Sun Oct 8 01:15:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0050490 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/USM_2/0050490/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0050490 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-114 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: 264574092 251297724 13276368 1729880 0 245238352 -/+ buffers/cache: 6059372 258514720 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-23:15:11-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-114 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-6.0.0/0050490 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/USM_2/0050490/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/USM_2/0050490/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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/USM_2/0050490/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-6.0.0/0050490/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Oct 8 01:15:26 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sun Oct 8 01:16:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-114 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sun Oct 8 01:16:44 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.460 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.460/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.460/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.460/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Oct 8 01:16:54 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.460/nu0.mnc ./tmp.mri_nu_correct.mni.460/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.460/0/ -iterations 1000 -distance 50 [ntraut@tars-114:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/] [2017-10-08 01:16:54] 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.460/0/ ./tmp.mri_nu_correct.mni.460/nu0.mnc ./tmp.mri_nu_correct.mni.460/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 Number of iterations: 37 CV of field change: 0.000975682 mri_convert ./tmp.mri_nu_correct.mni.460/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.460/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.460/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sun Oct 8 01:18:02 CEST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sun Oct 8 01:18:02 CEST 2017 Ended at Sun Oct 8 01:19:56 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sun Oct 8 01:19:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7061, pval=0.4932 >= threshold=0.0050) awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/transforms/talairach_avi.log TalAviQA: 0.98353 z-score: 1 #-------------------------------------------- #@# Nu Intensity Correction Sun Oct 8 01:19:58 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-6.0.0/0050490/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-114 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sun Oct 8 01:19:58 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.1256 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1256/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1256/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.1256/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Oct 8 01:20:09 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.1256/nu0.mnc ./tmp.mri_nu_correct.mni.1256/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1256/0/ [ntraut@tars-114:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/] [2017-10-08 01:20:09] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1256/0/ ./tmp.mri_nu_correct.mni.1256/nu0.mnc ./tmp.mri_nu_correct.mni.1256/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 Number of iterations: 30 CV of field change: 0.000983527 Reading Volume: ............................................................... Reading Volume: ............................................................... -------------------------------------------------------- Iteration 2 Sun Oct 8 01:21:25 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.1256/nu1.mnc ./tmp.mri_nu_correct.mni.1256/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.1256/1/ [ntraut@tars-114:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/] [2017-10-08 01:21:25] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1256/1/ ./tmp.mri_nu_correct.mni.1256/nu1.mnc ./tmp.mri_nu_correct.mni.1256/nu2.imp Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 18 CV of field change: 0.000985363 mri_binarize --i ./tmp.mri_nu_correct.mni.1256/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1256/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-6.0.0/0050490/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.1256/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1256/ones.mgz sysname Linux hostname tars-114 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.1256/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.1256/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.1256/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1256/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1256/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.1256/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1256/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1256/input.mean.dat sysname Linux hostname tars-114 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1256/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.1256/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1256/ones.mgz --i ./tmp.mri_nu_correct.mni.1256/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1256/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1256/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.1256/ones.mgz --i ./tmp.mri_nu_correct.mni.1256/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1256/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1256/output.mean.dat sysname Linux hostname tars-114 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1256/ones.mgz Loading ./tmp.mri_nu_correct.mni.1256/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.1256/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.1256/nu2.mnc ./tmp.mri_nu_correct.mni.1256/nu2.mnc mul 1.03906514931838336632 Saving result to './tmp.mri_nu_correct.mni.1256/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.1256/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.1256/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.1256/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 17 seconds. mapping ( 8, 113) to ( 3, 110) Sun Oct 8 01:24:07 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sun Oct 8 01:24:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 1.05834 -0.05780 -0.04230 -9.37296; 0.04197 0.94733 0.30468 -38.87525; 0.00133 -0.23165 1.06828 6.75354; 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 109 gm peak at 63 (63), valley at 35 (35) csf peak at 32, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 63 (63), valley at 24 (24) csf peak at 32, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 12 seconds. #-------------------------------------------- #@# Skull Stripping Sun Oct 8 01:26:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (41, 24, 0) --> (207, 182, 223) using (96, 77, 112) as brain centroid... mean wm in atlas = 108, using box (76,58,84) --> (116, 96,139) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 109 +- 5.4 after smoothing, mri peak at 109, scaling input intensities by 0.991 scaling channel 0 by 0.990826 initial log_p = -4.396 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.335263 @ (9.091, 9.091, -9.091) max log p = -4.156005 @ (-4.545, 4.545, 4.545) max log p = -4.091447 @ (-2.273, -2.273, 2.273) max log p = -4.083212 @ (-1.136, 1.136, 1.136) max log p = -4.078184 @ (-0.568, -1.705, 0.568) max log p = -4.078184 @ (0.000, 0.000, 0.000) Found translation: (0.6, 10.8, -0.6): log p = -4.078 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.788, old_max_log_p =-4.078 (thresh=-4.1) 1.05465 -0.03594 0.13412 -16.45666; 0.00000 1.11081 0.29764 -29.44774; -0.13885 -0.27296 1.01871 42.96675; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.782, old_max_log_p =-3.788 (thresh=-3.8) 1.06375 0.00000 0.00000 -6.37745; 0.00000 1.19413 0.31997 -42.31939; 0.00000 -0.25467 0.95044 31.53729; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.782, old_max_log_p =-3.782 (thresh=-3.8) 1.06375 0.00000 0.00000 -6.37745; 0.00000 1.19413 0.31997 -42.31939; 0.00000 -0.25467 0.95044 31.53729; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.687, old_max_log_p =-3.782 (thresh=-3.8) 1.04267 -0.00879 0.02780 -7.93726; 0.00241 1.17906 0.28077 -34.37264; -0.03795 -0.22207 0.97629 31.10920; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.684, old_max_log_p =-3.687 (thresh=-3.7) 1.04203 -0.04737 0.01860 -2.08969; 0.03652 1.17814 0.28153 -38.62361; -0.03795 -0.22207 0.97629 31.10920; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.662, old_max_log_p =-3.684 (thresh=-3.7) 1.04474 -0.01992 0.03319 -6.98353; 0.01113 1.17667 0.27160 -34.57709; -0.04587 -0.21170 0.97846 31.06960; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.656, old_max_log_p =-3.662 (thresh=-3.7) 1.04474 -0.01992 0.03319 -6.98353; 0.01074 1.17352 0.27927 -34.54782; -0.04591 -0.22106 0.97507 33.07893; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.655, old_max_log_p =-3.656 (thresh=-3.7) 1.04719 -0.01997 0.03327 -7.29258; 0.01074 1.17352 0.27927 -34.54782; -0.04591 -0.22106 0.97507 33.07893; 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 1.04719 -0.01997 0.03327 -7.29258; 0.01074 1.17352 0.27927 -34.54782; -0.04591 -0.22106 0.97507 33.07893; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.04719 -0.01997 0.03327 -7.29258; 0.01074 1.17352 0.27927 -34.54782; -0.04591 -0.22106 0.97507 33.07893; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.04719 -0.01997 0.03327 -7.29258; 0.01074 1.17352 0.27927 -34.54782; -0.04591 -0.22106 0.97507 33.07893; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.655 (old=-4.396) transform before final EM align: 1.04719 -0.01997 0.03327 -7.29258; 0.01074 1.17352 0.27927 -34.54782; -0.04591 -0.22106 0.97507 33.07893; 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 1.04719 -0.01997 0.03327 -7.29258; 0.01074 1.17352 0.27927 -34.54782; -0.04591 -0.22106 0.97507 33.07893; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.04719 -0.01997 0.03327 -7.29258; 0.01074 1.17352 0.27927 -34.54782; -0.04591 -0.22106 0.97507 33.07893; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.1 tol 0.000000 final transform: 1.04719 -0.01997 0.03327 -7.29258; 0.01074 1.17352 0.27927 -34.54782; -0.04591 -0.22106 0.97507 33.07893; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 5814.068127 mri_em_register stimesec 11.540245 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 157574 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 1789149 mri_em_register ru_nivcsw 14984 registration took 83 minutes and 39 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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=125 y=98 z=108 r=73 first estimation of the main basin volume: 1664660 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=109, y=82, z=74, Imax=255 CSF=18, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=9348481830 voxels, voxel volume =1.000 = 9348481830 mmm3 = 9348482.048 cm3 done. PostAnalyze...Basin Prior 12 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=125,y=105, z=104, r=10661 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=50 , nb = 45118 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=55 , nb = -1031211856 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=44 , nb = 1100087410 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=45 , nb = 1094517478 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=53 , nb = 1077211110 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1078909570 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 50, 38, 31, 56 after analyzing : 30, 38, 38, 42 RIGHT_CER before analyzing : 55, 43, 37, 64 after analyzing : 33, 43, 43, 48 LEFT_CER before analyzing : 44, 40, 38, 59 after analyzing : 29, 40, 40, 44 RIGHT_BRAIN before analyzing : 45, 36, 31, 56 after analyzing : 29, 36, 36, 41 LEFT_BRAIN before analyzing : 53, 38, 31, 56 after analyzing : 30, 38, 38, 42 OTHER before analyzing : 3, 2, 0, 9 after analyzing : 2, 17, 25, 19 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...60 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 72.019, std = 7.213 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.83, sigma = 2.91 after rotation: sse = 1.83, sigma = 2.91 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.95, its var is 3.00 before Erosion-Dilatation 0.27% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...41 iterations mri_strip_skull: done peeling brain Brain Size = 1763604 voxels, voxel volume = 1.000 mm3 = 1763604 mmm3 = 1763.604 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 62.087561 mri_watershed stimesec 1.084835 mri_watershed ru_maxrss 832900 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 215559 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2864 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 5566 mri_watershed ru_nivcsw 216 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sun Oct 8 02:51:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = (59, 43, 23) --> (193, 182, 200) using (104, 89, 112) as brain centroid... mean wm in atlas = 107, using box (88,72,90) --> (120, 106,133) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 109 +- 5.2 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.185 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.051234 @ (9.091, 9.091, -9.091) max log p = -3.745299 @ (-4.545, 4.545, 4.545) max log p = -3.626761 @ (-2.273, 2.273, 2.273) max log p = -3.623154 @ (-1.136, -1.136, 1.136) max log p = -3.612539 @ (0.568, -0.568, -1.705) max log p = -3.612539 @ (0.000, 0.000, 0.000) Found translation: (1.7, 14.2, -2.8): log p = -3.613 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.401, old_max_log_p =-3.613 (thresh=-3.6) 1.06580 -0.03087 0.11520 -15.75408; 0.00000 1.02750 0.27532 -18.49865; -0.14032 -0.23447 0.87506 60.37152; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.401, old_max_log_p =-3.401 (thresh=-3.4) 1.06580 -0.03087 0.11520 -15.75408; 0.00000 1.02750 0.27532 -18.49865; -0.14032 -0.23447 0.87506 60.37152; 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=-3.201, old_max_log_p =-3.401 (thresh=-3.4) 1.04896 0.01248 0.09083 -15.71046; -0.02894 1.07360 0.25300 -15.80520; -0.11395 -0.21304 0.93712 44.70525; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.201, old_max_log_p =-3.201 (thresh=-3.2) 1.04896 0.01248 0.09083 -15.71046; -0.02894 1.07360 0.25300 -15.80520; -0.11395 -0.21304 0.93712 44.70525; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.181, old_max_log_p =-3.201 (thresh=-3.2) 1.04809 -0.00502 0.08632 -13.30033; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86055; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.181, old_max_log_p =-3.181 (thresh=-3.2) 1.04809 -0.00502 0.08632 -13.30033; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86055; 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 1.04809 -0.00502 0.08632 -13.30033; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86055; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.04809 -0.00502 0.08632 -13.30033; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86055; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.04809 -0.00502 0.08632 -13.30033; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86055; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.181 (old=-4.185) transform before final EM align: 1.04809 -0.00502 0.08632 -13.30033; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86055; 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 1.04809 -0.00502 0.08632 -13.30033; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86055; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.04809 -0.00502 0.08632 -13.30033; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86055; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.7 tol 0.000000 final transform: 1.04809 -0.00502 0.08632 -13.30033; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86055; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 3479.343059 mri_em_register stimesec 6.534006 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 159485 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 875880 mri_em_register ru_nivcsw 8606 registration took 46 minutes and 9 seconds. #-------------------------------------- #@# CA Normalize Sun Oct 8 03:37:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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=22.9 skull bounding box = (59, 43, 24) --> (193, 182, 200) using (104, 89, 112) as brain centroid... mean wm in atlas = 107, using box (88,72,90) --> (120, 106,133) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 109 +- 5.2 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 246344 sample points... INFO: compute sample coordinates transform 1.04809 -0.00502 0.08632 -13.30033; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86055; 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 (122, 45, 26) --> (189, 153, 196) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 589 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 45, 22) --> (128, 149, 194) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 1 of 968 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 130, 56) --> (174, 168, 111) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 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 (85, 130, 49) --> (128, 168, 108) Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (109, 116, 90) --> (142, 181, 122) Brain_Stem: limiting intensities to 97.0 --> 132.0 5 of 18 (27.8%) samples deleted using 1591 total control points for intensity normalization... bias field = 0.974 +- 0.041 4 of 1585 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (122, 45, 26) --> (189, 153, 196) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 738 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 45, 22) --> (128, 149, 194) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 1 of 1411 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 130, 56) --> (174, 168, 111) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 74 (20.