms=2.045 (3.584%) rms = 2.02, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=804031.2, rms=2.022 (1.109%) rms = 1.98, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=798708.2, rms=1.983 (1.957%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 135 points - only 0.00% unknown deleting segment 3 with 37 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 80 points - only 1.25% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 88 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 26 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown mean border=84.8, 251 (90) missing vertices, mean dist -0.2 [0.4 (%76.1)->0.3 (%23.9))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.88 +- 0.28 (0.06-->5.66) (max @ vno 41855 --> 52144) face area 0.34 +- 0.18 (0.00-->6.99) mean absolute distance = 0.26 +- 0.38 3620 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1244423.8, rms=4.359 010: dt: 0.5000, sse=934223.2, rms=2.776 (36.303%) rms = 2.86, time step reduction 1 of 3 to 0.250... 011: dt: 0.2500, sse=849653.2, rms=2.189 (21.152%) 012: dt: 0.2500, sse=812410.2, rms=1.812 (17.228%) 013: dt: 0.2500, sse=797293.2, rms=1.677 (7.441%) rms = 1.64, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=799410.2, rms=1.641 (2.168%) rms = 1.60, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=796795.0, rms=1.598 (2.616%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 173 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 53 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown deleting segment 5 with 99 points - only 1.01% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 98 points - only 0.00% unknown deleting segment 8 with 68 points - only 0.00% unknown deleting segment 9 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown mean border=86.5, 280 (62) missing vertices, mean dist -0.1 [0.3 (%65.6)->0.2 (%34.4))] %88 local maxima, % 7 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 0.88 +- 0.28 (0.02-->6.17) (max @ vno 144523 --> 99492) face area 0.33 +- 0.18 (0.00-->6.76) mean absolute distance = 0.23 +- 0.33 3273 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=910425.6, rms=2.700 016: dt: 0.5000, sse=892113.8, rms=2.480 (8.124%) rms = 2.74, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=801667.6, rms=1.839 (25.866%) 018: dt: 0.2500, sse=781060.2, rms=1.564 (14.946%) rms = 1.52, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=772629.4, rms=1.515 (3.110%) 020: dt: 0.1250, sse=762512.5, rms=1.462 (3.550%) rms = 1.46, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=761136.9, rms=1.465 (-0.215%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 8 points - only 0.00% unknown deleting segment 1 with 224 points - only 0.00% unknown deleting segment 2 with 51 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 109 points - only 3.67% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 92 points - only 0.00% unknown deleting segment 7 with 85 points - only 0.00% unknown deleting segment 8 with 16 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown mean border=87.2, 356 (51) missing vertices, mean dist -0.0 [0.2 (%54.1)->0.2 (%45.9))] %90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=772832.8, rms=1.641 rms = 1.61, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=784003.3, rms=1.610 (1.883%) 023: dt: 0.2500, sse=750423.9, rms=1.412 (12.352%) 024: dt: 0.2500, sse=731587.2, rms=1.201 (14.948%) rms = 1.28, time step reduction 2 of 3 to 0.125... rms = 1.16, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=727564.8, rms=1.156 (3.733%) positioning took 0.5 minutes generating cortex label... 12 non-cortical segments detected only using segment with 8258 vertices erasing segment 0 (vno[0] = 21566) erasing segment 2 (vno[0] = 55077) erasing segment 3 (vno[0] = 80379) erasing segment 4 (vno[0] = 85465) erasing segment 5 (vno[0] = 88894) erasing segment 6 (vno[0] = 91230) erasing segment 7 (vno[0] = 100465) erasing segment 8 (vno[0] = 102306) erasing segment 9 (vno[0] = 103750) erasing segment 10 (vno[0] = 105689) erasing segment 11 (vno[0] = 109031) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.area vertex spacing 0.88 +- 0.28 (0.02-->6.57) (max @ vno 99492 --> 144523) face area 0.32 +- 0.17 (0.00-->6.56) 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 removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=60.3, 419 (419) missing vertices, mean dist 1.7 [0.3 (%0.0)->3.4 (%100.0))] %13 local maxima, %36 large gradients and %46 min vals, 302 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=22132696.0, rms=27.788 001: dt: 0.0500, sse=19361198.0, rms=25.930 (6.686%) 002: dt: 0.0500, sse=17414760.0, rms=24.541 (5.356%) 003: dt: 0.0500, sse=15956048.0, rms=23.446 (4.462%) 004: dt: 0.0500, sse=14805253.0, rms=22.545 (3.845%) 005: dt: 0.0500, sse=13860292.0, rms=21.776 (3.408%) 006: dt: 0.0500, sse=13060360.0, rms=21.104 (3.087%) 007: dt: 0.0500, sse=12367739.0, rms=20.504 (2.843%) 008: dt: 0.0500, sse=11757229.0, rms=19.960 (2.652%) 009: dt: 0.0500, sse=11212186.0, rms=19.462 (2.497%) 010: dt: 0.0500, sse=10720632.0, rms=19.001 (2.367%) positioning took 1.1 minutes mean border=60.2, 350 (220) missing vertices, mean dist 1.5 [0.1 (%0.1)->2.9 (%99.9))] %14 local maxima, %36 large gradients and %45 min vals, 277 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=11519686.0, rms=19.744 011: dt: 0.0500, sse=11068369.0, rms=19.328 (2.106%) 012: dt: 0.0500, sse=10655709.0, rms=18.940 (2.009%) 013: dt: 0.0500, sse=10276644.0, rms=18.576 (1.921%) 014: dt: 0.0500, sse=9927541.0, rms=18.234 (1.839%) 015: dt: 0.0500, sse=9605562.0, rms=17.913 (1.760%) 016: dt: 0.0500, sse=9307305.0, rms=17.611 (1.689%) 017: dt: 0.0500, sse=9030621.0, rms=17.325 (1.621%) 018: dt: 0.0500, sse=8773234.0, rms=17.055 (1.558%) 019: dt: 0.0500, sse=8533528.0, rms=16.800 (1.497%) 020: dt: 0.0500, sse=8310265.5, rms=16.559 (1.437%) positioning took 1.1 minutes mean border=60.1, 386 (167) missing vertices, mean dist 1.3 [0.1 (%0.7)->2.5 (%99.3))] %14 local maxima, %36 large gradients and %45 min vals, 268 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=8431804.0, rms=16.696 021: dt: 0.0500, sse=8219282.0, rms=16.465 (1.385%) 022: dt: 0.0500, sse=8020377.5, rms=16.245 (1.333%) 023: dt: 0.0500, sse=7833301.0, rms=16.036 (1.287%) 024: dt: 0.0500, sse=7657397.0, rms=15.837 (1.242%) 025: dt: 0.0500, sse=7491480.5, rms=15.646 (1.202%) 026: dt: 0.0500, sse=7334121.5, rms=15.464 (1.168%) 027: dt: 0.0500, sse=7184450.5, rms=15.288 (1.138%) 028: dt: 0.0500, sse=7041449.5, rms=15.118 (1.113%) 029: dt: 0.0500, sse=6903952.5, rms=14.952 (1.094%) 030: dt: 0.0500, sse=6772098.0, rms=14.792 (1.073%) positioning took 1.1 minutes mean border=60.0, 415 (137) missing vertices, mean dist 1.2 [0.1 (%3.5)->2.3 (%96.5))] %14 local maxima, %36 large gradients and %44 min vals, 249 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=6856944.0, rms=14.896 031: dt: 0.5000, sse=5888602.5, rms=13.670 (8.230%) 032: dt: 0.5000, sse=5177780.5, rms=12.688 (7.179%) 033: dt: 0.5000, sse=4613895.5, rms=11.851 (6.602%) 034: dt: 0.5000, sse=4146509.8, rms=11.105 (6.295%) 035: dt: 0.5000, sse=3736659.5, rms=10.408 (6.276%) 036: dt: 0.5000, sse=3362112.0, rms=9.726 (6.551%) 037: dt: 0.5000, sse=3013512.0, rms=9.048 (6.966%) 038: dt: 0.5000, sse=2707063.8, rms=8.407 (7.086%) 039: dt: 0.5000, sse=2454751.8, rms=7.841 (6.732%) 040: dt: 0.5000, sse=2248574.0, rms=7.346 (6.318%) 041: dt: 0.5000, sse=2090582.6, rms=6.942 (5.502%) 042: dt: 0.5000, sse=1968489.2, rms=6.612 (4.750%) 043: dt: 0.5000, sse=1877094.2, rms=6.355 (3.883%) 044: dt: 0.5000, sse=1806466.9, rms=6.148 (3.264%) 045: dt: 0.5000, sse=1758772.8, rms=6.004 (2.334%) 046: dt: 0.5000, sse=1723509.6, rms=5.894 (1.831%) 047: dt: 0.5000, sse=1699506.1, rms=5.819 (1.280%) 048: dt: 0.5000, sse=1681912.2, rms=5.761 (0.990%) rms = 5.72, time step reduction 1 of 3 to 0.250... 049: dt: 0.5000, sse=1668087.0, rms=5.718 (0.754%) 050: dt: 0.2500, sse=1574821.5, rms=5.372 (6.055%) 051: dt: 0.2500, sse=1541478.8, rms=5.258 (2.109%) rms = 5.27, time step reduction 2 of 3 to 0.125... rms = 5.22, time step reduction 3 of 3 to 0.062... 052: dt: 0.1250, sse=1530856.6, rms=5.219 (0.754%) positioning took 3.4 minutes mean border=59.1, 3100 (54) missing vertices, mean dist 0.2 [0.2 (%43.3)->0.7 (%56.7))] %28 local maxima, %26 large gradients and %40 min vals, 178 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=1787767.5, rms=5.295 053: dt: 0.5000, sse=1736785.1, rms=5.130 (3.119%) 054: dt: 0.5000, sse=1656761.4, rms=4.872 (5.031%) rms = 5.02, time step reduction 1 of 3 to 0.250... 055: dt: 0.2500, sse=1558106.5, rms=4.447 (8.712%) 056: dt: 0.2500, sse=1538610.2, rms=4.350 (2.183%) rms = 4.35, time step reduction 2 of 3 to 0.125... 057: dt: 0.2500, sse=1538449.4, rms=4.350 (0.006%) 058: dt: 0.1250, sse=1502240.5, rms=4.185 (3.779%) rms = 4.16, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1495141.1, rms=4.156 (0.708%) positioning took 1.4 minutes mean border=58.6, 3362 (47) missing vertices, mean dist 0.1 [0.2 (%43.2)->0.5 (%56.8))] %38 local maxima, %16 large gradients and %39 min vals, 225 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=1529577.9, rms=4.294 rms = 4.65, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1500595.4, rms=4.164 (3.005%) rms = 4.14, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1493996.2, rms=4.142 (0.534%) 062: dt: 0.1250, sse=1481034.0, rms=4.080 (1.499%) rms = 4.05, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1473755.0, rms=4.051 (0.709%) positioning took 1.0 minutes mean border=58.2, 7178 (42) missing vertices, mean dist 0.1 [0.2 (%44.0)->0.4 (%56.0))] %39 local maxima, %14 large gradients and %37 min vals, 226 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-6.0.0/0051348/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1489057.2, rms=4.112 rms = 4.33, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1468518.6, rms=4.022 (2.173%) 065: dt: 0.2500, sse=1448120.5, rms=3.954 (1.698%) rms = 3.94, time step reduction 2 of 3 to 0.125... 066: dt: 0.2500, sse=1441680.8, rms=3.936 (0.441%) 067: dt: 0.1250, sse=1414598.0, rms=3.806 (3.311%) rms = 3.77, time step reduction 3 of 3 to 0.062... 068: dt: 0.1250, sse=1406282.4, rms=3.772 (0.893%) positioning took 1.2 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.area.pial vertex spacing 1.02 +- 0.49 (0.01-->7.42) (max @ vno 142655 --> 142771) face area 0.41 +- 0.36 (0.00-->9.71) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 145874 vertices processed 25000 of 145874 vertices processed 50000 of 145874 vertices processed 75000 of 145874 vertices processed 100000 of 145874 vertices processed 125000 of 145874 vertices processed 0 of 145874 vertices processed 25000 of 145874 vertices processed 50000 of 145874 vertices processed 75000 of 145874 vertices processed 100000 of 145874 vertices processed 125000 of 145874 vertices processed thickness calculation complete, 704:2293 truncations. 23080 vertices at 0 distance 78689 vertices at 1 distance 89152 vertices at 2 distance 52712 vertices at 3 distance 22098 vertices at 4 distance 7772 vertices at 5 distance 2744 vertices at 6 distance 1033 vertices at 7 distance 476 vertices at 8 distance 234 vertices at 9 distance 134 vertices at 10 distance 111 vertices at 11 distance 81 vertices at 12 distance 53 vertices at 13 distance 46 vertices at 14 distance 35 vertices at 15 distance 34 vertices at 16 distance 21 vertices at 17 distance 25 vertices at 18 distance 22 vertices at 19 distance 34 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.thickness positioning took 17.9 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051348 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-6.0.0/0051348/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... 34293 bright wm thresholded. 656 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.orig... computing class statistics... border white: 276628 voxels (1.65%) border gray 335243 voxels (2.00%) WM (96.0): 96.6 +- 8.7 [70.0 --> 110.0] GM (73.0) : 72.5 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.9 (was 70) setting MAX_BORDER_WHITE to 108.7 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 52.7 (was 40) setting MAX_GRAY to 91.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.6 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=100+-7.8, GM=73+-6.1 mean inside = 92.5, mean outside = 76.6 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 0.88 +- 0.27 (0.04-->6.49) (max @ vno 35333 --> 143154) face area 0.32 +- 0.16 (0.00-->3.43) mean absolute distance = 0.60 +- 0.80 3710 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 344 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown deleting segment 4 with 77 points - only 0.00% unknown deleting segment 5 with 15 points - only 0.00% unknown mean border=82.1, 401 (401) missing vertices, mean dist 0.4 [0.9 (%13.3)->0.5 (%86.7))] %69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.27 (0.06-->6.42) (max @ vno 35333 --> 143154) face area 0.32 +- 0.17 (0.00-->3.97) mean absolute distance = 0.36 +- 0.56 3815 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1928981.6, rms=6.702 001: dt: 0.5000, sse=1129069.0, rms=3.971 (40.750%) 002: dt: 0.5000, sse=966667.2, rms=3.173 (20.091%) 003: dt: 0.5000, sse=944354.2, rms=3.122 (1.605%) 004: dt: 0.5000, sse=924102.3, rms=3.002 (3.845%) rms = 3.12, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=827519.1, rms=2.345 (21.886%) 006: dt: 0.2500, sse=796939.9, rms=2.046 (12.760%) 007: dt: 0.2500, sse=788934.7, rms=1.979 (3.255%) rms = 1.96, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=819760.0, rms=1.964 (0.795%) rms = 1.93, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=783494.0, rms=1.929 (1.776%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 174 points - only 0.00% unknown deleting segment 2 with 69 points - only 0.00% unknown deleting segment 3 with 22 points - only 0.00% unknown mean border=85.2, 292 (106) missing vertices, mean dist -0.2 [0.4 (%73.7)->0.3 (%26.3))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.88 +- 0.27 (0.03-->6.56) (max @ vno 35333 --> 143154) face area 0.33 +- 0.18 (0.00-->4.07) mean absolute distance = 0.27 +- 0.40 3623 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1150116.6, rms=4.014 010: dt: 0.5000, sse=937153.2, rms=2.704 (32.635%) rms = 2.74, time step reduction 1 of 3 to 0.250... 011: dt: 0.2500, sse=836995.9, rms=2.156 (20.248%) 012: dt: 0.2500, sse=805730.5, rms=1.803 (16.372%) 013: dt: 0.2500, sse=809552.6, rms=1.691 (6.238%) rms = 1.66, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=782555.9, rms=1.656 (2.043%) rms = 1.62, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=777586.9, rms=1.615 (2.479%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 230 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 71 points - only 0.00% unknown deleting segment 3 with 69 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown mean border=86.7, 288 (63) missing vertices, mean dist -0.1 [0.3 (%63.7)->0.2 (%36.3))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.27 (0.03-->6.60) (max @ vno 35333 --> 143154) face area 0.32 +- 0.17 (0.00-->3.98) mean absolute distance = 0.24 +- 0.35 3724 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=868461.6, rms=2.531 016: dt: 0.5000, sse=880415.6, rms=2.401 (5.112%) rms = 2.61, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=792988.7, rms=1.826 (23.958%) 018: dt: 0.2500, sse=793597.5, rms=1.574 (13.782%) rms = 1.54, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=764112.3, rms=1.536 (2.445%) rms = 1.49, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=757467.4, rms=1.490 (2.970%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 233 points - only 0.00% unknown deleting segment 2 with 24 points - only 0.00% unknown deleting segment 3 with 76 points - only 0.00% unknown deleting segment 4 with 70 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown mean border=87.3, 328 (46) missing vertices, mean dist -0.0 [0.3 (%53.4)->0.2 (%46.6))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=765395.2, rms=1.639 021: dt: 0.5000, sse=770163.9, rms=1.575 (3.928%) rms = 2.27, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=726946.9, rms=1.214 (22.908%) rms = 1.22, time step reduction 2 of 3 to 0.125... rms = 1.18, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=722509.5, rms=1.184 (2.513%) positioning took 0.5 minutes generating cortex label... 11 non-cortical segments detected only using segment with 7396 vertices erasing segment 1 (vno[0] = 54668) erasing segment 2 (vno[0] = 76066) erasing segment 3 (vno[0] = 77481) erasing segment 4 (vno[0] = 80021) erasing segment 5 (vno[0] = 96968) erasing segment 6 (vno[0] = 98092) erasing segment 7 (vno[0] = 100203) erasing segment 8 (vno[0] = 103185) erasing segment 9 (vno[0] = 106167) erasing segment 10 (vno[0] = 106209) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.area vertex spacing 0.88 +- 0.27 (0.04-->6.76) (max @ vno 35333 --> 143154) face area 0.32 +- 0.17 (0.00-->3.93) 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... smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=61.5, 416 (416) missing vertices, mean dist 1.7 [0.2 (%0.0)->3.4 (%100.0))] %13 local maxima, %34 large gradients and %48 min vals, 418 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=20520196.0, rms=26.716 001: dt: 0.0500, sse=17991420.0, rms=24.956 (6.590%) 002: dt: 0.0500, sse=16206763.0, rms=23.634 (5.296%) 003: dt: 0.0500, sse=14864570.0, rms=22.589 (4.422%) 004: dt: 0.0500, sse=13801326.0, rms=21.725 (3.824%) 005: dt: 0.0500, sse=12924272.0, rms=20.986 (3.403%) 006: dt: 0.0500, sse=12178957.0, rms=20.337 (3.095%) 007: dt: 0.0500, sse=11531230.0, rms=19.755 (2.861%) 008: dt: 0.0500, sse=10959714.0, rms=19.227 (2.673%) 009: dt: 0.0500, sse=10449420.0, rms=18.743 (2.518%) 010: dt: 0.0500, sse=9989320.0, rms=18.295 (2.388%) positioning took 1.1 minutes mean border=61.3, 337 (206) missing vertices, mean dist 1.4 [0.1 (%0.1)->2.8 (%99.9))] %14 local maxima, %34 large gradients and %47 min vals, 413 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=10784025.0, rms=19.061 011: dt: 0.0500, sse=10361136.0, rms=18.658 (2.116%) 012: dt: 0.0500, sse=9974506.0, rms=18.281 (2.018%) 013: dt: 0.0500, sse=9620483.0, rms=17.929 (1.924%) 014: dt: 0.0500, sse=9294502.0, rms=17.599 (1.842%) 015: dt: 0.0500, sse=8994681.0, rms=17.290 (1.758%) 016: dt: 0.0500, sse=8717550.0, rms=16.999 (1.683%) 017: dt: 0.0500, sse=8460822.0, rms=16.725 (1.613%) 018: dt: 0.0500, sse=8222816.0, rms=16.466 (1.544%) 019: dt: 0.0500, sse=8002075.5, rms=16.223 (1.477%) 020: dt: 0.0500, sse=7796357.0, rms=15.993 (1.419%) positioning took 1.0 minutes mean border=61.3, 358 (161) missing vertices, mean dist 1.3 [0.1 (%1.1)->2.5 (%98.9))] %15 local maxima, %34 large gradients and %47 min vals, 425 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=7889266.5, rms=16.104 021: dt: 0.0500, sse=7693398.5, rms=15.883 (1.370%) 022: dt: 0.0500, sse=7510562.5, rms=15.674 (1.315%) 023: dt: 0.0500, sse=7338380.5, rms=15.475 (1.272%) 024: dt: 0.0500, sse=7176774.5, rms=15.285 (1.224%) 025: dt: 0.0500, sse=7024301.0, rms=15.104 (1.184%) 026: dt: 0.0500, sse=6880308.5, rms=14.931 (1.146%) 027: dt: 0.0500, sse=6743063.5, rms=14.764 (1.118%) 028: dt: 0.0500, sse=6611835.0, rms=14.603 (1.093%) 029: dt: 0.0500, sse=6485641.0, rms=14.446 (1.075%) 030: dt: 0.0500, sse=6363869.0, rms=14.293 (1.061%) positioning took 1.1 minutes mean border=61.2, 376 (132) missing vertices, mean dist 1.1 [0.1 (%4.8)->2.3 (%95.2))] %15 local maxima, %34 large gradients and %46 min vals, 387 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=6422911.5, rms=14.367 031: dt: 0.5000, sse=5500829.0, rms=13.158 (8.416%) 032: dt: 0.5000, sse=4780914.5, rms=12.124 (7.861%) 033: dt: 0.5000, sse=4200959.0, rms=11.220 (7.458%) 034: dt: 0.5000, sse=3752715.8, rms=10.462 (6.751%) 035: dt: 0.5000, sse=3397909.8, rms=9.821 (6.126%) 036: dt: 0.5000, sse=3091365.5, rms=9.230 (6.024%) 037: dt: 0.5000, sse=2824522.0, rms=8.684 (5.911%) 038: dt: 0.5000, sse=2566864.5, rms=8.122 (6.467%) 039: dt: 0.5000, sse=2350258.0, rms=7.621 (6.179%) 040: dt: 0.5000, sse=2166930.8, rms=7.167 (5.949%) 041: dt: 0.5000, sse=2027087.6, rms=6.803 (5.089%) 042: dt: 0.5000, sse=1921119.4, rms=6.510 (4.296%) 043: dt: 0.5000, sse=1857344.2, rms=6.328 (2.793%) 044: dt: 0.5000, sse=1801126.2, rms=6.162 (2.625%) 045: dt: 0.5000, sse=1766811.2, rms=6.059 (1.683%) 046: dt: 0.5000, sse=1733037.4, rms=5.953 (1.740%) 047: dt: 0.5000, sse=1713136.8, rms=5.891 (1.053%) 048: dt: 0.5000, sse=1692935.1, rms=5.825 (1.104%) rms = 5.78, time step reduction 1 of 3 to 0.250... 