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 130, 49) --> (128, 168, 108) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 60 (13.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (109, 116, 90) --> (142, 181, 122) Brain_Stem: limiting intensities to 88.0 --> 132.0 18 of 72 (25.0%) samples deleted using 2355 total control points for intensity normalization... bias field = 1.012 +- 0.045 15 of 2297 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (122, 45, 26) --> (189, 153, 196) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 2 of 755 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 45, 22) --> (128, 149, 194) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 1 of 1465 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 130, 56) --> (174, 168, 111) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 50 of 94 (53.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 130, 49) --> (128, 168, 108) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 23 of 60 (38.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (109, 116, 90) --> (142, 181, 122) Brain_Stem: limiting intensities to 88.0 --> 132.0 106 of 189 (56.1%) samples deleted using 2563 total control points for intensity normalization... bias field = 1.013 +- 0.040 4 of 2343 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 29 seconds. #-------------------------------------- #@# CA Reg Sun Oct 8 03:39:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.12 (predicted orig area = 7.1) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.771, neg=0, invalid=762 0001: dt=209.097143, rms=0.715 (7.172%), neg=0, invalid=762 0002: dt=140.545455, rms=0.702 (1.850%), neg=0, invalid=762 0003: dt=369.920000, rms=0.693 (1.310%), neg=0, invalid=762 0004: dt=110.976000, rms=0.688 (0.657%), neg=0, invalid=762 0005: dt=887.808000, rms=0.682 (0.926%), neg=0, invalid=762 0006: dt=129.472000, rms=0.680 (0.329%), neg=0, invalid=762 0007: dt=295.936000, rms=0.679 (0.159%), neg=0, invalid=762 0008: dt=295.936000, rms=0.679 (0.002%), neg=0, invalid=762 0009: dt=295.936000, rms=0.675 (0.511%), neg=0, invalid=762 0010: dt=295.936000, rms=0.672 (0.484%), neg=0, invalid=762 0011: dt=295.936000, rms=0.670 (0.237%), neg=0, invalid=762 0012: dt=295.936000, rms=0.667 (0.486%), neg=0, invalid=762 0013: dt=295.936000, rms=0.665 (0.388%), neg=0, invalid=762 0014: dt=295.936000, rms=0.664 (0.136%), neg=0, invalid=762 0015: dt=295.936000, rms=0.662 (0.234%), neg=0, invalid=762 0016: dt=295.936000, rms=0.660 (0.290%), neg=0, invalid=762 0017: dt=295.936000, rms=0.659 (0.233%), neg=0, invalid=762 0018: dt=295.936000, rms=0.658 (0.179%), neg=0, invalid=762 0019: dt=295.936000, rms=0.657 (0.151%), neg=0, invalid=762 0020: dt=295.936000, rms=0.655 (0.302%), neg=0, invalid=762 0021: dt=295.936000, rms=0.653 (0.160%), neg=0, invalid=762 0022: dt=295.936000, rms=0.653 (0.024%), neg=0, invalid=762 0023: dt=295.936000, rms=0.651 (0.297%), neg=0, invalid=762 0024: dt=295.936000, rms=0.651 (0.126%), neg=0, invalid=762 0025: dt=295.936000, rms=0.650 (0.032%), neg=0, invalid=762 0026: dt=295.936000, rms=0.649 (0.214%), neg=0, invalid=762 0027: dt=295.936000, rms=0.648 (0.103%), neg=0, invalid=762 0028: dt=295.936000, rms=0.648 (0.048%), neg=0, invalid=762 0029: dt=129.472000, rms=0.647 (0.082%), neg=0, invalid=762 0030: dt=73.984000, rms=0.647 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.648, neg=0, invalid=762 0031: dt=295.936000, rms=0.647 (0.163%), neg=0, invalid=762 0032: dt=295.936000, rms=0.647 (0.045%), neg=0, invalid=762 0033: dt=295.936000, rms=0.647 (-0.023%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.653, neg=0, invalid=762 0034: dt=197.680473, rms=0.646 (1.025%), neg=0, invalid=762 0035: dt=108.547842, rms=0.640 (0.980%), neg=0, invalid=762 0036: dt=64.709534, rms=0.637 (0.401%), neg=0, invalid=762 0037: dt=414.720000, rms=0.630 (1.066%), neg=0, invalid=762 0038: dt=64.831169, rms=0.626 (0.651%), neg=0, invalid=762 0039: dt=145.152000, rms=0.624 (0.374%), neg=0, invalid=762 0040: dt=36.288000, rms=0.623 (0.145%), neg=0, invalid=762 0041: dt=36.288000, rms=0.623 (0.080%), neg=0, invalid=762 0042: dt=36.288000, rms=0.622 (0.124%), neg=0, invalid=762 0043: dt=36.288000, rms=0.621 (0.186%), neg=0, invalid=762 0044: dt=36.288000, rms=0.619 (0.255%), neg=0, invalid=762 0045: dt=36.288000, rms=0.617 (0.283%), neg=0, invalid=762 0046: dt=36.288000, rms=0.616 (0.283%), neg=0, invalid=762 0047: dt=36.288000, rms=0.614 (0.291%), neg=0, invalid=762 0048: dt=36.288000, rms=0.612 (0.286%), neg=0, invalid=762 0049: dt=36.288000, rms=0.610 (0.277%), neg=0, invalid=762 0050: dt=36.288000, rms=0.609 (0.277%), neg=0, invalid=762 0051: dt=36.288000, rms=0.607 (0.274%), neg=0, invalid=762 0052: dt=36.288000, rms=0.605 (0.256%), neg=0, invalid=762 0053: dt=36.288000, rms=0.604 (0.224%), neg=0, invalid=762 0054: dt=36.288000, rms=0.603 (0.210%), neg=0, invalid=762 0055: dt=36.288000, rms=0.602 (0.190%), neg=0, invalid=762 0056: dt=36.288000, rms=0.601 (0.177%), neg=0, invalid=762 0057: dt=36.288000, rms=0.600 (0.168%), neg=0, invalid=762 0058: dt=36.288000, rms=0.599 (0.152%), neg=0, invalid=762 0059: dt=36.288000, rms=0.598 (0.137%), neg=0, invalid=762 0060: dt=36.288000, rms=0.597 (0.120%), neg=0, invalid=762 0061: dt=36.288000, rms=0.596 (0.102%), neg=0, invalid=762 0062: dt=145.152000, rms=0.596 (0.013%), neg=0, invalid=762 0063: dt=145.152000, rms=0.596 (0.020%), neg=0, invalid=762 0064: dt=145.152000, rms=0.596 (0.032%), neg=0, invalid=762 0065: dt=145.152000, rms=0.596 (0.047%), neg=0, invalid=762 0066: dt=145.152000, rms=0.595 (0.059%), neg=0, invalid=762 0067: dt=145.152000, rms=0.595 (0.064%), neg=0, invalid=762 0068: dt=145.152000, rms=0.594 (0.113%), neg=0, invalid=762 0069: dt=145.152000, rms=0.594 (0.095%), neg=0, invalid=762 0070: dt=145.152000, rms=0.593 (0.122%), neg=0, invalid=762 0071: dt=145.152000, rms=0.592 (0.180%), neg=0, invalid=762 0072: dt=145.152000, rms=0.591 (0.133%), neg=0, invalid=762 0073: dt=145.152000, rms=0.590 (0.231%), neg=0, invalid=762 0074: dt=145.152000, rms=0.589 (0.147%), neg=0, invalid=762 0075: dt=145.152000, rms=0.588 (0.146%), neg=0, invalid=762 0076: dt=145.152000, rms=0.587 (0.179%), neg=0, invalid=762 0077: dt=145.152000, rms=0.587 (0.106%), neg=0, invalid=762 0078: dt=145.152000, rms=0.586 (0.172%), neg=0, invalid=762 0079: dt=145.152000, rms=0.585 (0.056%), neg=0, invalid=762 0080: dt=145.152000, rms=0.585 (0.096%), neg=0, invalid=762 0081: dt=145.152000, rms=0.584 (0.123%), neg=0, invalid=762 0082: dt=145.152000, rms=0.584 (0.018%), neg=0, invalid=762 0083: dt=82.944000, rms=0.584 (0.041%), neg=0, invalid=762 0084: dt=0.006328, rms=0.584 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.584, neg=0, invalid=762 0085: dt=124.416000, rms=0.583 (0.285%), neg=0, invalid=762 0086: dt=62.208000, rms=0.582 (0.050%), neg=0, invalid=762 0087: dt=62.208000, rms=0.582 (0.021%), neg=0, invalid=762 0088: dt=62.208000, rms=0.582 (0.020%), neg=0, invalid=762 0089: dt=62.208000, rms=0.582 (0.015%), neg=0, invalid=762 0090: dt=248.832000, rms=0.582 (0.021%), neg=0, invalid=762 0091: dt=9.072000, rms=0.582 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.605, neg=0, invalid=762 0092: dt=0.000000, rms=0.605 (0.090%), neg=0, invalid=762 0093: dt=0.000000, rms=0.605 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.605, neg=0, invalid=762 0094: dt=0.000000, rms=0.605 (0.090%), neg=0, invalid=762 0095: dt=0.000000, rms=0.605 (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=0.674, neg=0, invalid=762 0096: dt=5.323810, rms=0.650 (3.449%), neg=0, invalid=762 0097: dt=2.637681, rms=0.650 (0.147%), neg=0, invalid=762 0098: dt=2.637681, rms=0.650 (-0.037%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.650, neg=0, invalid=762 0099: dt=0.000000, rms=0.650 (0.074%), neg=0, invalid=762 0100: dt=0.000000, rms=0.650 (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=0.706, neg=0, invalid=762 0101: dt=1.536000, rms=0.701 (0.736%), neg=0, invalid=762 0102: dt=2.170886, rms=0.694 (0.955%), neg=0, invalid=762 0103: dt=0.448000, rms=0.694 (0.053%), neg=0, invalid=762 0104: dt=0.448000, rms=0.693 (0.029%), neg=0, invalid=762 0105: dt=0.448000, rms=0.693 (0.028%), neg=0, invalid=762 0106: dt=0.448000, rms=0.693 (0.021%), neg=0, invalid=762 0107: dt=1.792000, rms=0.691 (0.274%), neg=0, invalid=762 0108: dt=0.000000, rms=0.691 (-0.000%), neg=0, invalid=762 0109: dt=0.100000, rms=0.691 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.692, neg=0, invalid=762 0110: dt=0.448000, rms=0.691 (0.111%), neg=0, invalid=762 0111: dt=0.448000, rms=0.691 (0.015%), neg=0, invalid=762 0112: dt=0.448000, rms=0.691 (0.015%), neg=0, invalid=762 0113: dt=0.448000, rms=0.691 (0.009%), neg=0, invalid=762 0114: dt=0.448000, rms=0.691 (-0.008%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.663, neg=0, invalid=762 0115: dt=0.814962, rms=0.645 (2.597%), neg=0, invalid=762 0116: dt=0.080000, rms=0.645 (0.127%), neg=0, invalid=762 0117: dt=0.080000, rms=0.645 (-0.098%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.645, neg=0, invalid=762 0118: dt=0.028000, rms=0.645 (0.090%), neg=0, invalid=762 0119: dt=0.000000, rms=0.645 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.09359 (16) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (1068 voxels, overlap=0.628) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (1068 voxels, peak = 15), gca=14.9 gca peak = 0.15565 (16) mri peak = 0.07212 (17) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (775 voxels, overlap=0.818) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (775 voxels, peak = 17), gca=16.6 gca peak = 0.26829 (96) mri peak = 0.08229 (95) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1028 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1028 voxels, peak = 96), gca=96.5 gca peak = 0.20183 (93) mri peak = 0.08190 (96) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (846 voxels, overlap=1.002) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (846 voxels, peak = 94), gca=94.4 gca peak = 0.21683 (55) mri peak = 0.07240 (64) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (707 voxels, overlap=0.716) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (707 voxels, peak = 57), gca=57.5 gca peak = 0.30730 (58) mri peak = 0.09161 (63) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (848 voxels, overlap=0.997) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (848 voxels, peak = 64), gca=63.5 gca peak = 0.11430 (101) mri peak = 0.11192 (105) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65922 voxels, overlap=0.549) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65922 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.10490 (105) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (65364 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (65364 voxels, peak = 108), gca=107.6 gca peak = 0.14995 (59) mri peak = 0.04769 (52) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (27850 voxels, overlap=0.988) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (27850 voxels, peak = 54), gca=54.0 gca peak = 0.15082 (58) mri peak = 0.03747 (52) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28840 voxels, overlap=0.997) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28840 voxels, peak = 59), gca=59.4 gca peak = 0.14161 (67) mri peak = 0.10177 (70) Right_Caudate (50): linear fit = 1.05 x + 0.0 (960 voxels, overlap=0.879) Right_Caudate (50): linear fit = 1.05 x + 0.0 (960 voxels, peak = 71), gca=70.7 gca peak = 0.15243 (71) mri peak = 0.10115 (72) Left_Caudate (11): linear fit = 0.95 x + 0.0 (1125 voxels, overlap=0.905) Left_Caudate (11): linear fit = 0.95 x + 0.0 (1125 voxels, peak = 68), gca=67.8 gca peak = 0.13336 (57) mri peak = 0.04316 (55) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (27569 voxels, overlap=0.984) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (27569 voxels, peak = 60), gca=59.6 gca peak = 0.13252 (56) mri peak = 0.04617 (61) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (29302 voxels, overlap=0.944) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (29302 voxels, peak = 59), gca=58.5 gca peak = 0.18181 (84) mri peak = 0.07413 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (8773 voxels, overlap=0.784) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (8773 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.07956 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8325 voxels, overlap=0.806) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8325 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.08469 (62) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (456 voxels, overlap=0.991) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (456 voxels, peak = 60), gca=59.6 gca peak = 0.39313 (56) mri peak = 0.08413 (57) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (527 voxels, overlap=0.996) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (527 voxels, peak = 59), gca=58.5 gca peak = 0.14181 (85) mri peak = 0.05492 (90) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5866 voxels, overlap=0.911) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5866 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.06106 (87) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4831 voxels, overlap=0.929) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4831 voxels, peak = 87), gca=86.7 gca peak = 0.13399 (79) mri peak = 0.07592 (79) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2675 voxels, overlap=0.995) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2675 voxels, peak = 80), gca=80.2 gca peak = 0.14159 (79) mri peak = 0.08762 (80) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2695 voxels, overlap=0.973) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2695 voxels, peak = 81), gca=81.0 gca peak = 0.10025 (80) mri peak = 0.08399 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11973 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11973 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07352 (92) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1356 voxels, overlap=0.651) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1356 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.06529 (92) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1516 voxels, overlap=0.670) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1516 voxels, peak = 97), gca=96.6 gca peak = 0.20494 (23) mri peak = 0.07026 (23) gca peak = 0.15061 (21) mri peak = 0.07500 (15) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (436 voxels, overlap=0.605) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (436 voxels, peak = 17), gca=17.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak 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 1.03 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.87 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=0.675, neg=0, invalid=762 0120: dt=151.327103, rms=0.670 (0.856%), neg=0, invalid=762 0121: dt=129.472000, rms=0.668 (0.278%), neg=0, invalid=762 0122: dt=295.936000, rms=0.666 (0.249%), neg=0, invalid=762 0123: dt=110.976000, rms=0.665 (0.178%), neg=0, invalid=762 0124: dt=221.952000, rms=0.664 (0.141%), neg=0, invalid=762 0125: dt=110.976000, rms=0.663 (0.094%), neg=0, invalid=762 0126: dt=369.920000, rms=0.662 (0.127%), neg=0, invalid=762 0127: dt=92.480000, rms=0.662 (0.111%), neg=0, invalid=762 0128: dt=517.888000, rms=0.661 (0.175%), neg=0, invalid=762 0129: dt=110.976000, rms=0.660 (0.066%), neg=0, invalid=762 0130: dt=295.936000, rms=0.660 (0.070%), neg=0, invalid=762 0131: dt=110.976000, rms=0.659 (0.062%), neg=0, invalid=762 0132: dt=295.936000, rms=0.659 (0.062%), neg=0, invalid=762 0133: dt=110.976000, rms=0.659 (0.054%), neg=0, invalid=762 0134: dt=295.936000, rms=0.658 (0.056%), neg=0, invalid=762 0135: dt=110.976000, rms=0.658 (0.044%), neg=0, invalid=762 0136: dt=110.976000, rms=0.658 (0.031%), neg=0, invalid=762 0137: dt=110.976000, rms=0.657 (0.042%), neg=0, invalid=762 0138: dt=110.976000, rms=0.657 (0.066%), neg=0, invalid=762 0139: dt=110.976000, rms=0.656 (0.071%), neg=0, invalid=762 0140: dt=110.976000, rms=0.656 (0.078%), neg=0, invalid=762 0141: dt=110.976000, rms=0.655 (0.077%), neg=0, invalid=762 0142: dt=110.976000, rms=0.655 (0.074%), neg=0, invalid=762 0143: dt=110.976000, rms=0.654 (0.074%), neg=0, invalid=762 0144: dt=110.976000, rms=0.654 (0.069%), neg=0, invalid=762 0145: dt=110.976000, rms=0.654 (0.058%), neg=0, invalid=762 0146: dt=110.976000, rms=0.653 (0.055%), neg=0, invalid=762 0147: dt=110.976000, rms=0.653 (0.054%), neg=0, invalid=762 0148: dt=110.976000, rms=0.653 (0.056%), neg=0, invalid=762 0149: dt=110.976000, rms=0.652 (0.053%), neg=0, invalid=762 0150: dt=110.976000, rms=0.652 (0.053%), neg=0, invalid=762 0151: dt=110.976000, rms=0.652 (0.048%), neg=0, invalid=762 0152: dt=110.976000, rms=0.651 (0.048%), neg=0, invalid=762 0153: dt=110.976000, rms=0.651 (0.049%), neg=0, invalid=762 0154: dt=110.976000, rms=0.651 (0.046%), neg=0, invalid=762 0155: dt=110.976000, rms=0.650 (0.043%), neg=0, invalid=762 0156: dt=110.976000, rms=0.650 (0.042%), neg=0, invalid=762 0157: dt=110.976000, rms=0.650 (0.043%), neg=0, invalid=762 0158: dt=110.976000, rms=0.650 (0.041%), neg=0, invalid=762 0159: dt=110.976000, rms=0.649 (0.038%), neg=0, invalid=762 0160: dt=110.976000, rms=0.649 (0.038%), neg=0, invalid=762 0161: dt=110.976000, rms=0.649 (0.039%), neg=0, invalid=762 0162: dt=110.976000, rms=0.649 (0.040%), neg=0, invalid=762 0163: dt=110.976000, rms=0.648 (0.041%), neg=0, invalid=762 0164: dt=110.976000, rms=0.648 (0.040%), neg=0, invalid=762 0165: dt=110.976000, rms=0.648 (0.038%), neg=0, invalid=762 0166: dt=110.976000, rms=0.648 (0.037%), neg=0, invalid=762 0167: dt=110.976000, rms=0.647 (0.037%), neg=0, invalid=762 0168: dt=110.976000, rms=0.647 (0.035%), neg=0, invalid=762 0169: dt=110.976000, rms=0.647 (0.033%), neg=0, invalid=762 0170: dt=110.976000, rms=0.647 (0.033%), neg=0, invalid=762 0171: dt=110.976000, rms=0.646 (0.032%), neg=0, invalid=762 0172: dt=110.976000, rms=0.646 (0.032%), neg=0, invalid=762 0173: dt=110.976000, rms=0.646 (0.031%), neg=0, invalid=762 0174: dt=110.976000, rms=0.646 (0.030%), neg=0, invalid=762 0175: dt=110.976000, rms=0.646 (0.028%), neg=0, invalid=762 0176: dt=110.976000, rms=0.645 (0.028%), neg=0, invalid=762 0177: dt=110.976000, rms=0.645 (0.027%), neg=0, invalid=762 0178: dt=110.976000, rms=0.645 (0.026%), neg=0, invalid=762 0179: dt=110.976000, rms=0.645 (0.028%), neg=0, invalid=762 0180: dt=110.976000, rms=0.645 (0.027%), neg=0, invalid=762 0181: dt=110.976000, rms=0.645 (0.025%), neg=0, invalid=762 0182: dt=110.976000, rms=0.644 (0.025%), neg=0, invalid=762 0183: dt=110.976000, rms=0.644 (0.025%), neg=0, invalid=762 0184: dt=110.976000, rms=0.644 (0.025%), neg=0, invalid=762 0185: dt=110.976000, rms=0.644 (0.024%), neg=0, invalid=762 0186: dt=2071.552000, rms=0.644 (0.014%), neg=0, invalid=762 0187: dt=2071.552000, rms=0.644 (-4.863%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.645, neg=0, invalid=762 0188: dt=129.472000, rms=0.643 (0.186%), neg=0, invalid=762 0189: dt=443.904000, rms=0.643 (0.082%), neg=0, invalid=762 0190: dt=92.480000, rms=0.643 (0.027%), neg=0, invalid=762 0191: dt=92.480000, rms=0.643 (0.010%), neg=0, invalid=762 0192: dt=92.480000, rms=0.642 (0.014%), neg=0, invalid=762 0193: dt=92.480000, rms=0.642 (0.018%), neg=0, invalid=762 0194: dt=92.480000, rms=0.642 (0.023%), neg=0, invalid=762 0195: dt=92.480000, rms=0.642 (0.028%), neg=0, invalid=762 0196: dt=92.480000, rms=0.642 (0.028%), neg=0, invalid=762 0197: dt=92.480000, rms=0.642 (0.024%), neg=0, invalid=762 0198: dt=92.480000, rms=0.642 (0.023%), neg=0, invalid=762 0199: dt=517.888000, rms=0.641 (0.009%), neg=0, invalid=762 0200: dt=517.888000, rms=0.641 (0.029%), neg=0, invalid=762 0201: dt=517.888000, rms=0.641 (-0.117%), neg=0, invalid=762 0202: dt=55.488000, rms=0.641 (0.004%), neg=0, invalid=762 0203: dt=55.488000, rms=0.641 (-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=0.643, neg=0, invalid=762 0204: dt=199.804878, rms=0.636 (1.022%), neg=0, invalid=762 0205: dt=103.680000, rms=0.630 (0.922%), neg=0, invalid=762 0206: dt=62.208000, rms=0.627 (0.460%), neg=0, invalid=762 0207: dt=145.152000, rms=0.624 (0.574%), neg=0, invalid=762 0208: dt=62.208000, rms=0.622 (0.353%), neg=0, invalid=762 0209: dt=145.152000, rms=0.619 (0.399%), neg=0, invalid=762 0210: dt=36.288000, rms=0.617 (0.269%), neg=0, invalid=762 0211: dt=497.664000, rms=0.612 (0.811%), neg=0, invalid=762 0212: dt=36.288000, rms=0.609 (0.514%), neg=0, invalid=762 0213: dt=76.952381, rms=0.608 (0.242%), neg=0, invalid=762 0214: dt=82.944000, rms=0.607 (0.146%), neg=0, invalid=762 0215: dt=103.680000, rms=0.606 (0.169%), neg=0, invalid=762 0216: dt=36.288000, rms=0.605 (0.105%), neg=0, invalid=762 0217: dt=580.608000, rms=0.602 (0.611%), neg=0, invalid=762 0218: dt=36.288000, rms=0.600 (0.253%), neg=0, invalid=762 0219: dt=145.152000, rms=0.599 (0.158%), neg=0, invalid=762 0220: dt=36.288000, rms=0.599 (0.092%), neg=0, invalid=762 0221: dt=414.720000, rms=0.597 (0.222%), neg=0, invalid=762 0222: dt=36.288000, rms=0.596 (0.217%), neg=0, invalid=762 0223: dt=145.152000, rms=0.595 (0.144%), neg=0, invalid=762 0224: dt=36.288000, rms=0.595 (0.066%), neg=0, invalid=762 0225: dt=331.776000, rms=0.594 (0.156%), neg=0, invalid=762 0226: dt=36.288000, rms=0.593 (0.145%), neg=0, invalid=762 0227: dt=145.152000, rms=0.592 (0.137%), neg=0, invalid=762 0228: dt=36.288000, rms=0.592 (0.043%), neg=0, invalid=762 0229: dt=36.288000, rms=0.592 (0.029%), neg=0, invalid=762 0230: dt=36.288000, rms=0.591 (0.049%), neg=0, invalid=762 0231: dt=36.288000, rms=0.591 (0.077%), neg=0, invalid=762 0232: dt=36.288000, rms=0.590 (0.104%), neg=0, invalid=762 0233: dt=36.288000, rms=0.590 (0.123%), neg=0, invalid=762 0234: dt=36.288000, rms=0.589 (0.134%), neg=0, invalid=762 0235: dt=36.288000, rms=0.588 (0.138%), neg=0, invalid=762 0236: dt=36.288000, rms=0.587 (0.145%), neg=0, invalid=762 0237: dt=36.288000, rms=0.586 (0.148%), neg=0, invalid=762 0238: dt=36.288000, rms=0.585 (0.155%), neg=0, invalid=762 0239: dt=36.288000, rms=0.584 (0.157%), neg=0, invalid=762 0240: dt=36.288000, rms=0.583 (0.154%), neg=0, invalid=762 0241: dt=36.288000, rms=0.583 (0.155%), neg=0, invalid=762 0242: dt=36.288000, rms=0.582 (0.149%), neg=0, invalid=762 0243: dt=36.288000, rms=0.581 (0.140%), neg=0, invalid=762 0244: dt=36.288000, rms=0.581 (0.014%), neg=0, invalid=762 0245: dt=36.288000, rms=0.581 (0.025%), neg=0, invalid=762 0246: dt=36.288000, rms=0.580 (0.037%), neg=0, invalid=762 0247: dt=36.288000, rms=0.580 (0.049%), neg=0, invalid=762 0248: dt=36.288000, rms=0.580 (0.059%), neg=0, invalid=762 0249: dt=36.288000, rms=0.579 (0.068%), neg=0, invalid=762 0250: dt=36.288000, rms=0.579 (0.071%), neg=0, invalid=762 0251: dt=36.288000, rms=0.579 (0.074%), neg=0, invalid=762 0252: dt=36.288000, rms=0.578 (0.078%), neg=0, invalid=762 0253: dt=36.288000, rms=0.578 (0.082%), neg=0, invalid=762 0254: dt=36.288000, rms=0.577 (0.087%), neg=0, invalid=762 0255: dt=36.288000, rms=0.577 (0.011%), neg=0, invalid=762 0256: dt=36.288000, rms=0.577 (0.022%), neg=0, invalid=762 0257: dt=36.288000, rms=0.577 (0.030%), neg=0, invalid=762 0258: dt=36.288000, rms=0.577 (0.010%), neg=0, invalid=762 0259: dt=36.288000, rms=0.577 (0.010%), neg=0, invalid=762 0260: dt=9.072000, rms=0.577 (0.003%), neg=0, invalid=762 0261: dt=2.268000, rms=0.577 (0.001%), neg=0, invalid=762 0262: dt=2.268000, rms=0.577 (0.001%), neg=0, invalid=762 0263: dt=0.141750, rms=0.577 (0.000%), neg=0, invalid=762 0264: dt=0.070875, rms=0.577 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.577, neg=0, invalid=762 0265: dt=145.152000, rms=0.574 (0.527%), neg=0, invalid=762 0266: dt=82.944000, rms=0.574 (0.113%), neg=0, invalid=762 0267: dt=124.416000, rms=0.573 (0.107%), neg=0, invalid=762 0268: dt=36.288000, rms=0.573 (0.060%), neg=0, invalid=762 0269: dt=331.776000, rms=0.572 (0.138%), neg=0, invalid=762 0270: dt=36.288000, rms=0.571 (0.091%), neg=0, invalid=762 0271: dt=145.152000, rms=0.571 (0.056%), neg=0, invalid=762 0272: dt=62.208000, rms=0.571 (0.033%), neg=0, invalid=762 0273: dt=62.208000, rms=0.571 (0.031%), neg=0, invalid=762 0274: dt=62.208000, rms=0.571 (0.045%), neg=0, invalid=762 0275: dt=62.208000, rms=0.570 (0.063%), neg=0, invalid=762 0276: dt=62.208000, rms=0.570 (0.072%), neg=0, invalid=762 0277: dt=62.208000, rms=0.570 (0.023%), neg=0, invalid=762 0278: dt=31.104000, rms=0.570 (0.009%), neg=0, invalid=762 0279: dt=25.920000, rms=0.569 (0.009%), neg=0, invalid=762 0280: dt=1.620000, rms=0.569 (0.001%), neg=0, invalid=762 0281: dt=0.101250, rms=0.569 (0.000%), neg=0, invalid=762 0282: dt=0.050625, rms=0.569 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.577, neg=0, invalid=762 0283: dt=79.520958, rms=0.570 (1.375%), neg=0, invalid=762 0284: dt=55.334917, rms=0.561 (1.575%), neg=0, invalid=762 0285: dt=22.456140, rms=0.557 (0.683%), neg=0, invalid=762 0286: dt=225.676538, rms=0.547 (1.770%), neg=0, invalid=762 0287: dt=23.746479, rms=0.541 (1.082%), neg=0, invalid=762 0288: dt=44.800000, rms=0.539 (0.362%), neg=0, invalid=762 0289: dt=32.000000, rms=0.538 (0.125%), neg=0, invalid=762 0290: dt=44.800000, rms=0.537 (0.183%), neg=0, invalid=762 0291: dt=25.600000, rms=0.537 (0.148%), neg=0, invalid=762 0292: dt=38.400000, rms=0.536 (0.120%), neg=0, invalid=762 0293: dt=32.000000, rms=0.535 (0.150%), neg=0, invalid=762 0294: dt=25.600000, rms=0.535 (0.104%), neg=0, invalid=762 0295: dt=44.800000, rms=0.534 (0.137%), neg=0, invalid=762 0296: dt=2.800000, rms=0.534 (0.016%), neg=0, invalid=762 0297: dt=0.087500, rms=0.534 (0.004%), neg=0, invalid=762 0298: dt=0.010937, rms=0.534 (0.000%), neg=0, invalid=762 0299: dt=0.005469, rms=0.534 (0.000%), neg=0, invalid=762 0300: dt=0.002734, rms=0.534 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0301: dt=32.000000, rms=0.532 (0.437%), neg=0, invalid=762 0302: dt=32.000000, rms=0.531 (0.235%), neg=0, invalid=762 0303: dt=25.600000, rms=0.530 (0.113%), neg=0, invalid=762 0304: dt=32.000000, rms=0.529 (0.134%), neg=0, invalid=762 0305: dt=25.600000, rms=0.529 (0.072%), neg=0, invalid=762 0306: dt=32.000000, rms=0.528 (0.105%), neg=0, invalid=762 0307: dt=19.200000, rms=0.528 (0.058%), neg=0, invalid=762 0308: dt=44.800000, rms=0.527 (0.121%), neg=0, invalid=762 0309: dt=25.600000, rms=0.527 (0.044%), neg=0, invalid=762 0310: dt=25.600000, rms=0.527 (0.085%), neg=0, invalid=762 0311: dt=25.600000, rms=0.526 (0.111%), neg=0, invalid=762 0312: dt=25.600000, rms=0.525 (0.139%), neg=0, invalid=762 0313: dt=25.600000, rms=0.525 (0.077%), neg=0, invalid=762 0314: dt=25.600000, rms=0.524 (0.098%), neg=0, invalid=762 0315: dt=25.600000, rms=0.524 (0.121%), neg=0, invalid=762 0316: dt=25.600000, rms=0.523 (0.187%), neg=0, invalid=762 0317: dt=25.600000, rms=0.522 (0.191%), neg=0, invalid=762 0318: dt=25.600000, rms=0.521 (0.201%), neg=0, invalid=762 0319: dt=25.600000, rms=0.520 (0.191%), neg=0, invalid=762 0320: dt=25.600000, rms=0.519 (0.228%), neg=0, invalid=762 0321: dt=25.600000, rms=0.519 (0.026%), neg=0, invalid=762 0322: dt=25.600000, rms=0.518 (0.053%), neg=0, invalid=762 0323: dt=25.600000, rms=0.518 (0.071%), neg=0, invalid=762 0324: dt=25.600000, rms=0.517 (0.087%), neg=0, invalid=762 0325: dt=25.600000, rms=0.517 (0.094%), neg=0, invalid=762 0326: dt=25.600000, rms=0.516 (0.107%), neg=0, invalid=762 0327: dt=25.600000, rms=0.516 (0.111%), neg=0, invalid=762 0328: dt=25.600000, rms=0.515 (0.117%), neg=0, invalid=762 0329: dt=25.600000, rms=0.515 (0.128%), neg=0, invalid=762 0330: dt=25.600000, rms=0.514 (0.012%), neg=0, invalid=762 0331: dt=25.600000, rms=0.514 (0.035%), neg=0, invalid=762 0332: dt=25.600000, rms=0.514 (0.020%), neg=0, invalid=762 0333: dt=3.200000, rms=0.514 (-0.002%), neg=0, invalid=762 0334: dt=2.800000, rms=0.514 (0.002%), neg=0, invalid=762 0335: dt=2.000000, rms=0.514 (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=0.534, neg=0, invalid=762 0336: dt=0.000000, rms=0.534 (0.127%), neg=0, invalid=762 0337: dt=0.000000, rms=0.534 (0.000%), neg=0, invalid=762 0338: dt=0.150000, rms=0.534 (-0.017%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0339: dt=0.000000, rms=0.534 (0.127%), neg=0, invalid=762 0340: dt=0.000000, rms=0.534 (0.000%), neg=0, invalid=762 0341: dt=0.150000, rms=0.534 (-0.018%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.573, neg=0, invalid=762 0342: dt=1.024000, rms=0.571 (0.458%), neg=0, invalid=762 0343: dt=0.256000, rms=0.571 (0.013%), neg=0, invalid=762 0344: dt=0.256000, rms=0.571 (-0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.571, neg=0, invalid=762 0345: dt=0.448000, rms=0.570 (0.161%), neg=0, invalid=762 0346: dt=0.112000, rms=0.570 (0.005%), neg=0, invalid=762 0347: dt=0.112000, rms=0.570 (0.001%), neg=0, invalid=762 0348: dt=0.112000, rms=0.570 (-0.006%), 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=0.522, neg=0, invalid=762 0349: dt=0.448000, rms=0.508 (2.724%), neg=0, invalid=762 0350: dt=0.448000, rms=0.505 (0.619%), neg=0, invalid=762 0351: dt=0.448000, rms=0.503 (0.352%), neg=0, invalid=762 0352: dt=0.448000, rms=0.502 (0.216%), neg=0, invalid=762 0353: dt=0.466667, rms=0.501 (0.163%), neg=0, invalid=762 0354: dt=0.448000, rms=0.500 (0.112%), neg=0, invalid=762 0355: dt=0.448000, rms=0.500 (0.092%), neg=0, invalid=762 0356: dt=0.448000, rms=0.500 (0.068%), neg=0, invalid=762 0357: dt=0.448000, rms=0.499 (0.062%), neg=0, invalid=762 0358: dt=0.448000, rms=0.499 (0.047%), neg=0, invalid=762 0359: dt=0.448000, rms=0.499 (0.042%), neg=0, invalid=762 0360: dt=0.448000, rms=0.498 (0.070%), neg=0, invalid=762 0361: dt=0.448000, rms=0.498 (0.085%), neg=0, invalid=762 0362: dt=0.448000, rms=0.498 (0.087%), neg=0, invalid=762 0363: dt=0.448000, rms=0.497 (0.077%), neg=0, invalid=762 0364: dt=0.448000, rms=0.497 (0.057%), neg=0, invalid=762 0365: dt=0.448000, rms=0.497 (0.037%), neg=0, invalid=762 0366: dt=0.448000, rms=0.497 (-0.009%), neg=0, invalid=762 0367: dt=0.000000, rms=0.497 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.498, neg=0, invalid=762 0368: dt=0.448000, rms=0.493 (0.964%), neg=0, invalid=762 0369: dt=0.448000, rms=0.492 (0.054%), neg=0, invalid=762 0370: dt=0.448000, rms=0.492 (0.014%), neg=0, invalid=762 0371: dt=0.448000, rms=0.492 (-0.013%), 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=0.491, neg=0, invalid=762 0372: dt=0.000000, rms=0.490 (0.158%), neg=0, invalid=762 0373: dt=0.000000, rms=0.490 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=762 0374: dt=295.936000, rms=0.490 (0.194%), neg=0, invalid=762 0375: dt=73.984000, rms=0.490 (0.010%), neg=0, invalid=762 0376: dt=73.984000, rms=0.490 (0.008%), neg=0, invalid=762 0377: dt=73.984000, rms=0.490 (0.007%), neg=0, invalid=762 0378: dt=73.984000, rms=0.490 (0.010%), neg=0, invalid=762 0379: dt=73.984000, rms=0.490 (0.013%), neg=0, invalid=762 0380: dt=73.984000, rms=0.489 (0.014%), neg=0, invalid=762 0381: dt=73.984000, rms=0.489 (0.012%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0382: dt=36.288000, rms=0.489 (0.200%), neg=0, invalid=762 0383: dt=36.288000, rms=0.489 (0.022%), neg=0, invalid=762 0384: dt=36.288000, rms=0.489 (0.014%), neg=0, invalid=762 0385: dt=36.288000, rms=0.489 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0386: dt=124.416000, rms=0.488 (0.457%), neg=0, invalid=762 0387: dt=36.288000, rms=0.487 (0.103%), neg=0, invalid=762 0388: dt=36.288000, rms=0.487 (0.045%), neg=0, invalid=762 0389: dt=36.288000, rms=0.487 (0.063%), neg=0, invalid=762 0390: dt=36.288000, rms=0.486 (0.079%), neg=0, invalid=762 0391: dt=36.288000, rms=0.486 (0.096%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0392: dt=36.288000, rms=0.485 (0.106%), neg=0, invalid=762 0393: dt=36.288000, rms=0.485 (0.096%), neg=0, invalid=762 0394: dt=36.288000, rms=0.484 (0.086%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0395: dt=124.416000, rms=0.484 (0.019%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.485, neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0396: dt=44.800000, rms=0.482 (0.665%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0397: dt=38.400000, rms=0.480 (0.379%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0398: dt=25.474510, rms=0.479 (0.267%), neg=0, invalid=762 0399: dt=23.200000, rms=0.478 (0.147%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0400: dt=23.200000, rms=0.477 (0.163%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0401: dt=23.200000, rms=0.476 (0.224%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 0402: dt=23.200000, rms=0.475 (0.186%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0403: dt=23.200000, rms=0.474 (0.261%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 11 iterations, nbhd size=1, neg = 0 0404: dt=23.200000, rms=0.473 (0.205%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0405: dt=23.200000, rms=0.472 (0.200%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 14 iterations, nbhd size=1, neg = 0 0406: dt=23.200000, rms=0.472 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 4 iterations, nbhd size=0, neg = 0 0407: dt=23.200000, rms=0.471 (0.192%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 3 iterations, nbhd size=0, neg = 0 0408: dt=23.200000, rms=0.470 (0.191%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0409: dt=23.200000, rms=0.469 (0.180%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0410: dt=23.200000, rms=0.469 (0.114%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0411: dt=23.200000, rms=0.468 (0.155%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0412: dt=23.200000, rms=0.467 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 10 iterations, nbhd size=1, neg = 0 0413: dt=23.200000, rms=0.467 (0.121%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0414: dt=23.200000, rms=0.466 (0.066%), neg=0, invalid=762 0415: dt=11.200000, rms=0.466 (0.074%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0416: dt=76.800000, rms=0.466 (0.063%), neg=0, invalid=762 