049: dt: 0.5000, sse=1679677.2, rms=5.784 (0.715%) 050: dt: 0.2500, sse=1593396.5, rms=5.468 (5.459%) 051: dt: 0.2500, sse=1564165.4, rms=5.370 (1.796%) rms = 5.37, time step reduction 2 of 3 to 0.125... 052: dt: 0.2500, sse=1564888.5, rms=5.369 (0.008%) 053: dt: 0.1250, sse=1538145.8, rms=5.272 (1.815%) rms = 5.25, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=1531917.1, rms=5.250 (0.413%) positioning took 3.7 minutes mean border=60.3, 3448 (44) missing vertices, mean dist 0.2 [0.2 (%42.0)->0.8 (%58.0))] %27 local maxima, %24 large gradients and %42 min vals, 228 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=1764203.1, rms=5.293 055: dt: 0.5000, sse=1726737.8, rms=5.180 (2.133%) 056: dt: 0.5000, sse=1627977.2, rms=4.847 (6.435%) rms = 5.03, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1542813.8, rms=4.481 (7.535%) 058: dt: 0.2500, sse=1521949.6, rms=4.382 (2.209%) rms = 4.39, time step reduction 2 of 3 to 0.125... 059: dt: 0.1250, sse=1510851.6, rms=4.332 (1.158%) 060: dt: 0.1250, sse=1495284.6, rms=4.260 (1.666%) rms = 4.23, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1489195.0, rms=4.233 (0.630%) positioning took 1.6 minutes mean border=59.8, 3865 (34) missing vertices, mean dist 0.1 [0.2 (%40.8)->0.5 (%59.2))] %36 local maxima, %16 large gradients and %41 min vals, 251 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=1527263.0, rms=4.365 rms = 4.65, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1501552.9, rms=4.253 (2.568%) rms = 4.22, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1491370.2, rms=4.217 (0.858%) 064: dt: 0.1250, sse=1478646.5, rms=4.157 (1.425%) rms = 4.13, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1470852.2, rms=4.126 (0.742%) positioning took 1.0 minutes mean border=59.4, 7625 (29) missing vertices, mean dist 0.1 [0.2 (%42.3)->0.4 (%57.7))] %37 local maxima, %14 large gradients and %40 min vals, 251 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-6.0.0/0051348/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1483253.2, rms=4.159 rms = 4.31, time step reduction 1 of 3 to 0.250... 066: dt: 0.2500, sse=1464275.0, rms=4.077 (1.964%) 067: dt: 0.2500, sse=1441790.1, rms=3.999 (1.913%) rms = 3.97, time step reduction 2 of 3 to 0.125... 068: dt: 0.2500, sse=1433126.2, rms=3.973 (0.653%) 069: dt: 0.1250, sse=1409773.8, rms=3.861 (2.829%) rms = 3.82, time step reduction 3 of 3 to 0.062... 070: dt: 0.1250, sse=1400238.9, rms=3.821 (1.041%) positioning took 1.2 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.area.pial vertex spacing 1.01 +- 0.49 (0.04-->8.53) (max @ vno 53052 --> 143015) face area 0.40 +- 0.36 (0.00-->10.04) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 145578 vertices processed 25000 of 145578 vertices processed 50000 of 145578 vertices processed 75000 of 145578 vertices processed 100000 of 145578 vertices processed 125000 of 145578 vertices processed 0 of 145578 vertices processed 25000 of 145578 vertices processed 50000 of 145578 vertices processed 75000 of 145578 vertices processed 100000 of 145578 vertices processed 125000 of 145578 vertices processed thickness calculation complete, 634:2599 truncations. 22912 vertices at 0 distance 78215 vertices at 1 distance 88903 vertices at 2 distance 52592 vertices at 3 distance 22570 vertices at 4 distance 8063 vertices at 5 distance 2950 vertices at 6 distance 1143 vertices at 7 distance 529 vertices at 8 distance 275 vertices at 9 distance 157 vertices at 10 distance 115 vertices at 11 distance 88 vertices at 12 distance 56 vertices at 13 distance 35 vertices at 14 distance 39 vertices at 15 distance 35 vertices at 16 distance 30 vertices at 17 distance 34 vertices at 18 distance 29 vertices at 19 distance 48 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.thickness positioning took 18.1 minutes PIDs (17210 17213) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 03:51:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label Total face volume 298461 Total vertex volume 295075 (mask=0) #@# 0051348 lh 295075 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 03:51:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label Total face volume 295119 Total vertex volume 291788 (mask=0) #@# 0051348 rh 291788 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 03:51:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 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 = 314 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/ribbon.mgz mris_volmask took 22.04 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 04:13:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 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 0051348 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 04:13:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 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 0051348 rh pial Waiting for PID 20413 of (20413 20416 20419 20422) to complete... Waiting for PID 20416 of (20413 20416 20419 20422) to complete... Waiting for PID 20419 of (20413 20416 20419 20422) to complete... Waiting for PID 20422 of (20413 20416 20419 20422) 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 0051348 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 298461 Total vertex volume 295075 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 1295 862 2558 3.108 0.408 0.086 0.016 7 0.8 bankssts 1291 817 2982 3.141 0.615 0.136 0.032 24 1.6 caudalanteriorcingulate 3991 2586 8713 2.938 0.572 0.126 0.049 54 8.6 caudalmiddlefrontal 2277 1358 3500 2.251 0.583 0.125 0.041 30 3.8 cuneus 681 446 1833 3.198 0.915 0.139 0.048 11 1.4 entorhinal 4359 3009 10659 3.085 0.609 0.143 0.042 80 7.8 fusiform 8501 5613 17859 2.863 0.579 0.135 0.040 142 14.2 inferiorparietal 5389 3549 13909 3.066 0.654 0.136 0.044 99 9.6 inferiortemporal 1753 1129 3372 2.633 0.840 0.136 0.039 32 2.4 isthmuscingulate 7896 4799 14201 2.567 0.601 0.131 0.035 110 11.4 lateraloccipital 3675 2465 8793 3.177 0.743 0.135 0.044 56 6.5 lateralorbitofrontal 4583 2974 8146 2.485 0.678 0.135 0.041 70 7.3 lingual 2761 1781 5626 2.622 0.815 0.144 0.057 69 7.3 medialorbitofrontal 4480 2939 12382 3.261 0.678 0.141 0.049 85 8.2 middletemporal 911 581 2234 3.128 0.637 0.119 0.036 11 1.2 parahippocampal 2427 1524 4560 2.691 0.633 0.115 0.038 25 4.0 paracentral 2805 1817 6740 3.004 0.585 0.137 0.045 45 5.3 parsopercularis 936 595 2932 3.448 0.682 0.153 0.065 24 2.6 parsorbitalis 1695 1126 3827 2.904 0.591 0.121 0.036 22 2.6 parstriangularis 1844 1291 2003 1.800 0.453 0.135 0.041 20 3.6 pericalcarine 7271 4512 12205 2.373 0.660 0.130 0.047 130 14.6 postcentral 1837 1202 3970 2.919 0.990 0.155 0.043 37 3.0 posteriorcingulate 8785 5298 15921 2.749 0.608 0.125 0.050 129 17.9 precentral 5797 3826 12456 2.992 0.611 0.121 0.032 82 7.3 precuneus 1334 867 3645 3.523 0.761 0.147 0.054 35 2.8 rostralanteriorcingulate 9136 6102 22006 2.891 0.692 0.138 0.043 153 16.8 rostralmiddlefrontal 10656 6984 25467 3.084 0.736 0.134 0.049 175 22.9 superiorfrontal 9304 6148 17892 2.616 0.572 0.134 0.043 160 17.6 superiorparietal 5849 3850 13683 3.055 0.668 0.128 0.045 106 11.4 superiortemporal 7492 5011 17145 2.950 0.568 0.122 0.039 115 13.2 supramarginal 406 263 1081 2.757 0.552 0.160 0.058 16 0.8 frontalpole 857 550 2959 3.606 0.677 0.155 0.065 17 2.4 temporalpole 835 478 1519 2.627 0.574 0.121 0.056 15 1.8 transversetemporal 4054 2645 8208 3.080 0.775 0.134 0.056 59 10.5 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0051348 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 298461 Total vertex volume 295075 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 1295 801 2558 3.108 0.408 0.126 0.041 32 2.1 bankssts 1291 1194 2982 3.141 0.615 0.191 0.056 33 3.2 caudalanteriorcingulate 3991 3202 8713 2.938 0.572 0.145 0.041 61 7.2 caudalmiddlefrontal 2277 1762 3500 2.251 0.583 0.135 0.033 28 3.4 cuneus 681 700 1833 3.198 0.915 0.182 0.053 18 1.6 entorhinal 4359 4008 10659 3.085 0.609 0.175 0.047 76 9.6 fusiform 8501 6770 17859 2.863 0.579 0.149 0.044 172 16.8 inferiorparietal 5389 5394 13909 3.066 0.654 0.187 0.050 98 12.8 inferiortemporal 1753 1478 3372 2.633 0.840 0.186 0.054 50 4.1 isthmuscingulate 7896 6253 14201 2.567 0.601 0.133 0.032 160 11.6 lateraloccipital 3675 2995 8793 3.177 0.743 0.158 0.046 69 7.3 lateralorbitofrontal 4583 3738 8146 2.485 0.678 0.150 0.042 66 8.6 lingual 2761 2512 5626 2.622 0.815 0.200 0.071 83 9.9 medialorbitofrontal 4480 4315 12382 3.261 0.678 0.177 0.044 73 9.5 middletemporal 911 886 2234 3.128 0.637 0.180 0.044 14 1.7 parahippocampal 2427 1872 4560 2.691 0.633 0.137 0.037 26 4.1 paracentral 2805 2598 6740 3.004 0.585 0.167 0.043 39 5.5 parsopercularis 936 1000 2932 3.448 0.682 0.190 0.043 12 1.9 parsorbitalis 1695 1465 3827 2.904 0.591 0.162 0.042 26 3.4 parstriangularis 1844 976 2003 1.800 0.453 0.101 0.029 25 2.1 pericalcarine 7271 5601 12205 2.373 0.660 0.129 0.035 141 12.2 postcentral 1837 1475 3970 2.919 0.990 0.167 0.047 45 3.4 posteriorcingulate 8785 5971 15921 2.749 0.608 0.120 0.035 114 12.7 precentral 5797 4566 12456 2.992 0.611 0.143 0.037 99 9.7 precuneus 1334 1355 3645 3.523 0.761 0.206 0.064 36 4.6 rostralanteriorcingulate 9136 8523 22006 2.891 0.692 0.184 0.050 166 21.7 rostralmiddlefrontal 10656 9133 25467 3.084 0.736 0.166 0.055 306 30.1 superiorfrontal 9304 7343 17892 2.616 0.572 0.145 0.039 147 16.3 superiorparietal 5849 4833 13683 3.055 0.668 0.156 0.042 120 11.1 superiortemporal 7492 6392 17145 2.950 0.568 0.149 0.040 117 12.9 supramarginal 406 521 1081 2.757 0.552 0.230 0.051 6 1.1 frontalpole 857 1113 2959 3.606 0.677 0.216 0.049 12 2.2 temporalpole 835 686 1519 2.627 0.574 0.146 0.038 8 1.4 transversetemporal 4054 2460 8208 3.080 0.775 0.142 0.050 104 8.0 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 0051348 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 295119 Total vertex volume 291788 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 1866 1249 3599 3.078 0.450 0.105 0.025 13 1.8 bankssts 897 549 1619 2.749 0.707 0.136 0.036 17 1.3 caudalanteriorcingulate 3651 2404 7992 2.985 0.560 0.126 0.043 59 6.4 caudalmiddlefrontal 2550 1602 4312 2.345 0.593 0.150 0.041 43 4.1 cuneus 392 264 1431 3.604 0.782 0.137 0.042 5 0.7 entorhinal 3955 2686 9504 3.056 0.679 0.133 0.046 69 7.7 fusiform 9552 6227 20799 2.987 0.600 0.131 0.041 152 15.9 inferiorparietal 4186 2672 10144 3.007 0.753 0.137 0.053 75 10.1 inferiortemporal 1477 940 2764 2.659 0.979 0.142 0.037 28 2.0 isthmuscingulate 6844 4180 12169 2.614 0.578 0.127 0.035 95 9.6 lateraloccipital 3524 2301 8421 3.114 0.801 0.135 0.051 63 6.9 lateralorbitofrontal 5122 3210 8947 2.547 0.707 0.136 0.042 79 8.8 lingual 2656 1840 6657 2.855 0.634 0.146 0.058 59 7.0 medialorbitofrontal 5169 3326 14311 3.260 0.682 0.133 0.046 92 9.8 middletemporal 1043 648 2374 3.015 0.683 0.122 0.063 22 3.1 parahippocampal 2779 1779 5278 2.769 0.596 0.110 0.035 33 3.9 paracentral 1886 1273 4602 2.972 0.635 0.127 0.040 24 3.4 parsopercularis 1086 724 3828 3.483 0.711 0.141 0.048 17 2.1 parsorbitalis 1858 1305 4629 3.074 0.609 0.126 0.038 23 2.8 parstriangularis 2404 1542 2435 1.802 0.510 0.142 0.041 34 4.0 pericalcarine 7413 4639 12470 2.384 0.673 0.129 0.049 125 16.1 postcentral 1907 1271 3874 2.855 0.665 0.135 0.031 29 2.4 posteriorcingulate 9842 5967 17557 2.643 0.634 0.135 0.055 176 22.4 precentral 5879 3942 12145 2.862 0.626 0.127 0.035 89 8.5 precuneus 1035 666 2673 3.490 0.578 0.133 0.048 20 2.2 rostralanteriorcingulate 9282 6081 20269 2.661 0.667 0.140 0.049 191 19.5 rostralmiddlefrontal 9683 6527 24690 3.103 0.710 0.134 0.050 158 21.1 superiorfrontal 10818 6723 18241 2.513 0.556 0.125 0.044 165 19.9 superiorparietal 6521 4251 16193 3.138 0.677 0.117 0.040 94 11.2 superiortemporal 6951 4431 14404 2.915 0.609 0.132 0.062 166 22.1 supramarginal 411 281 1394 2.944 0.690 0.182 0.056 12 1.0 frontalpole 642 415 2287 3.469 0.692 0.172 0.074 19 2.1 temporalpole 705 441 1402 2.611 0.448 0.130 0.036 11 0.8 transversetemporal 3890 2517 8317 3.141 1.073 0.124 0.052 55 7.8 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051348 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 295119 Total vertex volume 291788 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 1866 1111 3599 3.078 0.450 0.133 0.042 32 3.4 bankssts 897 670 1619 2.749 0.707 0.163 0.046 16 1.9 caudalanteriorcingulate 3651 2838 7992 2.985 0.560 0.159 0.049 68 8.2 caudalmiddlefrontal 2550 2137 4312 2.345 0.593 0.156 0.041 46 4.6 cuneus 392 519 1431 3.604 0.782 0.237 0.060 9 1.3 entorhinal 3955 3420 9504 3.056 0.679 0.165 0.045 71 8.3 fusiform 9552 7578 20799 2.987 0.600 0.144 0.040 161 16.9 inferiorparietal 4186 3870 10144 3.007 0.753 0.179 0.052 84 9.8 inferiortemporal 1477 1134 2764 2.659 0.979 0.167 0.048 42 3.2 isthmuscingulate 6844 5033 12169 2.614 0.578 0.124 0.030 98 9.4 lateraloccipital 3524 2939 8421 3.114 0.801 0.172 0.052 73 8.3 lateralorbitofrontal 5122 4001 8947 2.547 0.707 0.148 0.040 84 9.0 lingual 2656 2804 6657 2.855 0.634 0.215 0.062 56 8.0 medialorbitofrontal 5169 5215 14311 3.260 0.682 0.179 0.048 83 11.6 middletemporal 1043 873 2374 3.015 0.683 0.153 0.046 16 2.6 parahippocampal 2779 2056 5278 2.769 0.596 0.132 0.037 42 4.8 paracentral 1886 1738 4602 2.972 0.635 0.175 0.045 26 4.0 parsopercularis 1086 1391 3828 3.483 0.711 0.199 0.043 13 2.0 parsorbitalis 1858 1655 4629 3.074 0.609 0.157 0.042 26 3.3 parstriangularis 2404 1279 2435 1.802 0.510 0.107 0.032 39 3.2 pericalcarine 7413 5677 12470 2.384 0.673 0.135 0.037 89 12.2 postcentral 1907 1551 3874 2.855 0.665 0.172 0.051 51 4.6 posteriorcingulate 9842 6886 17557 2.643 0.634 0.125 0.035 125 15.6 precentral 5879 4572 12145 2.862 0.626 0.148 0.044 107 10.0 precuneus 1035 897 2673 3.490 0.578 0.187 0.051 26 2.4 rostralanteriorcingulate 9282 8783 20269 2.661 0.667 0.199 0.058 180 26.7 rostralmiddlefrontal 9683 8987 24690 3.103 0.710 0.177 0.051 186 23.4 superiorfrontal 10818 7605 18241 2.513 0.556 0.133 0.039 167 18.9 superiorparietal 6521 5872 16193 3.138 0.677 0.163 0.043 103 12.9 superiortemporal 6951 5240 14404 2.915 0.609 0.148 0.045 131 13.7 supramarginal 411 636 1394 2.944 0.690 0.262 0.061 5 1.3 frontalpole 642 874 2287 3.469 0.692 0.221 0.055 8 1.7 temporalpole 705 600 1402 2.611 0.448 0.151 0.037 9 1.1 transversetemporal 3890 2472 8317 3.141 1.073 0.153 0.071 151 8.9 insula PIDs (20413 20416 20419 20422) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 04:15:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Sun Oct 8 04:15:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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 20595 of (20595 20598) to complete... Waiting for PID 20598 of (20595 20598) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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... 34 labels changed using aseg relabeling using gibbs priors... 000: 9676 changed, 145874 examined... 001: 2278 changed, 37039 examined... 002: 666 changed, 11859 examined... 003: 286 changed, 3878 examined... 004: 124 changed, 1571 examined... 005: 62 changed, 744 examined... 006: 26 changed, 354 examined... 007: 9 changed, 131 examined... 008: 6 changed, 55 examined... 009: 4 changed, 31 examined... 010: 4 changed, 24 examined... 011: 1 changed, 21 examined... 012: 0 changed, 6 examined... 9 labels changed using aseg 000: 272 total segments, 188 labels (2279 vertices) changed 001: 96 total segments, 12 labels (33 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 46 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1279 vertices marked for relabeling... 1279 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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: 9413 changed, 145578 examined... 001: 2147 changed, 36725 examined... 002: 631 changed, 11344 examined... 003: 254 changed, 3571 examined... 004: 99 changed, 1477 examined... 005: 59 changed, 576 examined... 006: 34 changed, 351 examined... 007: 16 changed, 177 examined... 008: 11 changed, 90 examined... 009: 3 changed, 61 examined... 010: 0 changed, 21 examined... 5 labels changed using aseg 000: 270 total segments, 187 labels (2925 vertices) changed 001: 98 total segments, 15 labels (63 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 27 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1337 vertices marked for relabeling... 1337 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. PIDs (20595 20598) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 04:15:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 04:15:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 rh white Waiting for PID 20641 of (20641 20644) to complete... Waiting for PID 20644 of (20641 20644) 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 0051348 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 298461 Total vertex volume 295075 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 1420 977 3392 2.803 0.718 0.153 0.047 32 2.7 G&S_frontomargin 1429 908 3098 2.762 0.493 0.130 0.030 19 1.7 G&S_occipital_inf 2034 1160 3528 2.440 0.704 0.132 0.058 36 5.5 G&S_paracentral 1747 1148 3837 2.971 0.571 0.145 0.046 31 2.9 G&S_subcentral 740 508 2484 3.050 0.599 0.159 0.060 23 1.7 G&S_transv_frontopol 2300 1549 5525 3.154 0.654 0.123 0.039 39 3.5 G&S_cingul-Ant 1361 914 3113 3.010 0.563 0.116 0.028 18 1.5 G&S_cingul-Mid-Ant 1306 888 3032 3.140 0.775 0.138 0.034 18 1.8 G&S_cingul-Mid-Post 759 499 2363 3.375 0.834 0.172 0.060 22 1.9 G_cingul-Post-dorsal 339 200 659 2.766 0.721 0.150 0.067 8 0.7 G_cingul-Post-ventral 2159 1281 3523 2.195 0.699 0.138 0.051 42 4.8 G_cuneus 1676 1088 4665 3.215 0.542 0.151 0.055 36 3.7 G_front_inf-Opercular 387 251 1302 3.381 0.764 0.187 0.093 17 1.9 G_front_inf-Orbital 885 564 2503 3.037 0.534 0.145 0.045 17 1.5 G_front_inf-Triangul 5407 3431 15756 3.111 0.695 0.152 0.063 126 14.7 G_front_middle 7236 4596 19000 3.151 0.807 0.154 0.064 164 20.7 G_front_sup 998 612 2065 3.014 0.847 0.150 0.081 17 4.2 G_Ins_lg&S_cent_ins 847 547 2557 3.434 0.901 0.151 0.075 22 2.8 G_insular_short 2499 1447 6515 3.053 0.599 0.140 0.038 50 3.6 G_occipital_middle 1754 1029 3506 2.673 0.558 0.135 0.041 31 2.9 G_occipital_sup 1676 1136 4753 3.317 0.585 0.158 0.044 40 3.2 G_oc-temp_lat-fusifor 3206 1983 5895 2.374 0.707 0.142 0.048 60 6.0 G_oc-temp_med-Lingual 1426 893 3965 3.302 0.778 0.137 0.052 27 2.7 G_oc-temp_med-Parahip 2306 1522 7400 3.384 0.746 0.144 0.056 53 5.0 G_orbital 3399 2218 8590 2.850 0.697 0.157 0.062 91 9.1 G_pariet_inf-Angular 3473 2247 8822 2.956 0.606 0.136 0.058 81 9.4 G_pariet_inf-Supramar 3508 2220 7318 2.534 0.621 0.155 0.060 87 9.5 G_parietal_sup 2822 1599 5064 2.396 0.659 0.146 0.069 81 8.5 G_postcentral 3308 1773 6479 2.755 0.664 0.137 0.074 72 9.9 G_precentral 2971 1921 8097 3.133 0.625 0.144 0.050 69 5.9 G_precuneus 884 540 2246 2.730 0.594 0.163 0.060 26 2.3 G_rectus 776 470 1361 2.547 1.157 0.151 0.093 34 3.6 G_subcallosal 662 371 1283 2.551 0.571 0.124 0.053 13 1.3 G_temp_sup-G_T_transv 2000 1290 6528 3.340 0.684 0.153 0.059 53 4.4 G_temp_sup-Lateral 849 568 2264 3.510 0.615 0.097 0.044 22 2.1 G_temp_sup-Plan_polar 1363 883 3259 3.007 0.543 0.129 0.049 22 2.7 G_temp_sup-Plan_tempo 3098 2012 9172 3.117 0.684 0.151 0.055 81 6.8 G_temporal_inf 2378 1519 7635 3.415 0.660 0.158 0.062 56 5.7 G_temporal_middle 284 194 596 3.092 0.457 0.086 0.016 1 0.2 Lat_Fis-ant-Horizont 308 205 521 2.724 0.440 0.089 0.023 1 0.3 Lat_Fis-ant-Vertical 1301 869 1993 2.959 0.564 0.109 0.029 9 1.6 Lat_Fis-post 2379 1372 3294 2.148 0.616 0.127 0.039 34 3.8 Pole_occipital 1942 1294 6491 3.392 0.776 0.163 0.061 43 5.1 Pole_temporal 2308 1581 2989 2.180 0.679 0.121 0.033 22 3.5 S_calcarine 3734 2477 4942 2.269 0.588 0.111 0.029 27 4.8 S_central 1163 792 1852 2.642 0.398 0.089 0.014 6 0.6 S_cingul-Marginalis 520 347 889 3.163 0.509 0.105 0.033 3 0.7 S_circular_insula_ant 1494 1003 2399 3.045 0.631 0.111 0.037 10 2.5 S_circular_insula_inf 1868 1255 2855 2.706 0.527 0.106 0.028 12 2.2 S_circular_insula_sup 839 586 1916 3.023 0.705 0.127 0.038 10 1.5 S_collat_transv_ant 465 323 657 2.467 0.473 0.133 0.031 3 0.7 S_collat_transv_post 2347 1559 3941 2.667 0.514 0.112 0.028 16 2.7 S_front_inf 1685 1151 2532 2.649 0.515 0.122 0.030 12 2.1 S_front_middle 3314 2224 6093 2.781 0.452 0.102 0.025 18 3.5 S_front_sup 780 514 1182 2.834 0.431 0.100 0.020 4 0.7 S_interm_prim-Jensen 3814 2710 6645 2.770 0.458 0.117 0.024 29 3.8 S_intrapariet&P_trans 962 669 1464 2.610 0.383 0.108 0.018 5 0.7 S_oc_middle&Lunatus 1920 1266 2999 2.673 0.368 0.100 0.018 10 1.5 S_oc_sup&transversal 812 527 1657 2.986 0.467 0.125 0.026 9 0.8 S_occipital_ant 1213 819 2146 2.906 0.419 0.101 0.022 7 1.0 S_oc-temp_lat 2044 1474 3790 2.814 0.471 0.129 0.031 25 2.6 S_oc-temp_med&Lingual 278 204 531 2.602 0.752 0.143 0.035 3 0.5 S_orbital_lateral 625 437 1029 2.487 0.789 0.138 0.038 6 1.0 S_orbital_med-olfact 1465 981 3103 3.245 0.756 0.131 0.036 16 2.3 S_orbital-H_Shaped 2194 1492 3472 2.574 0.476 