0417: dt=76.800000, rms=0.466 (-0.341%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=762 0418: dt=38.400000, rms=0.463 (0.709%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0419: dt=25.600000, rms=0.462 (0.185%), neg=0, invalid=762 0420: dt=25.600000, rms=0.462 (0.147%), neg=0, invalid=762 0421: dt=25.600000, rms=0.461 (0.181%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0422: dt=25.600000, rms=0.460 (0.096%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 0423: dt=25.600000, rms=0.460 (0.157%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0424: dt=25.600000, rms=0.459 (0.043%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0425: dt=25.600000, rms=0.459 (0.034%), neg=0, invalid=762 0426: dt=11.200000, rms=0.459 (0.052%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0427: dt=44.800000, rms=0.459 (0.066%), neg=0, invalid=762 0428: dt=11.200000, rms=0.459 (0.016%), neg=0, invalid=762 0429: dt=11.200000, rms=0.459 (0.010%), neg=0, invalid=762 0430: dt=11.200000, rms=0.459 (0.015%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0431: dt=11.200000, rms=0.458 (0.023%), neg=0, invalid=762 0432: dt=11.200000, rms=0.458 (0.025%), neg=0, invalid=762 0433: dt=11.200000, rms=0.458 (0.021%), neg=0, invalid=762 0434: dt=11.200000, rms=0.458 (0.025%), neg=0, invalid=762 0435: dt=11.200000, rms=0.458 (0.022%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=762 0436: dt=0.000000, rms=0.464 (0.173%), neg=0, invalid=762 0437: dt=0.000000, rms=0.464 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.465, neg=0, invalid=762 0438: dt=2.304000, rms=0.464 (0.187%), neg=0, invalid=762 0439: dt=1.008000, rms=0.464 (0.005%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0440: dt=1.008000, rms=0.464 (-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=0.475, neg=0, invalid=762 0441: dt=1.280000, rms=0.474 (0.352%), neg=0, invalid=762 0442: dt=0.112000, rms=0.474 (0.002%), neg=0, invalid=762 0443: dt=0.112000, rms=0.474 (0.004%), neg=0, invalid=762 0444: dt=0.112000, rms=0.474 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=762 0445: dt=1.536000, rms=0.473 (0.336%), neg=0, invalid=762 0446: dt=0.448000, rms=0.473 (0.014%), neg=0, invalid=762 0447: dt=0.448000, rms=0.473 (0.005%), neg=0, invalid=762 0448: dt=0.448000, rms=0.473 (-0.014%), 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=0.465, neg=0, invalid=762 iter 0, gcam->neg = 709 after 16 iterations, nbhd size=1, neg = 0 0449: dt=2.292771, rms=0.434 (6.731%), neg=0, invalid=762 0450: dt=0.096000, rms=0.434 (0.075%), neg=0, invalid=762 0451: dt=0.096000, rms=0.434 (-0.063%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=762 0452: dt=0.080000, rms=0.433 (0.254%), neg=0, invalid=762 0453: dt=0.000000, rms=0.433 (0.001%), neg=0, invalid=762 0454: dt=0.050000, rms=0.433 (-0.017%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0455: 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 0456: dt=55.488000, rms=0.418 (0.005%), neg=0, invalid=762 0457: dt=92.480000, rms=0.418 (0.002%), neg=0, invalid=762 0458: dt=92.480000, rms=0.418 (0.001%), neg=0, invalid=762 0459: dt=92.480000, rms=0.418 (0.001%), neg=0, invalid=762 0460: dt=92.480000, rms=0.418 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0461: dt=-0.001465, rms=0.418 (0.000%), neg=0, invalid=762 0462: 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 0463: dt=145.152000, rms=0.418 (0.080%), neg=0, invalid=762 0464: dt=145.152000, rms=0.418 (0.050%), neg=0, invalid=762 0465: dt=145.152000, rms=0.418 (-0.013%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0466: dt=11.200000, rms=0.418 (0.097%), neg=0, invalid=762 0467: dt=11.200000, rms=0.418 (0.039%), neg=0, invalid=762 0468: dt=11.200000, rms=0.418 (0.015%), neg=0, invalid=762 0469: dt=11.200000, rms=0.418 (-0.028%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0470: dt=60.595745, rms=0.416 (0.512%), neg=0, invalid=762 0471: dt=25.600000, rms=0.415 (0.255%), neg=0, invalid=762 0472: dt=44.800000, rms=0.414 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 9 iterations, nbhd size=1, neg = 0 0473: dt=44.800000, rms=0.414 (0.036%), neg=0, invalid=762 0474: dt=44.800000, rms=0.413 (0.321%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0475: dt=44.800000, rms=0.412 (0.144%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0476: dt=44.800000, rms=0.411 (0.248%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0477: dt=44.800000, rms=0.410 (0.221%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0478: dt=44.800000, rms=0.410 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0479: dt=44.800000, rms=0.409 (0.201%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 11 iterations, nbhd size=1, neg = 0 0480: dt=44.800000, rms=0.408 (0.085%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0481: dt=44.800000, rms=0.408 (0.121%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0482: dt=44.800000, rms=0.408 (0.119%), neg=0, invalid=762 0483: dt=25.600000, rms=0.407 (0.014%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=0, neg = 0 0484: dt=25.600000, rms=0.407 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0485: dt=25.600000, rms=0.407 (0.009%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0486: dt=25.600000, rms=0.407 (0.010%), neg=0, invalid=762 0487: dt=25.600000, rms=0.407 (0.004%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0488: dt=25.600000, rms=0.407 (0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.412, neg=0, invalid=762 0489: dt=0.000246, rms=0.412 (0.000%), neg=0, invalid=762 0490: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.412, neg=0, invalid=762 0491: dt=1.500000, rms=0.412 (0.005%), neg=0, invalid=762 0492: dt=0.750000, rms=0.412 (0.001%), neg=0, invalid=762 0493: dt=0.750000, rms=0.412 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.421, neg=0, invalid=762 0494: dt=0.000000, rms=0.421 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.421, neg=0, invalid=762 0495: dt=0.000000, rms=0.421 (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=0.406, neg=0, invalid=762 iter 0, gcam->neg = 638 after 20 iterations, nbhd size=1, neg = 0 0496: dt=1.280000, rms=0.397 (2.251%), neg=0, invalid=762 0497: dt=0.000013, rms=0.397 (0.000%), neg=0, invalid=762 0498: dt=0.000013, rms=0.397 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.397, neg=0, invalid=762 0499: dt=0.096000, rms=0.396 (0.045%), neg=0, invalid=762 0500: dt=0.028000, rms=0.396 (0.005%), neg=0, invalid=762 0501: dt=0.028000, rms=0.396 (0.003%), neg=0, invalid=762 0502: dt=0.028000, rms=0.396 (-0.005%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 53 minutes and 53 seconds. mri_ca_register utimesec 11318.304356 mri_ca_register stimesec 11.715219 mri_ca_register ru_maxrss 1343100 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4785063 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63592 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 10632 mri_ca_register ru_nivcsw 36667 FSRUNTIME@ mri_ca_register 2.8981 hours 2 threads #-------------------------------------- #@# SubCort Seg Sun Oct 8 06:33:35 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-114 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-6.0.0/0050490/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 2 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.14 Atlas used for the 3D morph was /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.09531 (16) Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (1326 voxels, overlap=0.741) Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (1326 voxels, peak = 15), gca=15.3 gca peak = 0.17677 (13) mri peak = 0.09173 (18) Right_Lateral_Ventricle (43): linear fit = 1.20 x + 0.0 (1316 voxels, overlap=0.866) Right_Lateral_Ventricle (43): linear fit = 1.20 x + 0.0 (1316 voxels, peak = 16), gca=15.5 gca peak = 0.28129 (95) mri peak = 0.09444 (91) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (715 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (715 voxels, peak = 92), gca=91.7 gca peak = 0.16930 (96) mri peak = 0.10200 (95) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (798 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (798 voxels, peak = 96), gca=95.5 gca peak = 0.24553 (55) mri peak = 0.09026 (60) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (981 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (981 voxels, peak = 59), gca=59.1 gca peak = 0.30264 (59) mri peak = 0.09751 (63) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (968 voxels, overlap=1.009) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (968 voxels, peak = 62), gca=61.7 gca peak = 0.07580 (103) mri peak = 0.12302 (105) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (44092 voxels, overlap=0.597) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (44092 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.10848 (105) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46449 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46449 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.04938 (52) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (38278 voxels, overlap=0.978) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (38278 voxels, peak = 56), gca=56.0 gca peak = 0.11620 (58) mri peak = 0.04476 (52) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (37424 voxels, overlap=0.984) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (37424 voxels, peak = 56), gca=56.0 gca peak = 0.30970 (66) mri peak = 0.09771 (74) Right_Caudate (50): linear fit = 1.07 x + 0.0 (1269 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.07 x + 0.0 (1269 voxels, peak = 70), gca=70.3 gca peak = 0.15280 (69) mri peak = 0.10579 (72) Left_Caudate (11): linear fit = 0.96 x + 0.0 (1190 voxels, overlap=0.937) Left_Caudate (11): linear fit = 0.96 x + 0.0 (1190 voxels, peak = 67), gca=66.6 gca peak = 0.13902 (56) mri peak = 0.04663 (59) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (26156 voxels, overlap=0.984) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (26156 voxels, peak = 59), gca=58.5 gca peak = 0.14777 (55) mri peak = 0.05413 (59) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (30314 voxels, overlap=0.987) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (30314 voxels, peak = 59), gca=58.6 gca peak = 0.16765 (84) mri peak = 0.09096 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6077 voxels, overlap=0.865) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6077 voxels, peak = 89), gca=88.6 gca peak = 0.18739 (84) mri peak = 0.09687 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6138 voxels, overlap=0.862) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6138 voxels, peak = 87), gca=86.9 gca peak = 0.29869 (57) mri peak = 0.08256 (59) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (591 voxels, overlap=1.031) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (591 voxels, peak = 60), gca=59.6 gca peak = 0.33601 (57) mri peak = 0.11715 (62) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (468 voxels, overlap=0.999) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (468 voxels, peak = 60), gca=59.6 gca peak = 0.11131 (90) mri peak = 0.06079 (90) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5210 voxels, overlap=0.953) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5210 voxels, peak = 91), gca=91.3 gca peak = 0.11793 (83) mri peak = 0.06680 (90) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4970 voxels, overlap=0.979) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4970 voxels, peak = 87), gca=86.7 gca peak = 0.08324 (81) mri peak = 0.07906 (81) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2754 voxels, overlap=0.905) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2754 voxels, peak = 81), gca=81.0 gca peak = 0.10360 (77) mri peak = 0.07630 (80) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2824 voxels, overlap=0.984) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2824 voxels, peak = 76), gca=75.8 gca peak = 0.08424 (78) mri peak = 0.08097 (87) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12302 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12302 voxels, peak = 85), gca=85.4 gca peak = 0.12631 (89) mri peak = 0.07186 (92) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1436 voxels, overlap=0.786) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1436 voxels, peak = 97), gca=96.6 gca peak = 0.14500 (87) mri peak = 0.06384 (93) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1557 voxels, overlap=0.844) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1557 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) mri peak = 0.12633 (18) gca peak = 0.19357 (14) mri peak = 0.12961 (18) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (279 voxels, overlap=0.815) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (279 voxels, peak = 14), gca=14.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.18464 (14) mri peak = 0.09531 (16) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (1326 voxels, overlap=0.958) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (1326 voxels, peak = 14), gca=14.5 gca peak = 0.16350 (15) mri peak = 0.09173 (18) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (1316 voxels, overlap=0.710) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (1316 voxels, peak = 16), gca=15.5 gca peak = 0.26422 (90) mri peak = 0.09444 (91) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (715 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (715 voxels, peak = 90), gca=89.6 gca peak = 0.18432 (96) mri peak = 0.10200 (95) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (798 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (798 voxels, peak = 97), gca=97.4 gca peak = 0.27675 (60) mri peak = 0.09026 (60) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (981 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (981 voxels, peak = 59), gca=59.1 gca peak = 0.31447 (59) mri peak = 0.09751 (63) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (968 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (968 voxels, peak = 60), gca=59.9 gca peak = 0.07772 (104) mri peak = 0.12302 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (44092 voxels, overlap=0.666) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (44092 voxels, peak = 104), gca=104.0 gca peak = 0.07686 (107) mri peak = 0.10848 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46449 voxels, overlap=0.722) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46449 voxels, peak = 106), gca=106.5 gca peak = 0.10057 (56) mri peak = 0.04938 (52) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (38278 voxels, overlap=0.989) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (38278 voxels, peak = 57), gca=57.4 gca peak = 0.11969 (56) mri peak = 0.04476 (52) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (37424 voxels, overlap=0.973) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (37424 voxels, peak = 59), gca=58.5 gca peak = 0.26195 (71) mri peak = 0.09771 (74) Right_Caudate (50): linear fit = 1.03 x + 0.0 (1269 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.03 x + 0.0 (1269 voxels, peak = 73), gca=73.5 gca peak = 0.14125 (66) mri peak = 0.10579 (72) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1190 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1190 voxels, peak = 66), gca=66.0 gca peak = 0.13225 (57) mri peak = 0.04663 (59) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (26156 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (26156 voxels, peak = 58), gca=58.4 gca peak = 0.13860 (58) mri peak = 0.05413 (59) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (30314 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (30314 voxels, peak = 59), gca=59.4 gca peak = 0.16050 (89) mri peak = 0.09096 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6077 voxels, overlap=0.979) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6077 voxels, peak = 89), gca=88.6 gca peak = 0.18302 (87) mri peak = 0.09687 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6138 voxels, overlap=0.963) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6138 voxels, peak = 87), gca=86.6 gca peak = 0.26844 (61) mri peak = 0.08256 (59) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (591 voxels, overlap=1.020) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (591 voxels, peak = 63), gca=62.5 gca peak = 0.31426 (60) mri peak = 0.11715 (62) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (468 voxels, overlap=1.024) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (468 voxels, peak = 62), gca=61.5 gca peak = 0.11210 (90) mri peak = 0.06079 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5210 voxels, overlap=0.973) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5210 voxels, peak = 90), gca=89.6 gca peak = 0.09869 (90) mri peak = 0.06680 (90) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4970 voxels, overlap=0.996) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4970 voxels, peak = 92), gca=92.2 gca peak = 0.08313 (81) mri peak = 0.07906 (81) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2754 voxels, overlap=0.905) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2754 voxels, peak = 81), gca=81.0 gca peak = 0.09873 (76) mri peak = 0.07630 (80) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2824 voxels, overlap=0.938) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2824 voxels, peak = 78), gca=77.9 gca peak = 0.07843 (86) mri peak = 0.08097 (87) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12302 voxels, overlap=0.767) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12302 voxels, peak = 86), gca=86.4 gca peak = 0.10980 (96) mri peak = 0.07186 (92) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1436 voxels, overlap=0.879) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1436 voxels, peak = 96), gca=95.5 gca peak = 0.17061 (92) mri peak = 0.06384 (93) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1557 voxels, overlap=0.934) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1557 voxels, peak = 92), gca=91.5 gca peak = 0.16923 (26) mri peak = 0.12633 (18) gca peak = 0.18343 (17) mri peak = 0.12961 (18) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (279 voxels, overlap=0.796) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (279 voxels, peak = 17), gca=17.