0.101 0.018 17 1.6 S_parieto_occipital 1704 1060 2235 2.560 1.108 0.136 0.027 26 1.6 S_pericallosal 3064 2125 4915 2.574 0.484 0.110 0.025 24 3.2 S_postcentral 1828 1203 3257 2.820 0.544 0.104 0.026 12 2.0 S_precentral-inf-part 1554 1040 2618 2.797 0.488 0.112 0.030 13 1.9 S_precentral-sup-part 764 522 1417 2.875 0.669 0.122 0.027 6 0.9 S_suborbital 1060 710 1899 3.105 0.607 0.115 0.024 6 1.1 S_subparietal 1565 1057 2520 2.994 0.517 0.109 0.021 8 1.6 S_temporal_inf 5708 3888 11041 2.909 0.497 0.116 0.027 55 5.9 S_temporal_sup 473 313 642 2.546 0.292 0.100 0.018 2 0.4 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0051348 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 295119 Total vertex volume 291788 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 884 584 2105 2.701 0.642 0.147 0.037 15 1.6 G&S_frontomargin 849 492 1916 2.885 0.565 0.130 0.039 15 1.1 G&S_occipital_inf 2198 1257 3792 2.423 0.693 0.133 0.070 51 6.9 G&S_paracentral 1828 1230 4223 2.992 0.595 0.134 0.038 24 2.8 G&S_subcentral 1261 807 3302 2.724 0.662 0.164 0.077 46 4.2 G&S_transv_frontopol 2964 2035 6939 3.124 0.671 0.132 0.043 48 5.5 G&S_cingul-Ant 1338 888 2914 2.985 0.642 0.127 0.036 22 2.0 G&S_cingul-Mid-Ant 1484 991 3134 3.063 0.603 0.125 0.031 17 1.9 G&S_cingul-Mid-Post 656 396 1863 3.260 0.697 0.158 0.049 16 1.2 G_cingul-Post-dorsal 312 207 736 2.839 0.704 0.166 0.046 7 0.6 G_cingul-Post-ventral 2370 1494 3886 2.196 0.632 0.151 0.046 41 4.0 G_cuneus 1432 968 4826 3.318 0.511 0.159 0.062 34 3.9 G_front_inf-Opercular 366 250 1364 3.401 0.489 0.173 0.060 8 0.9 G_front_inf-Orbital 608 418 2006 3.280 0.525 0.149 0.054 12 1.3 G_front_inf-Triangul 4311 2730 12559 3.004 0.650 0.158 0.066 123 11.6 G_front_middle 6077 3944 17799 3.235 0.735 0.148 0.063 130 16.6 G_front_sup 699 454 1823 3.528 0.949 0.140 0.086 15 2.8 G_Ins_lg&S_cent_ins 631 403 2463 3.830 0.900 0.147 0.057 10 1.3 G_insular_short 2189 1332 5276 2.920 0.596 0.144 0.044 45 3.9 G_occipital_middle 1878 1129 3615 2.567 0.533 0.131 0.041 32 3.0 G_occipital_sup 1916 1225 5318 3.191 0.771 0.151 0.066 53 5.7 G_oc-temp_lat-fusifor 3381 2022 6085 2.499 0.707 0.143 0.053 64 7.1 G_oc-temp_med-Lingual 1223 765 3897 3.376 0.827 0.143 0.071 29 4.0 G_oc-temp_med-Parahip 2516 1634 8589 3.470 0.806 0.152 0.061 65 6.1 G_orbital 4148 2493 10209 3.014 0.742 0.153 0.068 117 11.6 G_pariet_inf-Angular 2957 1832 7341 3.019 0.675 0.149 0.092 113 14.6 G_pariet_inf-Supramar 3920 2290 6712 2.320 0.614 0.152 0.068 93 11.5 G_parietal_sup 2593 1487 4520 2.331 0.658 0.151 0.069 72 8.3 G_postcentral 3857 2096 7154 2.603 0.698 0.153 0.077 107 12.3 G_precentral 2428 1608 5860 2.789 0.551 0.130 0.038 49 3.8 G_precuneus 774 540 2651 3.151 0.586 0.190 0.076 27 2.6 G_rectus 729 408 846 1.932 1.259 0.087 0.036 12 1.1 G_subcallosal 516 316 1222 2.763 0.530 0.138 0.042 10 0.7 G_temp_sup-G_T_transv 2586 1655 8106 3.394 0.630 0.146 0.068 66 7.7 G_temp_sup-Lateral 1117 772 2601 3.161 0.818 0.127 0.043 11 1.9 G_temp_sup-Plan_polar 1466 969 3319 3.045 0.520 0.132 0.040 18 2.7 G_temp_sup-Plan_tempo 2422 1459 6799 3.166 0.783 0.141 0.066 53 7.3 G_temporal_inf 3124 1987 10355 3.408 0.700 0.150 0.056 73 6.9 G_temporal_middle 324 238 624 3.086 0.570 0.099 0.020 1 0.3 Lat_Fis-ant-Horizont 198 139 353 2.837 0.633 0.115 0.024 1 0.2 Lat_Fis-ant-Vertical 1707 1143 2799 3.017 0.478 0.113 0.029 14 2.0 Lat_Fis-post 3458 2031 5331 2.329 0.684 0.133 0.038 52 5.6 Pole_occipital 1503 1003 4615 3.202 0.815 0.165 0.067 43 4.2 Pole_temporal 2469 1616 3088 2.253 0.799 0.126 0.031 23 3.2 S_calcarine 3921 2543 4795 2.176 0.505 0.114 0.036 34 5.9 S_central 1563 1070 2453 2.574 0.443 0.097 0.020 9 1.2 S_cingul-Marginalis 537 367 1024 3.189 0.519 0.107 0.058 10 0.8 S_circular_insula_ant 1228 801 1858 2.788 0.669 0.086 0.018 5 1.0 S_circular_insula_inf 1461 976 2378 2.947 0.554 0.103 0.026 7 1.7 S_circular_insula_sup 636 461 1404 2.945 0.474 0.122 0.031 5 0.9 S_collat_transv_ant 517 361 914 2.913 0.644 0.138 0.033 5 0.7 S_collat_transv_post 2110 1444 3659 2.650 0.563 0.112 0.035 33 3.3 S_front_inf 2568 1719 4186 2.378 0.564 0.129 0.037 30 4.0 S_front_middle 2987 2095 5167 2.609 0.501 0.107 0.026 16 3.4 S_front_sup 670 421 974 2.759 0.417 0.110 0.027 4 0.8 S_interm_prim-Jensen 4536 2992 7538 2.700 0.428 0.107 0.027 38 4.7 S_intrapariet&P_trans 699 473 957 2.355 0.410 0.108 0.018 5 0.5 S_oc_middle&Lunatus 1753 1193 2631 2.624 0.442 0.108 0.022 11 1.6 S_oc_sup&transversal 574 382 930 2.808 0.549 0.108 0.024 4 0.5 S_occipital_ant 1222 833 2005 2.721 0.469 0.120 0.024 10 1.3 S_oc-temp_lat 1803 1287 3220 2.921 0.536 0.107 0.021 11 1.5 S_oc-temp_med&Lingual 372 270 687 2.894 0.576 0.125 0.031 3 0.5 S_orbital_lateral 530 356 937 2.606 0.724 0.124 0.036 4 0.7 S_orbital_med-olfact 1304 853 2659 3.077 0.665 0.118 0.039 14 1.8 S_orbital-H_Shaped 2413 1627 4113 2.783 0.562 0.126 0.030 31 3.0 S_parieto_occipital 1490 932 1600 2.259 0.757 0.131 0.027 23 1.3 S_pericallosal 3455 2260 5289 2.619 0.450 0.104 0.028 26 4.1 S_postcentral 2127 1425 3593 2.898 0.542 0.103 0.023 11 2.2 S_precentral-inf-part 1598 1069 2612 2.674 0.472 0.117 0.029 12 2.0 S_precentral-sup-part 338 248 573 2.395 0.491 0.121 0.046 3 0.7 S_suborbital 1150 800 2528 3.317 0.569 0.111 0.025 9 1.0 S_subparietal 919 626 1696 2.954 0.609 0.111 0.028 5 1.1 S_temporal_inf 7302 4970 13924 3.026 0.494 0.105 0.023 53 7.3 S_temporal_sup 443 299 548 2.333 0.410 0.115 0.023 3 0.4 S_temporal_transverse PIDs (20641 20644) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 04:16:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Sun Oct 8 04:16:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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 20745 of (20745 20748) to complete... Waiting for PID 20748 of (20745 20748) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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... 2041 labels changed using aseg relabeling using gibbs priors... 000: 2159 changed, 145874 examined... 001: 511 changed, 10044 examined... 002: 143 changed, 2959 examined... 003: 60 changed, 806 examined... 004: 29 changed, 341 examined... 005: 22 changed, 172 examined... 006: 19 changed, 109 examined... 007: 11 changed, 88 examined... 008: 10 changed, 66 examined... 009: 7 changed, 61 examined... 010: 9 changed, 41 examined... 011: 4 changed, 43 examined... 012: 2 changed, 26 examined... 013: 1 changed, 12 examined... 014: 1 changed, 5 examined... 015: 1 changed, 7 examined... 016: 0 changed, 9 examined... 310 labels changed using aseg 000: 78 total segments, 45 labels (492 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 887 vertices marked for relabeling... 887 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 17 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051348 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... 1589 labels changed using aseg relabeling using gibbs priors... 000: 2302 changed, 145578 examined... 001: 555 changed, 10437 examined... 002: 149 changed, 3148 examined... 003: 62 changed, 893 examined... 004: 38 changed, 342 examined... 005: 29 changed, 213 examined... 006: 25 changed, 158 examined... 007: 10 changed, 123 examined... 008: 9 changed, 62 examined... 009: 6 changed, 44 examined... 010: 3 changed, 28 examined... 011: 1 changed, 22 examined... 012: 2 changed, 7 examined... 013: 3 changed, 12 examined... 014: 4 changed, 15 examined... 015: 4 changed, 24 examined... 016: 4 changed, 20 examined... 017: 6 changed, 20 examined... 018: 4 changed, 25 examined... 019: 9 changed, 18 examined... 020: 3 changed, 31 examined... 021: 1 changed, 17 examined... 022: 2 changed, 7 examined... 023: 1 changed, 12 examined... 024: 1 changed, 7 examined... 025: 1 changed, 7 examined... 026: 0 changed, 7 examined... 334 labels changed using aseg 000: 63 total segments, 30 labels (661 vertices) changed 001: 36 total segments, 3 labels (3 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 12 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 736 vertices marked for relabeling... 736 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 18 seconds. PIDs (20745 20748) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 04:16:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 04:16:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 rh white Waiting for PID 20791 of (20791 20794) to complete... Waiting for PID 20794 of (20791 20794) 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 0051348 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 298461 Total vertex volume 295075 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 1797 1159 3776 3.025 0.610 0.128 0.029 27 2.1 caudalanteriorcingulate 4379 2832 9327 2.914 0.567 0.125 0.049 59 9.3 caudalmiddlefrontal 3082 1882 5057 2.326 0.595 0.116 0.038 45 5.0 cuneus 644 412 1746 3.182 0.931 0.138 0.047 11 1.4 entorhinal 3932 2716 9414 3.069 0.599 0.140 0.039 71 6.6 fusiform 8956 5901 19297 2.884 0.585 0.135 0.040 150 15.0 inferiorparietal 5398 3576 13895 3.036 0.655 0.140 0.046 103 10.3 inferiortemporal 1712 1114 3326 2.645 0.812 0.140 0.040 32 2.4 isthmuscingulate 7886 4781 13977 2.568 0.584 0.129 0.035 110 11.1 lateraloccipital 4255 2855 10522 3.174 0.802 0.141 0.047 71 8.3 lateralorbitofrontal 4711 3048 8282 2.463 0.686 0.136 0.041 72 7.7 lingual 2259 1455 4812 2.689 0.765 0.152 0.055 52 5.6 medialorbitofrontal 5887 3855 15519 3.230 0.657 0.134 0.044 98 9.6 middletemporal 945 605 2327 3.146 0.637 0.119 0.036 12 1.2 parahippocampal 2715 1695 5195 2.744 0.658 0.117 0.043 30 5.1 paracentral 2635 1713 6239 2.992 0.597 0.136 0.046 42 5.0 parsopercularis 941 612 2335 3.159 0.528 0.133 0.052 17 2.1 parsorbitalis 2116 1389 4572 2.859 0.605 0.123 0.036 26 3.2 parstriangularis 1795 1256 1945 1.810 0.455 0.137 0.042 20 3.6 pericalcarine 8118 5047 13540 2.383 0.661 0.131 0.049 144 17.2 postcentral 2015 1335 4248 2.898 0.995 0.151 0.041 37 3.1 posteriorcingulate 8627 5216 15680 2.754 0.603 0.126 0.049 126 17.3 precentral 5808 3826 12786 3.000 0.610 0.125 0.034 90 7.8 precuneus 1895 1213 4673 3.247 0.924 0.140 0.059 59 4.8 rostralanteriorcingulate 6728 4425 17223 2.974 0.725 0.141 0.047 125 13.3 rostralmiddlefrontal 11854 7821 28643 3.032 0.736 0.135 0.049 201 24.9 superiorfrontal 7452 4998 14265 2.616 0.558 0.134 0.039 116 13.0 superiorparietal 7703 5081 18915 3.142 0.668 0.127 0.044 131 14.7 superiortemporal 6790 4554 15089 2.929 0.557 0.123 0.041 108 12.6 supramarginal 