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16507 (28) gca peak Left_Thalamus = 1.00000 (96) gca peak Third_Ventricle = 0.16923 (26) gca peak CSF = 0.23651 (36) gca peak Left_Accumbens_area = 0.81130 (60) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24205 (25) gca peak Right_Accumbens_area = 0.29950 (69) 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 = 0.07134 (78) gca peak non_WM_hypointensities = 0.08683 (44) gca peak Optic_Chiasm = 0.70610 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.03 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 63163 voxels changed in iteration 0 of unlikely voxel relabeling 198 voxels changed in iteration 1 of unlikely voxel relabeling 10 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 35010 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 368 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 71539 changed. image ll: -2.124, PF=0.500 pass 2: 20395 changed. image ll: -2.124, PF=0.500 pass 3: 6675 changed. pass 4: 2379 changed. 37445 voxels changed in iteration 0 of unlikely voxel relabeling 192 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 6548 voxels changed in iteration 0 of unlikely voxel relabeling 77 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 5766 voxels changed in iteration 0 of unlikely voxel relabeling 47 voxels changed in iteration 1 of unlikely voxel relabeling 10 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4782 voxels changed in iteration 0 of unlikely voxel relabeling 24 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 4547.695645 mri_ca_label stimesec 5.390180 mri_ca_label ru_maxrss 2100388 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 829856 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 512 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 381 mri_ca_label ru_nivcsw 15328 auto-labeling took 75 minutes and 6 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/transforms/cc_up.lta 0050490 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-6.0.0/0050490/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/norm.mgz 53197 voxels in left wm, 58180 in right wm, xrange [119, 130] searching rotation angles z=[-7 7], y=[-4 10] searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 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 global minimum found at slice 125.0, rotations (3.04, 0.41) final transformation (x=125.0, yr=3.037, zr=0.410): 0.99857 -0.00716 0.05298 -1.43615; 0.00715 0.99997 0.00038 39.07113; -0.05298 -0.00000 0.99860 35.76150; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 88 99 eigenvectors: 0.00004 -0.00129 1.00000; -0.08572 -0.99632 -0.00128; 0.99632 -0.08572 -0.00015; error in mid anterior detected - correcting... writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aseg.auto.mgz... corpus callosum segmentation took 1.3 minutes #-------------------------------------- #@# Merge ASeg Sun Oct 8 07:49:58 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sun Oct 8 07:49:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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... 1473 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 58 (58), valley at 0 (-1) csf peak at 29, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 58 (58), valley at 0 (-1) csf peak at 29, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 23 seconds. #-------------------------------------------- #@# Mask BFS Sun Oct 8 07:54:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1746576 voxels in mask (pct= 10.41) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sun Oct 8 07:54:28 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 (105.0): 105.5 +- 4.8 [79.0 --> 125.0] GM (70.0) : 68.5 +- 9.1 [30.0 --> 95.0] setting bottom of white matter range to 77.6 setting top of gray matter range to 86.7 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... 5980 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5134 filled 496 bright non-wm voxels segmented. 3154 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.82 minutes reading wm segmentation from wm.seg.mgz... 307 voxels added to wm to prevent paths from MTL structures to cortex 3105 additional wm voxels added 0 additional wm voxels added SEG EDIT: 50593 voxels turned on, 47427 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+): 11 found - 11 modified | TOTAL: 11 pass 2 (xy+): 0 found - 11 modified | TOTAL: 11 pass 1 (xy-): 17 found - 17 modified | TOTAL: 28 pass 2 (xy-): 0 found - 17 modified | TOTAL: 28 pass 1 (yz+): 9 found - 9 modified | TOTAL: 37 pass 2 (yz+): 0 found - 9 modified | TOTAL: 37 pass 1 (yz-): 18 found - 18 modified | TOTAL: 55 pass 2 (yz-): 0 found - 18 modified | TOTAL: 55 pass 1 (xz+): 7 found - 7 modified | TOTAL: 62 pass 2 (xz+): 0 found - 7 modified | TOTAL: 62 pass 1 (xz-): 10 found - 10 modified | TOTAL: 72 pass 2 (xz-): 0 found - 10 modified | TOTAL: 72 Iteration Number : 1 pass 1 (+++): 7 found - 7 modified | TOTAL: 7 pass 2 (+++): 0 found - 7 modified | TOTAL: 7 pass 1 (+++): 13 found - 13 modified | TOTAL: 20 pass 2 (+++): 0 found - 13 modified | TOTAL: 20 pass 1 (+++): 6 found - 6 modified | TOTAL: 26 pass 2 (+++): 0 found - 6 modified | TOTAL: 26 pass 1 (+++): 20 found - 20 modified | TOTAL: 46 pass 2 (+++): 0 found - 20 modified | TOTAL: 46 Iteration Number : 1 pass 1 (++): 98 found - 98 modified | TOTAL: 98 pass 2 (++): 0 found - 98 modified | TOTAL: 98 pass 1 (+-): 57 found - 57 modified | TOTAL: 155 pass 2 (+-): 0 found - 57 modified | TOTAL: 155 pass 1 (--): 99 found - 99 modified | TOTAL: 254 pass 2 (--): 0 found - 99 modified | TOTAL: 254 pass 1 (-+): 61 found - 61 modified | TOTAL: 315 pass 2 (-+): 0 found - 61 modified | TOTAL: 315 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 5 found - 5 modified | TOTAL: 11 pass 2 (yz+): 0 found - 5 modified | TOTAL: 11 pass 1 (yz-): 3 found - 3 modified | TOTAL: 14 pass 2 (yz-): 0 found - 3 modified | TOTAL: 14 pass 1 (xz+): 6 found - 6 modified | TOTAL: 20 pass 2 (xz+): 0 found - 6 modified | TOTAL: 20 pass 1 (xz-): 2 found - 2 modified | TOTAL: 22 pass 2 (xz-): 0 found - 2 modified | TOTAL: 22 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 (+-): 5 found - 5 modified | TOTAL: 5 pass 2 (+-): 0 found - 5 modified | TOTAL: 5 pass 1 (--): 2 found - 2 modified | TOTAL: 7 pass 2 (--): 0 found - 2 modified | TOTAL: 7 pass 1 (-+): 0 found - 0 modified | TOTAL: 7 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 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 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 464 (out of 598344: 0.077547) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sun Oct 8 07:57:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 1.04809 -0.00502 0.08632 -13.30034; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86054; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.04809 -0.00502 0.08632 -13.30034; -0.01272 1.07313 0.26244 -19.71896; -0.11331 -0.22127 0.93285 46.86054; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1143 (min = 350, max = 1400), aspect = 0.60 (min = 0.10, max = 0.75) no need to search using seed (126, 114, 89), TAL = (2.0, -39.0, 14.0) talairach voxel to voxel transform 0.94490 -0.01286 -0.08382 16.24174; -0.01594 0.88098 -0.24637 28.70499; 0.11099 0.20741 1.00337 -41.45222; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 114, 89) --> (2.0, -39.0, 14.0) done. writing output to filled.mgz... filling took 1.3 minutes talairach cc position changed to (2.00, -39.00, 14.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -39.00, 14.00) SRC: (109.36, 105.49, 83.48) search lh wm seed point around talairach space (-16.00, -39.00, 14.00), SRC: (143.38, 104.91, 87.47) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sun Oct 8 07:58:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 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 = 2 (out of 286167: 0.000699) 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 30: 665 vertices, 768 faces slice 40: 6929 vertices, 7200 faces slice 50: 16085 vertices, 16430 faces slice 60: 27421 vertices, 27815 faces slice 70: 39321 vertices, 39729 faces slice 80: 50975 vertices, 51374 faces slice 90: 62652 vertices, 63078 faces slice 100: 74560 vertices, 74975 faces slice 110: 85825 vertices, 86215 faces slice 120: 96753 vertices, 97160 faces slice 130: 107890 vertices, 108278 faces slice 140: 118518 vertices, 118897 faces slice 150: 127631 vertices, 128009 faces slice 160: 136136 vertices, 136453 faces slice 170: 143334 vertices, 143627 faces slice 180: 149033 vertices, 149264 faces slice 190: 153234 vertices, 153416 faces slice 200: 154422 vertices, 154490 faces slice 210: 154422 vertices, 154490 faces slice 220: 154422 vertices, 154490 faces slice 230: 154422 vertices, 154490 faces slice 240: 154422 vertices, 154490 faces slice 250: 154422 vertices, 154490 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... 154422 voxel in cpt #1: X=-68 [v=154422,e=463470,f=308980] located at (-24.351089, -24.472206, 28.391066) For the whole surface: X=-68 [v=154422,e=463470,f=308980] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sun Oct 8 07:58:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 3 found - 3 modified | TOTAL: 3 pass 2 (xy-): 0 found - 3 modified | TOTAL: 3 pass 1 (yz+): 4 found - 4 modified | TOTAL: 7 pass 2 (yz+): 0 found - 4 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 0 found - 0 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 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 = 14 (out of 291514: 0.004803) 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 30: 647 vertices, 730 faces slice 40: 6085 vertices, 6363 faces slice 50: 15423 vertices, 15783 faces slice 60: 26866 vertices, 27277 faces slice 70: 40135 vertices, 40592 faces slice 80: 53374 vertices, 53834 faces slice 90: 66440 vertices, 66867 faces slice 100: 78690 vertices, 79126 faces slice 110: 90296 vertices, 90725 faces slice 120: 101042 vertices, 101444 faces slice 130: 111975 vertices, 112376 faces slice 140: 122269 vertices, 122624 faces slice 150: 130691 vertices, 131042 faces slice 160: 138861 vertices, 139196 faces slice 170: 145901 vertices, 146180 faces slice 180: 151170 vertices, 151410 faces slice 190: 155064 vertices, 155220 faces slice 200: 156170 vertices, 156236 faces slice 210: 156170 vertices, 156236 faces slice 220: 156170 vertices, 156236 faces slice 230: 156170 vertices, 156236 faces slice 240: 156170 vertices, 156236 faces slice 250: 156170 vertices, 156236 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... 156170 voxel in cpt #1: X=-66 [v=156170,e=468708,f=312472] located at (30.636024, -25.891964, 29.509291) For the whole surface: X=-66 [v=156170,e=468708,f=312472] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sun Oct 8 07:58:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sun Oct 8 07:58:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 23775 of (23775 23778) to complete... Waiting for PID 23778 of (23775 23778) 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 (23775 23778) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sun Oct 8 07:58:55 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sun Oct 8 07:58:55 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 23821 of (23821 23824) to complete... Waiting for PID 23824 of (23821 23824) 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 = 49.3 mm, total surface area = 81268 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.4 minutes step 000: RMS=0.157 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.039 (target=0.015) step 045: RMS=0.036 (target=0.015) step 050: RMS=0.035 (target=0.015) step 055: RMS=0.033 (target=0.015) step 060: RMS=0.033 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 94.883575 mris_inflate stimesec 0.379942 mris_inflate ru_maxrss 225172 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 32214 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10864 mris_inflate ru_oublock 10880 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1657 mris_inflate ru_nivcsw 4707 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.9 mm, total surface area = 82400 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.156 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.050 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.043 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.037 (target=0.015) step 060: RMS=0.036 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 44.285267 mris_inflate stimesec 0.104984 mris_inflate ru_maxrss 227696 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 32331 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11008 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2528 mris_inflate ru_nivcsw 3472 PIDs (23821 23824) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sun Oct 8 08:00:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sun Oct 8 08:00:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 23931 of (23931 23935) to complete... Waiting for PID 23935 of (23931 23935) 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 0.93 +- 0.56 (0.00-->5.87) (max @ vno 84155 --> 84168) face area 0.02 +- 0.03 (-0.04-->0.48) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.293... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.610, avgs=0 005/300: dt: 0.9000, rms radial error=176.350, avgs=0 010/300: dt: 0.9000, rms radial error=175.790, avgs=0 015/300: dt: 0.9000, rms radial error=175.055, avgs=0 020/300: dt: 0.9000, rms radial error=174.220, avgs=0 025/300: dt: 0.9000, rms radial error=173.332, avgs=0 030/300: dt: 0.9000, rms radial error=172.413, avgs=0 035/300: dt: 0.9000, rms radial error=171.478, avgs=0 040/300: dt: 0.9000, rms radial error=170.535, avgs=0 045/300: dt: 0.9000, rms radial error=169.590, avgs=0 050/300: dt: 0.9000, rms radial error=168.646, avgs=0 055/300: dt: 0.9000, rms radial error=167.704, avgs=0 060/300: dt: 0.9000, rms radial error=166.767, avgs=0 065/300: dt: 0.9000, rms radial error=165.833, avgs=0 070/300: dt: 0.9000, rms radial error=164.904, avgs=0 075/300: dt: 0.9000, rms radial error=163.980, avgs=0 080/300: dt: 0.9000, rms radial error=163.060, avgs=0 085/300: dt: 0.9000, rms radial error=162.144, avgs=0 090/300: dt: 0.9000, rms radial error=161.234, avgs=0 095/300: dt: 0.9000, rms radial error=160.328, avgs=0 100/300: dt: 0.9000, rms radial error=159.427, avgs=0 105/300: dt: 0.9000, rms radial error=158.534, avgs=0 110/300: dt: 0.9000, rms radial error=157.645, avgs=0 115/300: dt: 0.9000, rms radial error=156.761, avgs=0 120/300: dt: 0.9000, rms radial error=155.882, avgs=0 125/300: dt: 0.9000, rms radial error=155.008, avgs=0 130/300: dt: 0.9000, rms radial error=154.139, avgs=0 135/300: dt: 0.9000, rms radial error=153.274, avgs=0 140/300: dt: 0.9000, rms radial error=152.414, avgs=0 145/300: dt: 0.9000, rms radial error=151.558, avgs=0 150/300: dt: 0.9000, rms radial error=150.707, avgs=0 155/300: dt: 0.9000, rms radial error=149.861, avgs=0 160/300: dt: 0.9000, rms radial error=149.019, avgs=0 165/300: dt: 0.9000, rms radial error=148.182, avgs=0 170/300: dt: 0.9000, rms radial error=147.350, avgs=0 175/300: dt: 0.9000, rms radial error=146.522, avgs=0 180/300: dt: 0.9000, rms radial error=145.699, avgs=0 185/300: dt: 0.9000, rms radial error=144.880, avgs=0 190/300: dt: 0.9000, rms radial error=144.065, avgs=0 195/300: dt: 0.9000, rms radial error=143.255, avgs=0 200/300: dt: 0.9000, rms radial error=142.449, avgs=0 205/300: dt: 0.9000, rms radial error=141.648, avgs=0 210/300: dt: 0.9000, rms radial error=140.851, avgs=0 215/300: dt: 0.9000, rms radial error=140.059, avgs=0 220/300: dt: 0.9000, rms radial error=139.271, avgs=0 225/300: dt: 0.9000, rms radial error=138.487, avgs=0 230/300: dt: 0.9000, rms radial error=137.708, avgs=0 235/300: dt: 0.9000, rms radial error=136.933, avgs=0 240/300: dt: 0.9000, rms radial error=136.163, avgs=0 245/300: dt: 0.9000, rms radial error=135.397, avgs=0 250/300: dt: 0.9000, rms radial error=134.635, avgs=0 255/300: dt: 0.9000, rms radial error=133.877, avgs=0 260/300: dt: 0.9000, rms radial error=133.123, avgs=0 265/300: dt: 0.9000, rms radial error=132.374, avgs=0 270/300: dt: 0.9000, rms radial error=131.629, avgs=0 275/300: dt: 0.9000, rms radial error=130.888, avgs=0 280/300: dt: 0.9000, rms radial error=130.151, avgs=0 285/300: dt: 0.9000, rms radial error=129.418, avgs=0 290/300: dt: 0.9000, rms radial error=128.689, avgs=0 295/300: dt: 0.9000, rms radial error=127.964, avgs=0 300/300: dt: 0.9000, rms radial error=127.243, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18424.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 3228.84 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 3 (K=160.0), pass 1, starting sse = 364.85 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/11 = 0.00879 epoch 4 (K=640.0), pass 1, starting sse = 22.83 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.16/17 = 0.00939 final distance error %28.29 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.15 hours mris_sphere utimesec 620.806623 mris_sphere stimesec 0.679896 mris_sphere ru_maxrss 225372 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 32269 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10912 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 7446 mris_sphere ru_nivcsw 21018 FSRUNTIME@ mris_sphere 0.1525 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 +- 0.55 (0.00-->5.95) (max @ vno 118933 --> 118934) face area 0.02 +- 0.03 (-0.07-->0.64) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.288... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.705, avgs=0 005/300: dt: 0.9000, rms radial error=176.443, avgs=0 010/300: dt: 0.9000, rms radial error=175.882, avgs=0 015/300: dt: 0.9000, rms radial error=175.144, avgs=0 020/300: dt: 0.9000, rms radial error=174.304, avgs=0 025/300: dt: 0.9000, rms radial error=173.405, avgs=0 030/300: dt: 0.9000, rms radial error=172.481, avgs=0 035/300: dt: 0.9000, rms radial error=171.540, avgs=0 040/300: dt: 0.9000, rms radial error=170.593, avgs=0 045/300: dt: 0.9000, rms radial error=169.643, avgs=0 050/300: dt: 0.9000, rms radial error=168.694, avgs=0 055/300: dt: 0.9000, rms radial error=167.749, avgs=0 060/300: dt: 0.9000, rms radial error=166.809, avgs=0 065/300: dt: 0.9000, rms radial error=165.874, avgs=0 070/300: dt: 0.9000, rms radial error=164.943, avgs=0 075/300: dt: 0.9000, rms radial error=164.017, avgs=0 080/300: dt: 0.9000, rms radial error=163.096, avgs=0 085/300: dt: 0.9000, rms radial error=162.180, avgs=0 090/300: dt: 0.9000, rms radial error=161.269, avgs=0 095/300: dt: 0.9000, rms radial error=160.363, avgs=0 100/300: dt: 0.9000, rms radial error=159.462, avgs=0 105/300: dt: 0.9000, rms radial error=158.566, avgs=0 110/300: dt: 0.9000, rms radial error=157.675, avgs=0 115/300: dt: 0.9000, rms radial error=156.789, avgs=0 120/300: dt: 0.9000, rms radial error=155.909, avgs=0 125/300: dt: 0.9000, rms radial error=155.033, avgs=0 130/300: dt: 0.9000, rms radial error=154.162, avgs=0 135/300: dt: 0.9000, rms radial error=153.296, avgs=0 140/300: dt: 0.9000, rms radial error=152.436, avgs=0 145/300: dt: 0.9000, rms radial error=151.580, avgs=0 150/300: dt: 0.9000, rms radial error=150.729, avgs=0 155/300: dt: 0.9000, rms radial error=149.882, avgs=0 160/300: dt: 0.9000, rms radial error=149.040, avgs=0 165/300: dt: 0.9000, rms radial error=148.203, avgs=0 170/300: dt: 0.9000, rms radial error=147.370, avgs=0 175/300: dt: 0.9000, rms radial error=146.541, avgs=0 180/300: dt: 0.9000, rms radial error=145.717, avgs=0 185/300: dt: 0.9000, rms radial error=144.898, avgs=0 190/300: dt: 0.9000, rms radial error=144.083, avgs=0 195/300: dt: 0.9000, rms radial error=143.272, avgs=0 200/300: dt: 0.9000, rms radial error=142.466, avgs=0 205/300: dt: 0.9000, rms radial error=141.664, avgs=0 210/300: dt: 0.9000, rms radial error=140.867, avgs=0 215/300: dt: 0.9000, rms radial error=140.074, avgs=0 220/300: dt: 0.9000, rms radial error=139.286, avgs=0 225/300: dt: 0.9000, rms radial error=138.501, avgs=0 230/300: dt: 0.9000, rms radial error=137.722, avgs=0 235/300: dt: 0.9000, rms radial error=136.946, avgs=0 240/300: dt: 0.9000, rms radial error=136.175, avgs=0 245/300: dt: 0.9000, rms radial error=135.409, avgs=0 250/300: dt: 0.9000, rms radial error=134.646, avgs=0 255/300: dt: 0.9000, rms radial error=133.888, avgs=0 260/300: dt: 0.9000, rms radial error=133.134, avgs=0 265/300: dt: 0.9000, rms radial error=132.384, avgs=0 270/300: dt: 0.9000, rms radial error=131.639, avgs=0 275/300: dt: 0.9000, rms radial error=130.897, avgs=0 280/300: dt: 0.9000, rms radial error=130.160, avgs=0 285/300: dt: 0.9000, rms radial error=129.427, avgs=0 290/300: dt: 0.9000, rms radial error=128.697, avgs=0 295/300: dt: 0.9000, rms radial error=127.972, avgs=0 300/300: dt: 0.9000, rms radial error=127.251, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18694.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 3277.11 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 = 363.59 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00718 epoch 4 (K=640.0), pass 1, starting sse = 22.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.23/23 = 0.01006 final distance error %26.65 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.09 hours mris_sphere utimesec 309.462954 mris_sphere stimesec 0.142978 mris_sphere ru_maxrss 227892 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 32889 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 10992 mris_sphere ru_oublock 11032 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 10472 mris_sphere ru_nivcsw 24121 FSRUNTIME@ mris_sphere 0.0860 hours 1 threads PIDs (23931 23935) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sun Oct 8 08:09:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sun Oct 8 08:09:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sun Oct 8 08:09:28 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050490 lh #@# Fix Topology rh Sun Oct 8 08:09:28 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050490 rh Waiting for PID 24411 of (24411 24414) to complete... Waiting for PID 24414 of (24411 24414) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050490 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=-68 (nv=154422, nf=308980, ne=463470, g=35) 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 14 iterations marking ambiguous vertices... 4176 ambiguous faces found in tessellation segmenting defects... 46 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 38 into 24 45 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5872 (-4.7936) -vertex loglikelihood: -6.3859 (-3.1929) -normal dot loglikelihood: -3.5948 (-3.5948) -quad curv loglikelihood: -6.5552 (-3.2776) Total Loglikelihood : -26.1231 CORRECTING DEFECT 0 (vertices=46, convex hull=68, v0=3510) After retessellation of defect 0 (v0=3510), euler #=-43 (151818,454253,302392) : difference with theory (-42) = 1 CORRECTING DEFECT 1 (vertices=37, convex hull=71, v0=11236) After retessellation of defect 1 (v0=11236), euler #=-42 (151832,454321,302447) : difference with theory (-41) = 1 CORRECTING DEFECT 2 (vertices=91, convex hull=136, v0=13002) After retessellation of defect 2 (v0=13002), euler #=-41 (151881,454528,302606) : difference with theory (-40) = 1 CORRECTING DEFECT 3 (vertices=56, convex hull=80, v0=14142) After retessellation of defect 3 (v0=14142), euler #=-40 (151910,454648,302698) : difference with theory (-39) = 1 CORRECTING DEFECT 4 (vertices=34, convex hull=69, v0=16438) After retessellation of defect 4 (v0=16438), euler #=-39 (151926,454723,302758) : difference with theory (-38) = 1 CORRECTING DEFECT 5 (vertices=24, convex hull=26, v0=17225) After retessellation of defect 5 (v0=17225), euler #=-38 (151930,454741,302773) : difference with theory (-37) = 1 CORRECTING DEFECT 6 (vertices=25, convex hull=51, v0=19189) After retessellation of defect 6 (v0=19189), euler #=-37 (151937,454782,302808) : difference with theory (-36) = 1 CORRECTING DEFECT 7 (vertices=28, convex hull=66, v0=21241) After retessellation of defect 7 (v0=21241), euler #=-36 (151954,454859,302869) : difference with theory (-35) = 1 CORRECTING DEFECT 8 (vertices=67, convex hull=61, v0=23912) After retessellation of defect 8 (v0=23912), euler #=-35 (151970,454932,302927) : difference with theory (-34) = 1 CORRECTING DEFECT 9 (vertices=79, convex hull=108, v0=31040) After retessellation of defect 9 (v0=31040), euler #=-34 (151989,455035,303012) : difference with theory (-33) = 1 CORRECTING DEFECT 10 (vertices=75, convex hull=99, v0=34905) After retessellation of defect 10 (v0=34905), euler #=-33 (152023,455178,303122) : difference with theory (-32) = 1 CORRECTING DEFECT 11 (vertices=29, convex hull=75, v0=40424) After retessellation of defect 11 (v0=40424), euler #=-32 (152036,455244,303176) : difference with theory (-31) = 1 CORRECTING DEFECT 12 (vertices=79, convex hull=105, v0=42010) After retessellation of defect 12 (v0=42010), euler #=-31 (152081,455421,303309) : difference with theory (-30) = 1 CORRECTING DEFECT 13 (vertices=7, convex hull=23, v0=50580) After retessellation of defect 13 (v0=50580), euler #=-30 (152083,455433,303320) : difference with theory (-29) = 1 CORRECTING DEFECT 14 (vertices=57, convex hull=88, v0=54783) After retessellation of defect 14 (v0=54783), euler #=-29 (152094,455504,303381) : difference with theory (-28) = 1 CORRECTING DEFECT 15 (vertices=187, convex hull=102, v0=80080) After retessellation of defect 15 (v0=80080), euler #=-28 (152151,455718,303539) : difference with theory (-27) = 1 CORRECTING DEFECT 16 (vertices=31, convex hull=62, v0=99704) After retessellation of defect 16 (v0=99704), euler #=-27 (152170,455802,303605) : difference with theory (-26) = 1 CORRECTING DEFECT 17 (vertices=22, convex hull=30, v0=103019) After retessellation of defect 17 (v0=103019), euler #=-26 (152175,455824,303623) : difference with theory (-25) = 1 CORRECTING DEFECT 18 (vertices=13, convex hull=19, v0=104465) After retessellation of defect 18 (v0=104465), euler #=-25 (152178,455834,303631) : difference with theory (-24) = 1 CORRECTING DEFECT 19 (vertices=13, convex hull=19, v0=105204) After retessellation of defect 19 (v0=105204), euler #=-24 (152180,455847,303643) : difference with theory (-23) = 1 CORRECTING DEFECT 20 (vertices=43, convex hull=61, v0=105408) After retessellation of defect 20 (v0=105408), euler #=-23 (152207,455954,303724) : difference with theory (-22) = 1 CORRECTING DEFECT 21 (vertices=24, convex hull=26, v0=105626) After retessellation of defect 21 (v0=105626), euler #=-22 (152209,455969,303738) : difference with theory (-21) = 1 CORRECTING DEFECT 22 (vertices=5, convex hull=15, v0=108538) After retessellation of defect 22 (v0=108538), euler #=-21 (152210,455975,303744) : difference with theory (-20) = 1 CORRECTING DEFECT 23 (vertices=55, convex hull=82, v0=109655) After retessellation of defect 23 (v0=109655), euler #=-20 (152225,456051,303806) : difference with theory (-19) = 1 CORRECTING DEFECT 24 (vertices=780, convex hull=370, v0=110411) After retessellation of defect 24 (v0=110411), euler #=-18 (152280,456401,304103) : difference with theory (-18) = 0 CORRECTING DEFECT 25 (vertices=6, convex hull=26, v0=110595) After retessellation of defect 25 (v0=110595), euler #=-17 (152283,456417,304117) : difference with theory (-17) = 0 CORRECTING DEFECT 26 (vertices=33, convex hull=57, v0=112627) After retessellation of defect 26 (v0=112627), euler #=-16 (152294,456472,304162) : difference with theory (-16) = 0 CORRECTING DEFECT 27 (vertices=38, convex hull=56, v0=112639) After retessellation of defect 27 (v0=112639), euler #=-15 (152311,456544,304218) : difference with theory (-15) = 0 CORRECTING DEFECT 28 (vertices=81, convex hull=66, v0=112740) After retessellation of defect 28 (v0=112740), euler #=-14 (152329,456623,304280) : difference with theory (-14) = 0 CORRECTING DEFECT 29 (vertices=28, convex hull=69, v0=119476) After retessellation of defect 29 (v0=119476), euler #=-13 (152343,456694,304338) : difference with theory (-13) = 0 CORRECTING DEFECT 30 (vertices=22, convex hull=16, v0=119945) After retessellation of defect 30 (v0=119945), euler #=-12 (152347,456709,304350) : difference with theory (-12) = 0 CORRECTING DEFECT 31 (vertices=64, convex hull=72, v0=120325) After retessellation of defect 31 (v0=120325), euler #=-11 (152368,456799,304420) : difference with theory (-11) = 0 CORRECTING DEFECT 32 (vertices=8, convex hull=18, v0=120971) After retessellation of defect 32 (v0=120971), euler #=-10 (152369,456806,304427) : difference with theory (-10) = 0 CORRECTING DEFECT 33 (vertices=53, convex hull=88, v0=121871) After retessellation of defect 33 (v0=121871), euler #=-9 (152391,456909,304509) : difference with theory (-9) = 0 CORRECTING DEFECT 34 (vertices=9, convex hull=50, v0=126521) After retessellation of defect 34 (v0=126521), euler #=-8 (152395,456936,304533) : difference with theory (-8) = 0 CORRECTING DEFECT 35 (vertices=56, convex hull=90, v0=127703) After retessellation of defect 35 (v0=127703), euler #=-7 (152417,457039,304615) : difference with theory (-7) = 0 CORRECTING DEFECT 36 (vertices=6, convex hull=22, v0=128501) After retessellation of defect 36 (v0=128501), euler #=-6 (152418,457048,304624) : difference with theory (-6) = 0 CORRECTING DEFECT 37 (vertices=55, convex hull=68, v0=129154) After retessellation of defect 37 (v0=129154), euler #=-5 (152438,457135,304692) : difference with theory (-5) = 0 CORRECTING DEFECT 38 (vertices=73, convex hull=75, v0=131150) After retessellation of defect 38 (v0=131150), euler #=-4 (152450,457203,304749) : difference with theory (-4) = 0 CORRECTING DEFECT 39 (vertices=27, convex hull=51, v0=134424) After retessellation of defect 39 (v0=134424), euler #=-3 (152465,457269,304801) : difference with theory (-3) = 0 CORRECTING DEFECT 40 (vertices=28, convex hull=75, v0=138410) After retessellation of defect 40 (v0=138410), euler #=-2 (152478,457339,304859) : difference with theory (-2) = 0 CORRECTING DEFECT 41 (vertices=41, convex hull=63, v0=138663) After retessellation of defect 41 (v0=138663), euler #=-1 (152498,457425,304926) : difference with theory (-1) = 0 CORRECTING DEFECT 42 (vertices=28, convex hull=60, v0=142328) After retessellation of defect 42 (v0=142328), euler #=0 (152510,457483,304973) : difference with theory (0) = 0 CORRECTING DEFECT 43 (vertices=35, convex hull=73, v0=153694) After retessellation of defect 43 (v0=153694), euler #=1 (152523,457555,305033) : difference with theory (1) = 0 CORRECTING DEFECT 44 (vertices=26, convex hull=24, v0=154156) After retessellation of defect 44 (v0=154156), euler #=2 (152526,457572,305048) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.09-->8.73) (max @ vno 129768 --> 135089) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.09-->8.73) (max @ vno 129768 --> 135089) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 145 mutations (36.4%), 253 crossovers (63.6%), 293 vertices were eliminated building final representation... 1896 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=152526, nf=305048, ne=457572, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 41.1 minutes 0 defective edges removing intersecting faces 000: 290 intersecting 001: 11 intersecting 002: 6 intersecting mris_fix_topology utimesec 2466.722001 mris_fix_topology stimesec 1.328797 mris_fix_topology ru_maxrss 494976 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 55521 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 10864 mris_fix_topology ru_oublock 14680 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 757 mris_fix_topology ru_nivcsw 13624 FSRUNTIME@ mris_fix_topology lh 0.6852 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050490 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=-66 (nv=156170, nf=312472, ne=468708, g=34) 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... 3843 ambiguous faces found in tessellation segmenting defects... 