823 471 1504 2.621 0.578 0.123 0.057 15 1.8 transversetemporal 3308 2158 6947 3.138 0.749 0.129 0.054 47 8.5 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 0051348 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 295119 Total vertex volume 291788 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 951 591 1700 2.720 0.690 0.135 0.035 18 1.4 caudalanteriorcingulate 3834 2532 8413 2.987 0.557 0.127 0.043 61 6.8 caudalmiddlefrontal 3058 1929 5218 2.382 0.593 0.146 0.039 50 4.7 cuneus 385 260 1417 3.581 0.778 0.137 0.039 4 0.6 entorhinal 3770 2563 9083 3.057 0.674 0.134 0.046 68 7.5 fusiform 9516 6184 20429 2.977 0.599 0.131 0.040 150 15.8 inferiorparietal 4309 2785 10263 2.977 0.745 0.136 0.052 71 10.0 inferiortemporal 1445 917 2701 2.649 0.969 0.143 0.037 28 2.0 isthmuscingulate 6965 4265 12184 2.601 0.581 0.127 0.036 95 9.8 lateraloccipital 4004 2616 10087 3.116 0.815 0.145 0.054 80 8.7 lateralorbitofrontal 4952 3100 8697 2.548 0.710 0.136 0.042 77 8.5 lingual 2283 1508 5300 2.605 0.990 0.141 0.054 50 5.4 medialorbitofrontal 6450 4174 16984 3.209 0.660 0.128 0.042 105 11.1 middletemporal 1106 694 2554 3.061 0.695 0.123 0.061 22 3.1 parahippocampal 2882 1836 5467 2.768 0.621 0.112 0.039 38 4.6 paracentral 2264 1523 5374 2.958 0.623 0.129 0.043 30 4.2 parsopercularis 964 639 3099 3.394 0.641 0.138 0.046 15 1.8 parsorbitalis 1735 1228 4102 3.013 0.642 0.120 0.033 18 2.3 parstriangularis 2394 1526 2436 1.804 0.507 0.141 0.041 32 3.9 pericalcarine 8287 5152 13878 2.419 0.684 0.129 0.051 142 18.6 postcentral 1956 1300 3956 2.862 0.673 0.135 0.032 30 2.5 posteriorcingulate 9656 5836 17233 2.641 0.633 0.135 0.055 174 22.2 precentral 5995 4042 12579 2.871 0.621 0.125 0.034 90 8.0 precuneus 1432 936 3429 3.302 0.672 0.126 0.043 25 2.6 rostralanteriorcingulate 6949 4495 15683 2.693 0.718 0.140 0.050 144 15.2 rostralmiddlefrontal 12350 8358 30480 2.997 0.710 0.136 0.049 211 26.1 superiorfrontal 9210 5718 15542 2.508 0.552 0.125 0.044 140 16.9 superiorparietal 8389 5488 21034 3.185 0.662 0.121 0.042 125 15.0 superiortemporal 6616 4226 13764 2.899 0.613 0.134 0.064 165 21.8 supramarginal 686 426 1404 2.632 0.443 0.129 0.036 11 0.8 transversetemporal 3100 2044 7297 3.376 0.793 0.123 0.054 43 6.4 insula PIDs (20791 20794) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 04:17:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts pctsurfcon --s 0051348 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 04:17:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts pctsurfcon --s 0051348 --rh-only Waiting for PID 20861 of (20861 20872) to complete... Waiting for PID 20872 of (20861 20872) to complete... pctsurfcon --s 0051348 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts/pctsurfcon.log Sun Oct 8 04:17:37 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-6.0.0/0051348/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-553 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-6.0.0/0051348/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.wm.mgh --regheader 0051348 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 74697 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.wm.mgh Dim: 145874 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.gm.mgh --projfrac 0.3 --regheader 0051348 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 93173 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.gm.mgh Dim: 145874 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20861/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.w-g.pct.mgh --annot 0051348 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/lh.w-g.pct.mgh --annot 0051348 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-553 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/lh.w-g.pct.mgh Vertex Area is 0.64788 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 0051348 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/scripts/pctsurfcon.log Sun Oct 8 04:17:37 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-6.0.0/0051348/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-553 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-6.0.0/0051348/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.wm.mgh --regheader 0051348 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 74420 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.wm.mgh Dim: 145578 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.gm.mgh --projfrac 0.3 --regheader 0051348 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 92828 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.gm.mgh Dim: 145578 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/tmp.pctsurfcon.20872/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.w-g.pct.mgh --annot 0051348 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.w-g.pct.mgh --annot 0051348 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-553 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.w-g.pct.mgh Vertex Area is 0.645438 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 (20861 20872) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 04:17:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1626 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1436 voxels changed to hypointensity... 3006 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 04:18:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348 mri_aparc2aseg --s 0051348 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt #----------------------------------------- #@# AParc-to-ASeg a2009s Sun Oct 8 04:18:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348 mri_aparc2aseg --s 0051348 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s #----------------------------------------- #@# AParc-to-ASeg DKTatlas Sun Oct 8 04:18:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348 mri_aparc2aseg --s 0051348 --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 21038 of (21038 21041 21044) to complete... Waiting for PID 21041 of (21038 21041 21044) to complete... Waiting for PID 21044 of (21038 21041 21044) to complete... mri_aparc2aseg --s 0051348 --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 0051348 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/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-6.0.0/0051348/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 6.83 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 69 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 38 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 65 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 69 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 93 rescaling Third_Ventricle from 25 --> 38 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 53 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 87 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 69 rescaling Right_Lateral_Ventricle from 13 --> 22 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 83 rescaling Right_Cerebellum_Cortex from 59 --> 62 rescaling Right_Thalamus_Proper from 85 --> 83 rescaling Right_Caudate from 62 --> 76 rescaling Right_Putamen from 80 --> 81 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 66 rescaling Right_Amygdala from 55 --> 66 rescaling Right_Accumbens_area from 65 --> 74 rescaling Right_VentralDC from 86 --> 84 rescaling Fifth_Ventricle from 40 --> 46 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 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 = 579829 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 212 changed. pass 2: 13 changed. pass 3: 3 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/aparc+aseg.mgz mri_aparc2aseg --s 0051348 --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 0051348 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/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-6.0.0/0051348/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 6.83 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 69 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 38 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 65 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 69 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 93 rescaling Third_Ventricle from 25 --> 38 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 53 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 87 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 69 rescaling Right_Lateral_Ventricle from 13 --> 22 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 83 rescaling Right_Cerebellum_Cortex from 59 --> 62 rescaling Right_Thalamus_Proper from 85 --> 83 rescaling Right_Caudate from 62 --> 76 rescaling Right_Putamen from 80 --> 81 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 66 rescaling Right_Amygdala from 55 --> 66 rescaling Right_Accumbens_area from 65 --> 74 rescaling Right_VentralDC from 86 --> 84 rescaling Fifth_Ventricle from 40 --> 46 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 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 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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 0051348 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/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-6.0.0/0051348/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 6.83 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 69 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 38 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 65 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 69 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 93 rescaling Third_Ventricle from 25 --> 38 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 53 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 87 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 69 rescaling Right_Lateral_Ventricle from 13 --> 22 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 83 rescaling Right_Cerebellum_Cortex from 59 --> 62 rescaling Right_Thalamus_Proper from 85 --> 83 rescaling Right_Caudate from 62 --> 76 rescaling Right_Putamen from 80 --> 81 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 66 rescaling Right_Amygdala from 55 --> 66 rescaling Right_Accumbens_area from 65 --> 74 rescaling Right_VentralDC from 86 --> 84 rescaling Fifth_Ventricle from 40 --> 46 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 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 = 579907 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 212 changed. pass 2: 13 changed. pass 3: 3 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (21038 21041 21044) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 04:29:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 04:29:21 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-6.0.0/0051348/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-553 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-6.0.0/0051348/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-553 machine x86_64 user ntraut input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Sun Oct 8 04:29:21 CEST 2017 Ended at Sun Oct 8 04:29:28 CEST 2017 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 04:29:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348 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 0051348 $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 0051348 sysname Linux hostname tars-553 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1528850 mm^3 (det: 1.274229 ) Computing euler number orig.nofix lheno = -344, rheno = -294 orig.nofix lhholes = 173, rhholes = 148 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Sun Oct 8 04:33:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348 mri_aparc2aseg --s 0051348 --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 0051348 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-6.0.0/0051348/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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-6.0.0/0051348/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8711 vertices from left hemi Ripped 7702 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-6.0.0/0051348/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 = 963420 Used brute-force search on 30 voxels Fixing Parahip LH WM Found 6 clusters 0 k 1.000000 1 k 2.000000 2 k 976.000000 3 k 1.000000 4 k 1.000000 5 k 4.000000 Fixing Parahip RH WM Found 8 clusters 0 k 5.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 4.000000 5 k 1.000000 6 k 1.000000 7 k 1166.000000 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 0051348 --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 0051348 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-553 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1528850 mm^3 (det: 1.274229 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 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-6.0.0/0051348/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 04:43:42 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 22059 of (22059 22065 22071 22075 22082) to complete... Waiting for PID 22065 of (22059 22065 22071 22075 22082) to complete... Waiting for PID 22071 of (22059 22065 22071 22075 22082) to complete... Waiting for PID 22075 of (22059 22065 22071 22075 22082) to complete... Waiting for PID 22082 of (22059 22065 22071 22075 22082) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 554 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4683 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 772 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8681 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 262 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4339 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 519 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6502 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 986 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6770 mri_label2label: Done PIDs (22059 22065 22071 22075 22082) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 22144 of (22144 22150 22156 22161) to complete... Waiting for PID 22150 of (22144 22150 22156 22161) to complete... Waiting for PID 22156 of (22144 22150 22156 22161) to complete... Waiting for PID 22161 of (22144 22150 22156 22161) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 482 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4552 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 2062 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15651 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 597 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4778 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 582 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4004 mri_label2label: Done PIDs (22144 22150 22156 22161) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 22201 of (22201 22207 22213 22219 22223) to complete... Waiting for PID 22207 of (22201 22207 22213 22219 22223) to complete... Waiting for PID 22213 of (22201 22207 22213 22219 22223) to complete... Waiting for PID 22219 of (22201 22207 22213 22219 22223) to complete... Waiting for PID 22223 of (22201 22207 22213 22219 22223) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 1287 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5928 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 3171 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11285 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 372 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2390 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1411 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 114 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1313 mri_label2label: Done PIDs (22201 22207 22213 22219 22223) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 22313 of (22313 22319 22325 22331 22336) to complete... Waiting for PID 22319 of (22313 22319 22325 22331 22336) to complete... Waiting for PID 22325 of (22313 22319 22325 22331 22336) to complete... Waiting for PID 22331 of (22313 22319 22325 22331 22336) to complete... Waiting for PID 22336 of (22313 22319 22325 22331 22336) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 161 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1175 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 303 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2395 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1568 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 181 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2177 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 295 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2614 mri_label2label: Done PIDs (22313 22319 22325 22331 22336) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 22379 of (22379 22385 22391 22397) to complete... Waiting for PID 22385 of (22379 22385 22391 22397) to complete... Waiting for PID 22391 of (22379 22385 22391 22397) to complete... Waiting for PID 22397 of (22379 22385 22391 22397) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 204 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1753 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 1148 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8183 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 305 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2217 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 213 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1364 mri_label2label: Done PIDs (22379 22385 22391 22397) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 22436 of (22436 22442 22448 22454 22460) to complete... Waiting for PID 22442 of (22436 22442 22448 22454 22460) to complete... Waiting for PID 22448 of (22436 22442 22448 22454 22460) to complete... Waiting for PID 22454 of (22436 22442 22448 22454 22460) to complete... Waiting for PID 22460 of (22436 22442 22448 22454 22460) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 886 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4291 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 1388 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4722 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 598 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 509 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145874 Number of reverse mapping hits = 49 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 499 mri_label2label: Done PIDs (22436 22442 22448 22454 22460) completed and logs appended. mris_label2annot --s 0051348 --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-6.0.0/0051348/label cmdline mris_label2annot --s 0051348 --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-553 machine x86_64 user ntraut subject 0051348 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-6.0.0/0051348/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 101874 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/lh.BA_exvivo.annot mris_label2annot --s 0051348 --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-6.0.0/0051348/label cmdline mris_label2annot --s 0051348 --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-553 machine x86_64 user ntraut subject 0051348 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-6.0.0/0051348/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 119513 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 298461 Total vertex volume 295075 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 1327 725 2278 2.407 0.682 0.164 0.088 47 5.2 BA1_exvivo 4308 2826 7852 2.606 0.575 0.124 0.037 65 7.0 BA2_exvivo 1181 798 1329 2.070 0.477 0.129 0.031 11 1.5 BA3a_exvivo 2711 1737 4322 2.209 0.648 0.119 0.034 34 3.6 BA3b_exvivo 1868 1101 3548 2.687 0.636 0.125 0.052 25 4.3 BA4a_exvivo 1668 975 2569 2.697 0.507 0.111 0.047 19 3.5 BA4p_exvivo 10326 6396 22270 2.943 0.712 0.134 0.058 176 25.5 BA6_exvivo 2657 1747 6169 3.008 0.588 0.139 0.046 44 5.1 BA44_exvivo 2754 1827 6125 2.827 0.601 0.132 0.040 40 4.9 BA45_exvivo 3379 2190 3866 1.774 0.491 0.132 0.043 40 6.5 V1_exvivo 8629 5261 14332 2.428 0.583 0.132 0.042 138 14.4 V2_exvivo 1936 1200 4361 2.945 0.501 0.129 0.031 28 2.5 MT_exvivo 599 367 1676 3.249 0.737 0.126 0.048 8 1.2 perirhinal_exvivo 657 437 1588 3.111 0.848 0.132 0.040 9 1.0 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 0051348 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 298461 Total vertex volume 295075 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 837 449 1387 2.375 0.651 0.166 0.081 22 3.0 BA1_exvivo 1831 1132 3208 2.521 0.562 0.118 0.042 33 3.1 BA2_exvivo 1005 690 1070 2.046 0.477 0.136 0.032 9 1.3 BA3a_exvivo 1634 1077 2235 1.954 0.433 0.105 0.025 13 1.7 BA3b_exvivo 1865 1110 3451 2.764 0.579 0.122 0.048 22 4.1 BA4a_exvivo 1302 791 2008 2.639 0.516 0.111 0.046 15 2.6 BA4p_exvivo 