43 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 24 into 23 -merging segment 35 into 34 41 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.6031 (-4.8015) -vertex loglikelihood: -6.3247 (-3.1623) -normal dot loglikelihood: -3.6219 (-3.6219) -quad curv loglikelihood: -6.1991 (-3.0995) Total Loglikelihood : -25.7487 CORRECTING DEFECT 0 (vertices=20, convex hull=30, v0=8661) After retessellation of defect 0 (v0=8661), euler #=-39 (153747,460080,306294) : difference with theory (-38) = 1 CORRECTING DEFECT 1 (vertices=84, convex hull=122, v0=9725) After retessellation of defect 1 (v0=9725), euler #=-38 (153775,460225,306412) : difference with theory (-37) = 1 CORRECTING DEFECT 2 (vertices=162, convex hull=133, v0=21761) After retessellation of defect 2 (v0=21761), euler #=-37 (153822,460422,306563) : difference with theory (-36) = 1 CORRECTING DEFECT 3 (vertices=47, convex hull=48, v0=30542) After retessellation of defect 3 (v0=30542), euler #=-36 (153835,460478,306607) : difference with theory (-35) = 1 CORRECTING DEFECT 4 (vertices=56, convex hull=86, v0=30774) After retessellation of defect 4 (v0=30774), euler #=-35 (153859,460586,306692) : difference with theory (-34) = 1 CORRECTING DEFECT 5 (vertices=21, convex hull=47, v0=32745) After retessellation of defect 5 (v0=32745), euler #=-34 (153868,460629,306727) : difference with theory (-33) = 1 CORRECTING DEFECT 6 (vertices=167, convex hull=124, v0=32873) After retessellation of defect 6 (v0=32873), euler #=-33 (153896,460769,306840) : difference with theory (-32) = 1 CORRECTING DEFECT 7 (vertices=39, convex hull=30, v0=40113) After retessellation of defect 7 (v0=40113), euler #=-32 (153898,460783,306853) : difference with theory (-31) = 1 CORRECTING DEFECT 8 (vertices=14, convex hull=25, v0=67187) After retessellation of defect 8 (v0=67187), euler #=-31 (153900,460798,306867) : difference with theory (-30) = 1 CORRECTING DEFECT 9 (vertices=38, convex hull=68, v0=68584) After retessellation of defect 9 (v0=68584), euler #=-30 (153920,460886,306936) : difference with theory (-29) = 1 CORRECTING DEFECT 10 (vertices=25, convex hull=35, v0=77304) After retessellation of defect 10 (v0=77304), euler #=-29 (153924,460908,306955) : difference with theory (-28) = 1 CORRECTING DEFECT 11 (vertices=224, convex hull=100, v0=84346) After retessellation of defect 11 (v0=84346), euler #=-28 (153963,461072,307081) : difference with theory (-27) = 1 CORRECTING DEFECT 12 (vertices=14, convex hull=22, v0=87916) After retessellation of defect 12 (v0=87916), euler #=-27 (153963,461080,307090) : difference with theory (-26) = 1 CORRECTING DEFECT 13 (vertices=31, convex hull=18, v0=88005) After retessellation of defect 13 (v0=88005), euler #=-26 (153967,461095,307102) : difference with theory (-25) = 1 CORRECTING DEFECT 14 (vertices=45, convex hull=26, v0=94952) After retessellation of defect 14 (v0=94952), euler #=-25 (153970,461109,307114) : difference with theory (-24) = 1 CORRECTING DEFECT 15 (vertices=75, convex hull=116, v0=104106) After retessellation of defect 15 (v0=104106), euler #=-24 (154016,461300,307260) : difference with theory (-23) = 1 CORRECTING DEFECT 16 (vertices=22, convex hull=52, v0=106306) After retessellation of defect 16 (v0=106306), euler #=-23 (154025,461351,307303) : difference with theory (-22) = 1 CORRECTING DEFECT 17 (vertices=111, convex hull=106, v0=107727) After retessellation of defect 17 (v0=107727), euler #=-22 (154086,461587,307479) : difference with theory (-21) = 1 CORRECTING DEFECT 18 (vertices=83, convex hull=80, v0=110027) After retessellation of defect 18 (v0=110027), euler #=-21 (154121,461729,307587) : difference with theory (-20) = 1 CORRECTING DEFECT 19 (vertices=35, convex hull=72, v0=110656) After retessellation of defect 19 (v0=110656), euler #=-20 (154142,461823,307661) : difference with theory (-19) = 1 CORRECTING DEFECT 20 (vertices=40, convex hull=62, v0=111626) After retessellation of defect 20 (v0=111626), euler #=-19 (154162,461905,307724) : difference with theory (-18) = 1 CORRECTING DEFECT 21 (vertices=43, convex hull=56, v0=115443) After retessellation of defect 21 (v0=115443), euler #=-18 (154172,461961,307771) : difference with theory (-17) = 1 CORRECTING DEFECT 22 (vertices=30, convex hull=73, v0=116026) After retessellation of defect 22 (v0=116026), euler #=-17 (154191,462048,307840) : difference with theory (-16) = 1 CORRECTING DEFECT 23 (vertices=81, convex hull=129, v0=117715) After retessellation of defect 23 (v0=117715), euler #=-16 (154241,462259,308002) : difference with theory (-15) = 1 CORRECTING DEFECT 24 (vertices=21, convex hull=52, v0=119264) After retessellation of defect 24 (v0=119264), euler #=-15 (154250,462306,308041) : difference with theory (-14) = 1 CORRECTING DEFECT 25 (vertices=46, convex hull=45, v0=120144) After retessellation of defect 25 (v0=120144), euler #=-14 (154254,462336,308068) : difference with theory (-13) = 1 CORRECTING DEFECT 26 (vertices=31, convex hull=23, v0=123648) After retessellation of defect 26 (v0=123648), euler #=-13 (154263,462368,308092) : difference with theory (-12) = 1 CORRECTING DEFECT 27 (vertices=80, convex hull=114, v0=125516) After retessellation of defect 27 (v0=125516), euler #=-12 (154305,462551,308234) : difference with theory (-11) = 1 CORRECTING DEFECT 28 (vertices=48, convex hull=77, v0=126194) After retessellation of defect 28 (v0=126194), euler #=-11 (154333,462668,308324) : difference with theory (-10) = 1 CORRECTING DEFECT 29 (vertices=22, convex hull=24, v0=127194) After retessellation of defect 29 (v0=127194), euler #=-10 (154336,462685,308339) : difference with theory (-9) = 1 CORRECTING DEFECT 30 (vertices=27, convex hull=77, v0=131397) After retessellation of defect 30 (v0=131397), euler #=-9 (154351,462758,308398) : difference with theory (-8) = 1 CORRECTING DEFECT 31 (vertices=59, convex hull=82, v0=132258) After retessellation of defect 31 (v0=132258), euler #=-8 (154392,462919,308519) : difference with theory (-7) = 1 CORRECTING DEFECT 32 (vertices=51, convex hull=74, v0=132340) After retessellation of defect 32 (v0=132340), euler #=-7 (154405,462988,308576) : difference with theory (-6) = 1 CORRECTING DEFECT 33 (vertices=70, convex hull=59, v0=135476) After retessellation of defect 33 (v0=135476), euler #=-5 (154417,463050,308628) : difference with theory (-5) = 0 CORRECTING DEFECT 34 (vertices=35, convex hull=75, v0=141339) After retessellation of defect 34 (v0=141339), euler #=-4 (154439,463147,308704) : difference with theory (-4) = 0 CORRECTING DEFECT 35 (vertices=72, convex hull=105, v0=143500) After retessellation of defect 35 (v0=143500), euler #=-3 (154467,463278,308808) : difference with theory (-3) = 0 CORRECTING DEFECT 36 (vertices=214, convex hull=61, v0=144665) After retessellation of defect 36 (v0=144665), euler #=-2 (154489,463372,308881) : difference with theory (-2) = 0 CORRECTING DEFECT 37 (vertices=15, convex hull=29, v0=144765) After retessellation of defect 37 (v0=144765), euler #=-1 (154493,463394,308900) : difference with theory (-1) = 0 CORRECTING DEFECT 38 (vertices=29, convex hull=57, v0=149173) After retessellation of defect 38 (v0=149173), euler #=0 (154502,463440,308938) : difference with theory (0) = 0 CORRECTING DEFECT 39 (vertices=68, convex hull=89, v0=151834) After retessellation of defect 39 (v0=151834), euler #=1 (154516,463517,309002) : difference with theory (1) = 0 CORRECTING DEFECT 40 (vertices=29, convex hull=71, v0=154483) After retessellation of defect 40 (v0=154483), euler #=2 (154525,463569,309046) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.02-->11.96) (max @ vno 24078 --> 24098) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.02-->11.96) (max @ vno 24078 --> 24098) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 116 mutations (33.8%), 227 crossovers (66.2%), 56 vertices were eliminated building final representation... 1645 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=154525, nf=309046, ne=463569, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 19.3 minutes 0 defective edges removing intersecting faces 000: 214 intersecting 001: 7 intersecting mris_fix_topology utimesec 1158.689852 mris_fix_topology stimesec 0.152976 mris_fix_topology ru_maxrss 480300 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 56172 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 14768 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 926 mris_fix_topology ru_nivcsw 6161 FSRUNTIME@ mris_fix_topology rh 0.3220 hours 1 threads PIDs (24411 24414) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 152526 - 457572 + 305048 = 2 --> 0 holes F =2V-4: 305048 = 305052-4 (0) 2E=3F: 915144 = 915144 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 154525 - 463569 + 309046 = 2 --> 0 holes F =2V-4: 309046 = 309050-4 (0) 2E=3F: 927138 = 927138 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 31 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 5 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Oct 8 08:50:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050490 lh #-------------------------------------------- #@# Make White Surf rh Sun Oct 8 08:50:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050490 rh Waiting for PID 26267 of (26267 26270) to complete... Waiting for PID 26270 of (26267 26270) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050490 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-6.0.0/0050490/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... 18861 bright wm thresholded. 604 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.orig... computing class statistics... border white: 281912 voxels (1.68%) border gray 319696 voxels (1.91%) WM (96.0): 96.5 +- 9.0 [70.0 --> 110.0] GM (68.0) : 68.0 +- 10.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 52.8 (was 70) setting MAX_BORDER_WHITE to 110.0 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 42.5 (was 40) setting MAX_GRAY to 92.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.3 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->3.75) (max @ vno 128964 --> 129768) face area 0.28 +- 0.12 (0.00-->2.43) mean absolute distance = 0.65 +- 0.75 4960 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-7.8, GM=63+-8.7 mean inside = 91.3, mean outside = 71.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=76.6, 25 (25) missing vertices, mean dist 0.3 [0.5 (%36.6)->0.7 (%63.4))] %74 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 0.92 +- 0.25 (0.10-->4.02) (max @ vno 108380 --> 108379) face area 0.28 +- 0.13 (0.00-->2.43) mean absolute distance = 0.32 +- 0.52 3673 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3948342.0, rms=10.643 001: dt: 0.5000, sse=2215870.8, rms=7.431 (30.187%) 002: dt: 0.5000, sse=1517707.1, rms=5.616 (24.423%) 003: dt: 0.5000, sse=1205458.2, rms=4.573 (18.571%) 004: dt: 0.5000, sse=1065336.0, rms=4.017 (12.166%) 005: dt: 0.5000, sse=1009239.8, rms=3.766 (6.229%) 006: dt: 0.5000, sse=984131.8, rms=3.647 (3.167%) rms = 3.60, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=975687.3, rms=3.602 (1.229%) 008: dt: 0.2500, sse=758159.9, rms=2.249 (37.571%) 009: dt: 0.2500, sse=713704.2, rms=1.864 (17.114%) 010: dt: 0.2500, sse=702277.5, rms=1.750 (6.092%) 011: dt: 0.2500, sse=696095.1, rms=1.687 (3.623%) rms = 1.65, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=693576.9, rms=1.655 (1.924%) 013: dt: 0.1250, sse=687262.2, rms=1.586 (4.163%) rms = 1.58, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=686718.0, rms=1.577 (0.556%) positioning took 3.1 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 1 vertex label from ripped group mean border=79.7, 35 (6) missing vertices, mean dist -0.2 [0.4 (%72.0)->0.2 (%28.0))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.24 (0.05-->4.27) (max @ vno 108380 --> 108379) face area 0.35 +- 0.16 (0.00-->3.33) mean absolute distance = 0.26 +- 0.39 4820 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1402305.9, rms=4.628 015: dt: 0.5000, sse=1063699.5, rms=3.118 (32.617%) rms = 3.32, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=932639.1, rms=2.322 (25.550%) 017: dt: 0.2500, sse=868844.9, rms=1.787 (23.019%) 018: dt: 0.2500, sse=846297.3, rms=1.553 (13.098%) 019: dt: 0.2500, sse=838407.1, rms=1.463 (5.774%) 020: dt: 0.2500, sse=834537.9, rms=1.411 (3.570%) rms = 1.38, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=832683.9, rms=1.382 (2.048%) 022: dt: 0.1250, sse=827700.6, rms=1.329 (3.855%) rms = 1.32, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=827477.4, rms=1.325 (0.327%) positioning took 2.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=81.5, 34 (3) missing vertices, mean dist -0.1 [0.3 (%63.3)->0.2 (%36.7))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.03-->4.54) (max @ vno 108380 --> 108379) face area 0.34 +- 0.16 (0.00-->3.39) mean absolute distance = 0.26 +- 0.36 4318 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=977428.7, rms=2.743 024: dt: 0.5000, sse=963890.4, rms=2.645 (3.575%) rms = 3.06, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=848681.8, rms=1.750 (33.832%) 026: dt: 0.2500, sse=813081.6, rms=1.371 (21.694%) 027: dt: 0.2500, sse=805593.6, rms=1.271 (7.274%) rms = 1.26, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=803831.7, rms=1.263 (0.640%) 029: dt: 0.1250, sse=799307.2, rms=1.197 (5.217%) rms = 1.20, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=799544.6, rms=1.200 (-0.282%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.3, 36 (2) missing vertices, mean dist -0.0 [0.3 (%54.5)->0.2 (%45.5))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=832190.4, rms=1.690 rms = 1.85, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=790050.7, rms=1.183 (30.029%) 032: dt: 0.2500, sse=772827.8, rms=0.902 (23.745%) rms = 0.90, time step reduction 2 of 3 to 0.125... rms = 0.90, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=772043.2, rms=0.898 (0.450%) positioning took 0.6 minutes generating cortex label... 8 non-cortical segments detected only using segment with 8327 vertices erasing segment 1 (vno[0] = 94701) erasing segment 2 (vno[0] = 104655) erasing segment 3 (vno[0] = 107495) erasing segment 4 (vno[0] = 108417) erasing segment 5 (vno[0] = 108419) erasing segment 6 (vno[0] = 111556) erasing segment 7 (vno[0] = 120208) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.area vertex spacing 0.90 +- 0.25 (0.03-->4.57) (max @ vno 108379 --> 108380) face area 0.34 +- 0.16 (0.00-->3.40) refinement took 10.5 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050490 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-6.0.0/0050490/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... 18861 bright wm thresholded. 604 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.orig... computing class statistics... border white: 281912 voxels (1.68%) border gray 319696 voxels (1.91%) WM (96.0): 96.5 +- 9.0 [70.0 --> 110.0] GM (68.0) : 68.0 +- 10.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.8 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 65.0 (was 85) setting MAX_CSF to 44.5 (was 40) setting MAX_GRAY to 93.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.3 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.31) (max @ vno 22887 --> 24077) face area 0.28 +- 0.12 (0.00-->3.78) mean absolute distance = 0.64 +- 0.78 4173 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-7.8, GM=65+-7.8 mean inside = 91.7, mean outside = 72.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=78.4, 37 (37) missing vertices, mean dist 0.2 [0.5 (%39.8)->0.7 (%60.2))] %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.08-->4.08) (max @ vno 24076 --> 24077) face area 0.28 +- 0.13 (0.00-->3.53) mean absolute distance = 0.33 +- 0.55 4122 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3681038.8, rms=10.121 001: dt: 0.5000, sse=2018981.1, rms=6.886 (31.966%) 002: dt: 0.5000, sse=1404970.1, rms=5.181 (24.754%) 003: dt: 0.5000, sse=1155562.6, rms=4.307 (16.886%) 004: dt: 0.5000, sse=1050026.1, rms=3.862 (10.324%) 005: dt: 0.5000, sse=1004668.8, rms=3.662 (5.172%) 006: dt: 0.5000, sse=985681.0, rms=3.567 (2.597%) rms = 3.54, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=979759.2, rms=3.539 (0.793%) 008: dt: 0.2500, sse=766301.7, rms=2.195 (37.971%) 009: dt: 0.2500, sse=722744.2, rms=1.833 (16.485%) 010: dt: 0.2500, sse=712956.4, rms=1.732 (5.503%) 011: dt: 0.2500, sse=711361.0, rms=1.678 (3.117%) rms = 1.65, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=705002.7, rms=1.653 (1.484%) 013: dt: 0.1250, sse=697310.4, rms=1.565 (5.356%) rms = 1.56, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=696356.0, rms=1.556 (0.567%) positioning took 3.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.2, 64 (8) missing vertices, mean dist -0.2 [0.4 (%70.1)->0.2 (%29.9))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.24 (0.10-->3.95) (max @ vno 24076 --> 24077) face area 0.35 +- 0.16 (0.00-->4.44) mean absolute distance = 0.27 +- 0.44 4580 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1339157.5, rms=4.340 015: dt: 0.5000, sse=1049365.1, rms=2.990 (31.106%) rms = 3.21, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=926084.8, rms=2.210 (26.082%) 017: dt: 0.2500, sse=872998.6, rms=1.712 (22.536%) 018: dt: 0.2500, sse=848322.8, rms=1.513 (11.635%) 019: dt: 0.2500, sse=842345.5, rms=1.443 (4.601%) rms = 1.40, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=840730.0, rms=1.403 (2.807%) 021: dt: 0.1250, sse=834935.8, rms=1.348 (3.929%) rms = 1.34, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=834365.7, rms=1.342 (0.418%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.0, 68 (2) missing vertices, mean dist -0.1 [0.3 (%62.5)->0.2 (%37.5))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.09-->3.99) (max @ vno 24098 --> 25235) face area 0.34 +- 0.15 (0.00-->4.29) mean absolute distance = 0.26 +- 0.38 4275 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=989596.1, rms=2.760 023: dt: 0.5000, sse=968723.0, rms=2.559 (7.288%) rms = 2.97, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=854671.8, rms=1.737 (32.115%) 025: dt: 0.2500, sse=826022.1, rms=1.372 (20.997%) 026: dt: 0.2500, sse=813133.7, rms=1.281 (6.670%) rms = 1.27, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=811753.1, rms=1.266 (1.169%) 028: dt: 0.1250, sse=806791.3, rms=1.205 (4.810%) rms = 1.21, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=807784.2, rms=1.206 (-0.110%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.7, 78 (0) missing vertices, mean dist -0.0 [0.3 (%53.6)->0.2 (%46.4))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=836678.6, rms=1.658 rms = 1.83, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=796564.9, rms=1.181 (28.789%) 031: dt: 0.2500, sse=781054.4, rms=0.930 (21.261%) rms = 0.93, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=815665.3, rms=0.930 (0.016%) rms = 0.92, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=778004.3, rms=0.922 (0.880%) positioning took 0.5 minutes generating cortex label... 