5938 3541 11577 2.803 0.721 0.140 0.070 121 18.6 BA6_exvivo 1722 1137 4391 3.040 0.603 0.149 0.055 36 3.9 BA44_exvivo 1142 735 2894 2.962 0.505 0.132 0.037 17 1.7 BA45_exvivo 3645 2333 4208 1.787 0.491 0.132 0.044 46 7.1 V1_exvivo 4297 2578 6564 2.301 0.581 0.134 0.039 64 6.7 V2_exvivo 485 302 1151 2.942 0.515 0.141 0.037 7 0.7 MT_exvivo 300 183 819 3.253 0.616 0.111 0.031 2 0.4 perirhinal_exvivo 358 242 947 3.391 0.941 0.140 0.039 4 0.7 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 04:47:44 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 22623 of (22623 22629 22635 22639 22647) to complete... Waiting for PID 22629 of (22623 22629 22635 22639 22647) to complete... Waiting for PID 22635 of (22623 22629 22635 22639 22647) to complete... Waiting for PID 22639 of (22623 22629 22635 22639 22647) to complete... Waiting for PID 22647 of (22623 22629 22635 22639 22647) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 667 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4629 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 920 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7607 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 319 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4299 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 502 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5024 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 1170 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6917 mri_label2label: Done PIDs (22623 22629 22635 22639 22647) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 22704 of (22704 22710 22716 22721) to complete... Waiting for PID 22710 of (22704 22710 22716 22721) to complete... Waiting for PID 22716 of (22704 22710 22716 22721) to complete... Waiting for PID 22721 of (22704 22710 22716 22721) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 766 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 5239 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 1854 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 14110 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 1037 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7949 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 751 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6106 mri_label2label: Done PIDs (22704 22710 22716 22721) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 22761 of (22761 22767 22773 22779 22784) to complete... Waiting for PID 22767 of (22761 22767 22773 22779 22784) to complete... Waiting for PID 22773 of (22761 22767 22773 22779 22784) to complete... Waiting for PID 22779 of (22761 22767 22773 22779 22784) to complete... Waiting for PID 22784 of (22761 22767 22773 22779 22784) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 1848 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6575 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 3210 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11226 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 224 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2156 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 105 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1143 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 830 mri_label2label: Done PIDs (22761 22767 22773 22779 22784) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 22845 of (22845 22851 22856 22861 22869) to complete... Waiting for PID 22851 of (22845 22851 22856 22861 22869) to complete... Waiting for PID 22856 of (22845 22851 22856 22861 22869) to complete... Waiting for PID 22861 of (22845 22851 22856 22861 22869) to complete... Waiting for PID 22869 of (22845 22851 22856 22861 22869) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 176 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1052 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 353 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 3041 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1805 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 180 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2363 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 241 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1629 mri_label2label: Done PIDs (22845 22851 22856 22861 22869) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 22916 of (22916 22922 22928 22934) to complete... Waiting for PID 22922 of (22916 22922 22928 22934) to complete... Waiting for PID 22928 of (22916 22922 22928 22934) to complete... Waiting for PID 22934 of (22916 22922 22928 22934) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 249 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1738 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 1068 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 8027 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1145 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 118 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1296 mri_label2label: Done PIDs (22916 22922 22928 22934) 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 0051348 --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 0051348 --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 0051348 --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 0051348 --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 0051348 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 22973 of (22973 22979 22985 22990 22995) to complete... Waiting for PID 22979 of (22973 22979 22985 22990 22995) to complete... Waiting for PID 22985 of (22973 22979 22985 22990 22995) to complete... Waiting for PID 22990 of (22973 22979 22985 22990 22995) to complete... Waiting for PID 22995 of (22973 22979 22985 22990 22995) 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 1195 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4427 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 1594 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5031 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 19 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 287 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 744 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 0051348 --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 = 0051348 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-6.0.0/0051348/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 145578 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 324 mri_label2label: Done PIDs (22973 22979 22985 22990 22995) completed and logs appended. mris_label2annot --s 0051348 --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-6.0.0/0051348/label cmdline mris_label2annot --s 0051348 --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-553 machine x86_64 user ntraut subject 0051348 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-6.0.0/0051348/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 101178 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/label/rh.BA_exvivo.annot mris_label2annot --s 0051348 --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-6.0.0/0051348/label cmdline mris_label2annot --s 0051348 --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-553 machine x86_64 user ntraut subject 0051348 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-6.0.0/0051348/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 120056 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/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 0051348 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 295119 Total vertex volume 291788 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 1168 621 1987 2.306 0.629 0.156 0.083 38 4.7 BA1_exvivo 4029 2522 6633 2.574 0.540 0.119 0.042 60 7.3 BA2_exvivo 1309 863 1321 2.004 0.434 0.125 0.034 11 1.8 BA3a_exvivo 2367 1548 3651 2.044 0.524 0.123 0.042 31 4.1 BA3b_exvivo 2126 1212 3614 2.570 0.606 0.134 0.063 49 5.6 BA4a_exvivo 1751 1053 2679 2.577 0.461 0.115 0.048 17 3.3 BA4p_exvivo 8640 5364 18904 2.929 0.742 0.138 0.060 168 22.4 BA6_exvivo 4060 2739 9087 2.966 0.610 0.121 0.034 45 5.6 BA44_exvivo 3731 2538 9720 3.033 0.682 0.138 0.051 77 8.3 BA45_exvivo 4212 2582 4966 1.854 0.558 0.145 0.044 65 7.9 V1_exvivo 8513 5255 14687 2.552 0.597 0.135 0.041 129 13.7 V2_exvivo 1646 1036 3494 2.945 0.547 0.126 0.036 25 2.2 MT_exvivo 533 338 1747 3.607 0.657 0.148 0.050 10 1.2 perirhinal_exvivo 315 216 1211 3.672 0.690 0.141 0.053 6 0.6 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 0051348 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051348/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 295119 Total vertex volume 291788 (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) = 1528850 mm^3 (det: 1.274229 ) lhCtxGM: 292852.920 292167.000 diff= 685.9 pctdiff= 0.234 rhCtxGM: 289186.484 288228.000 diff= 958.5 pctdiff= 0.331 lhCtxWM: 195089.304 195334.000 diff= -244.7 pctdiff=-0.125 rhCtxWM: 189816.852 191319.000 diff=-1502.1 pctdiff=-0.791 SubCortGMVol 61024.000 SupraTentVol 1053515.560 (1050738.000) diff=2777.560 pctdiff=0.264 SupraTentVolNotVent 1030865.560 (1028088.000) diff=2777.560 pctdiff=0.269 BrainSegVol 1225672.000 (1222135.000) diff=3537.000 pctdiff=0.289 BrainSegVolNotVent 1198124.000 (1197916.560) diff=207.440 pctdiff=0.017 BrainSegVolNotVent 1198124.000 CerebellumVol 169931.000 VentChorVol 22650.000 3rd4th5thCSF 4898.000 CSFVol 1361.000, OptChiasmVol 105.000 MaskVol 1589178.000 797 426 1209 2.141 0.585 0.166 0.065 30 2.4 BA1_exvivo 2239 1374 3830 2.532 0.549 0.122 0.052 36 5.3 BA2_exvivo 1221 800 1118 1.978 0.404 0.125 0.031 10 1.6 BA3a_exvivo 1744 1176 2360 1.905 0.370 0.103 0.029 12 1.9 BA3b_exvivo 1241 704 2213 2.643 0.670 0.137 0.065 29 3.3 BA4a_exvivo 1405 841 2072 2.613 0.409 0.115 0.048 18 2.6 BA4p_exvivo 5768 3556 12025 2.830 0.749 0.146 0.067 127 17.0 BA6_exvivo 831 573 2362 3.187 0.605 0.130 0.040 12 1.3 BA44_exvivo 900 634 2815 3.189 0.556 0.155 0.060 18 2.4 BA45_exvivo 4000 2467 4587 1.846 0.558 0.143 0.043 60 7.4 V1_exvivo 4616 2817 7474 2.419 0.609 0.139 0.043 73 7.4 V2_exvivo 225 136 547 3.007 0.432 0.126 0.030 4 0.2 MT_exvivo 316 203 1092 3.658 0.468 0.140 0.045 4 0.6 perirhinal_exvivo 219 149 850 3.646 0.971 0.144 0.046 4 0.4 entorhinal_exvivo Started at Sat Oct 7 17:01:48 CEST 2017 Ended at Sun Oct 8 04:51:17 CEST 2017 #@#%# recon-all-run-time-hours 11.825 recon-all -s 0051348 finished without error at Sun Oct 8 04:51:17 CEST 2017