5 non-cortical segments detected only using segment with 7731 vertices erasing segment 1 (vno[0] = 109559) erasing segment 2 (vno[0] = 117438) erasing segment 3 (vno[0] = 124558) erasing segment 4 (vno[0] = 154232) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.area vertex spacing 0.90 +- 0.24 (0.02-->4.01) (max @ vno 24098 --> 25235) face area 0.34 +- 0.15 (0.00-->4.30) refinement took 10.3 minutes PIDs (26267 26270) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sun Oct 8 09:01:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sun Oct 8 09:01:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 27028 of (27028 27031) to complete... Waiting for PID 27031 of (27028 27031) 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 (27028 27031) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sun Oct 8 09:01:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sun Oct 8 09:01:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 27076 of (27076 27079) to complete... Waiting for PID 27079 of (27076 27079) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 49.4 mm, total surface area = 93935 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.181 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 1.3 minutes mris_inflate utimesec 88.673519 mris_inflate stimesec 0.200969 mris_inflate ru_maxrss 222576 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 32205 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10728 mris_inflate ru_oublock 11944 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1703 mris_inflate ru_nivcsw 3580 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 49.0 mm, total surface area = 94482 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.180 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 43.261423 mris_inflate stimesec 0.089986 mris_inflate ru_maxrss 225400 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 32907 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10872 mris_inflate ru_oublock 12096 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2562 mris_inflate ru_nivcsw 3387 PIDs (27076 27079) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sun Oct 8 09:02:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Sun Oct 8 09:02:46 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 27190 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... Waiting for PID 27193 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... Waiting for PID 27196 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... Waiting for PID 27199 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... Waiting for PID 27202 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... Waiting for PID 27205 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... Waiting for PID 27208 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... Waiting for PID 27211 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... Waiting for PID 27214 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... Waiting for PID 27217 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... Waiting for PID 27220 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... Waiting for PID 27223 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 3.839*4pi (48.242) --> -3 handles ICI = 199.2, FI = 1873.6, variation=30233.165 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 202 vertices thresholded to be in k1 ~ [-0.18 0.30], k2 ~ [-0.10 0.04] total integrated curvature = 0.616*4pi (7.746) --> 0 handles ICI = 1.5, FI = 10.8, variation=175.575 140 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 152 vertices thresholded to be in [-0.11 0.13] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022 done. mris_curvature -w rh.white.preaparc total integrated curvature = 2.485*4pi (31.224) --> -1 handles ICI = 202.4, FI = 1972.0, variation=31573.021 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 187 vertices thresholded to be in k1 ~ [-0.23 0.93], k2 ~ [-0.13 0.05] total integrated curvature = 0.547*4pi (6.868) --> 0 handles ICI = 1.5, FI = 10.2, variation=169.057 152 vertices thresholded to be in [-0.04 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 120 vertices thresholded to be in [-0.12 0.20] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.022 done. PIDs (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sun Oct 8 09:04:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050490 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 [ 0050490/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 [ 283 ] Gb_filter = 0 WARN: S lookup min: -0.234448 WARN: S explicit min: 0.000000 vertex = 43 #----------------------------------------- #@# Curvature Stats rh Sun Oct 8 09:04:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050490 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 [ 0050490/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 [ 287 ] Gb_filter = 0 WARN: S lookup min: -0.330693 WARN: S explicit min: 0.000000 vertex = 237 #-------------------------------------------- #@# Sphere lh Sun Oct 8 09:04:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sun Oct 8 09:04:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 27422 of (27422 27425) to complete... Waiting for PID 27425 of (27422 27425) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0.272... 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 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.33 pass 1: epoch 2 of 3 starting distance error %19.31 unfolding complete - removing small folds... starting distance error %19.25 removing remaining folds... final distance error %19.27 MRISunfold() return, current seed 1234 -01: dt=0.0000, 91 negative triangles 179: dt=0.9900, 91 negative triangles 180: dt=0.9900, 47 negative triangles 181: dt=0.9900, 22 negative triangles 182: dt=0.9900, 13 negative triangles 183: dt=0.9900, 9 negative triangles 184: dt=0.9900, 7 negative triangles 185: dt=0.9900, 9 negative triangles 186: dt=0.9900, 6 negative triangles 187: dt=0.9900, 3 negative triangles 188: dt=0.9900, 3 negative triangles 189: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.92 hours mris_sphere utimesec 3320.394223 mris_sphere stimesec 0.904862 mris_sphere ru_maxrss 313524 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 55072 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10776 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 146566 mris_sphere ru_nivcsw 275958 FSRUNTIME@ mris_sphere 0.9223 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0.269... 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 %19.95 pass 1: epoch 2 of 3 starting distance error %19.91 unfolding complete - removing small folds... starting distance error %19.85 removing remaining folds... final distance error %19.87 MRISunfold() return, current seed 1234 -01: dt=0.0000, 176 negative triangles 201: dt=0.9900, 176 negative triangles 202: dt=0.9900, 81 negative triangles 203: dt=0.9900, 76 negative triangles 204: dt=0.9900, 56 negative triangles 205: dt=0.9900, 54 negative triangles 206: dt=0.9900, 42 negative triangles 207: dt=0.9900, 41 negative triangles 208: dt=0.9900, 45 negative triangles 209: dt=0.9900, 41 negative triangles 210: dt=0.9900, 41 negative triangles 211: dt=0.9900, 37 negative triangles 212: dt=0.9900, 44 negative triangles 213: dt=0.9900, 44 negative triangles 214: dt=0.9900, 38 negative triangles 215: dt=0.9900, 33 negative triangles 216: dt=0.9900, 39 negative triangles 217: dt=0.9900, 37 negative triangles 218: dt=0.9900, 33 negative triangles 219: dt=0.9900, 27 negative triangles 220: dt=0.9900, 38 negative triangles 221: dt=0.9900, 31 negative triangles 222: dt=0.9900, 30 negative triangles 223: dt=0.9900, 35 negative triangles 224: dt=0.9900, 29 negative triangles 225: dt=0.9900, 32 negative triangles 226: dt=0.9900, 25 negative triangles 227: dt=0.9900, 26 negative triangles 228: dt=0.9900, 24 negative triangles 229: dt=0.9900, 24 negative triangles 230: dt=0.9900, 19 negative triangles 231: dt=0.9900, 25 negative triangles 232: dt=0.9900, 19 negative triangles 233: dt=0.9900, 16 negative triangles 234: dt=0.9900, 22 negative triangles 235: dt=0.9900, 15 negative triangles 236: dt=0.9900, 11 negative triangles 237: dt=0.9900, 12 negative triangles 238: dt=0.9900, 10 negative triangles 239: dt=0.9900, 13 negative triangles 240: dt=0.9900, 10 negative triangles 241: dt=0.9900, 8 negative triangles 242: dt=0.9900, 11 negative triangles 243: dt=0.9900, 13 negative triangles 244: dt=0.9900, 10 negative triangles 245: dt=0.9900, 7 negative triangles 246: dt=0.9900, 10 negative triangles 247: dt=0.9900, 8 negative triangles 248: dt=0.9900, 12 negative triangles 249: dt=0.9900, 10 negative triangles 250: dt=0.9900, 5 negative triangles 251: dt=0.9900, 9 negative triangles 252: dt=0.9900, 7 negative triangles 253: dt=0.9900, 10 negative triangles 254: dt=0.9900, 9 negative triangles 255: dt=0.9900, 4 negative triangles 256: dt=0.9900, 8 negative triangles 257: dt=0.9900, 4 negative triangles 258: dt=0.9900, 9 negative triangles 259: dt=0.9900, 8 negative triangles 260: dt=0.9900, 6 negative triangles 261: dt=0.9900, 2 negative triangles 262: dt=0.9900, 2 negative triangles 263: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.75 hours mris_sphere utimesec 7472.463012 mris_sphere stimesec 5.569153 mris_sphere ru_maxrss 317228 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 55998 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10928 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 110276 mris_sphere ru_nivcsw 341591 FSRUNTIME@ mris_sphere 1.7467 hours 1 threads PIDs (27422 27425) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sun Oct 8 10:49:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Sun Oct 8 10:49:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 31524 of (31524 31527) to complete... Waiting for PID 31527 of (31524 31527) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 5.580 curvature mean = 0.022, std = 0.818 curvature mean = 0.016, std = 0.855 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 361896.5, tmin=1.1238 d=32.00 min @ (0.00, 8.00, 0.00) sse = 289369.9, tmin=2.2698 d=16.00 min @ (4.00, 0.00, -4.00) sse = 262620.3, tmin=3.4242 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 259453.7, tmin=4.6244 d=4.00 min @ (1.00, 0.00, 1.00) sse = 257551.5, tmin=5.8339 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 257465.1, tmin=7.0473 d=1.00 min @ (0.25, 0.25, 0.00) sse = 257283.9, tmin=8.2474 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 9.44 min curvature mean = -0.006, std = 0.830 curvature mean = 0.007, std = 0.945 curvature mean = -0.010, std = 0.840 curvature mean = 0.003, std = 0.977 curvature mean = -0.012, std = 0.841 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.026, std = 0.284 curvature mean = 0.038, std = 0.246 curvature mean = 0.064, std = 0.340 curvature mean = 0.035, std = 0.302 curvature mean = 0.039, std = 0.534 curvature mean = 0.034, std = 0.329 curvature mean = 0.021, std = 0.682 curvature mean = 0.034, std = 0.340 curvature mean = 0.007, std = 0.794 MRISregister() return, current seed 0 -01: dt=0.0000, 25 negative triangles 117: dt=0.9900, 25 negative triangles expanding nbhd size to 1 118: dt=0.9900, 29 negative triangles 119: dt=0.9900, 25 negative triangles 120: dt=0.9900, 23 negative triangles 121: dt=0.9900, 23 negative triangles 122: dt=0.9900, 22 negative triangles 123: dt=0.9900, 18 negative triangles 124: dt=0.9900, 14 negative triangles 125: dt=0.9900, 15 negative triangles 126: dt=0.9900, 13 negative triangles 127: dt=0.9900, 11 negative triangles 128: dt=0.9900, 11 negative triangles 129: dt=0.9900, 9 negative triangles 130: dt=0.9900, 5 negative triangles 131: dt=0.9900, 5 negative triangles 132: dt=0.9900, 2 negative triangles 133: dt=0.9900, 1 negative triangles 134: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.34 hours mris_register utimesec 4806.365321 mris_register stimesec 1.869715 mris_register ru_maxrss 277188 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 39770 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10816 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 405322 mris_register ru_nivcsw 251630 FSRUNTIME@ mris_register 1.3353 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 5.698 curvature mean = 0.019, std = 0.817 curvature mean = 0.017, std = 0.852 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (8.00, -8.00, 0.00) sse = 369997.8, tmin=5.0650 d=16.00 min @ (-4.00, 0.00, -4.00) sse = 348248.9, tmin=7.6121 d=8.00 min @ (0.00, 2.00, 2.00) sse = 345031.7, tmin=10.1948 d=4.00 min @ (0.00, -1.00, -1.00) sse = 343818.1, tmin=12.8257 d=2.00 min @ (0.00, 0.50, 0.00) sse = 343675.9, tmin=15.4552 d=1.00 min @ (-0.25, -0.25, 0.00) sse = 343638.3, tmin=18.0755 d=0.50 min @ (0.12, 0.00, 0.12) sse = 343614.6, tmin=20.6925 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 20.69 min curvature mean = -0.008, std = 0.810 curvature mean = 0.007, std = 0.941 curvature mean = -0.014, std = 0.815 curvature mean = 0.003, std = 0.976 curvature mean = -0.017, std = 0.813 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.027, std = 0.293 curvature mean = 0.030, std = 0.235 curvature mean = 0.065, std = 0.332 curvature mean = 0.028, std = 0.292 curvature mean = 0.041, std = 0.514 curvature mean = 0.027, std = 0.318 curvature mean = 0.024, std = 0.655 curvature mean = 0.027, std = 0.329 curvature mean = 0.008, std = 0.766 MRISregister() return, current seed 0 -01: dt=0.0000, 85 negative triangles 123: dt=0.9900, 85 negative triangles expanding nbhd size to 1 124: dt=0.9900, 98 negative triangles 125: dt=0.9900, 71 negative triangles 126: dt=0.9900, 51 negative triangles 127: dt=0.9900, 41 negative triangles 128: dt=0.9900, 35 negative triangles 129: dt=0.9900, 35 negative triangles 130: dt=0.9900, 28 negative triangles 131: dt=0.9900, 27 negative triangles 132: dt=0.9900, 23 negative triangles 133: dt=0.9900, 20 negative triangles 134: dt=0.9900, 22 negative triangles 135: dt=0.9900, 21 negative triangles 136: dt=0.9900, 16 negative triangles 137: dt=0.9900, 16 negative triangles 138: dt=0.9900, 10 negative triangles 139: dt=0.9900, 13 negative triangles 140: dt=0.9900, 11 negative triangles 141: dt=0.9900, 7 negative triangles 142: dt=0.9900, 7 negative triangles 143: dt=0.9900, 3 negative triangles 144: dt=0.9900, 8 negative triangles 145: dt=0.9900, 5 negative triangles 146: dt=0.9900, 4 negative triangles 147: dt=0.9900, 3 negative triangles 148: dt=0.9900, 3 negative triangles 149: dt=0.9900, 1 negative triangles 150: dt=0.9900, 5 negative triangles 151: dt=0.9900, 1 negative triangles 152: dt=0.9900, 3 negative triangles 153: dt=0.9900, 1 negative triangles 154: dt=0.9900, 2 negative triangles 155: dt=0.9900, 1 negative triangles 156: dt=0.9900, 2 negative triangles 157: dt=0.9900, 2 negative triangles 158: dt=0.9900, 2 negative triangles 159: dt=0.9405, 3 negative triangles 160: dt=0.9405, 3 negative triangles 161: dt=0.9405, 2 negative triangles 162: dt=0.9405, 1 negative triangles 163: dt=0.9405, 1 negative triangles 164: dt=0.9405, 1 negative triangles 165: dt=0.9405, 1 negative triangles 166: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 3.04 hours mris_register utimesec 12482.820322 mris_register stimesec 9.242594 mris_register ru_maxrss 281244 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 40733 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 10872 mris_register ru_oublock 10968 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 252257 mris_register ru_nivcsw 396536 FSRUNTIME@ mris_register 3.0416 hours 1 threads PIDs (31524 31527) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 13:51:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 13:51:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 5119 of (5119 5122) to complete... Waiting for PID 5122 of (5119 5122) 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 (5119 5122) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 13:52:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 13:52:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 5172 of (5172 5175) to complete... Waiting for PID 5175 of (5172 5175) 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 (5172 5175) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 13:52:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 13:52:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 5219 of (5219 5222) to complete... Waiting for PID 5222 of (5219 5222) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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... 1409 labels changed using aseg relabeling using gibbs priors... 000: 3415 changed, 152526 examined... 001: 827 changed, 14385 examined... 002: 216 changed, 4587 examined... 003: 59 changed, 1277 examined... 004: 25 changed, 369 examined... 005: 11 changed, 150 examined... 006: 4 changed, 66 examined... 007: 4 changed, 26 examined... 008: 0 changed, 23 examined... 289 labels changed using aseg 000: 136 total segments, 93 labels (383 vertices) changed 001: 44 total segments, 2 labels (7 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1346 vertices marked for relabeling... 1346 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 30 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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... 1173 labels changed using aseg relabeling using gibbs priors... 000: 2988 changed, 154525 examined... 001: 734 changed, 12982 examined... 002: 179 changed, 4072 examined... 003: 52 changed, 1096 examined... 004: 18 changed, 324 examined... 005: 6 changed, 110 examined... 006: 2 changed, 36 examined... 007: 0 changed, 11 examined... 173 labels changed using aseg 000: 104 total segments, 67 labels (332 vertices) changed 001: 40 total segments, 3 labels (3 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1485 vertices marked for relabeling... 1485 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 15 seconds. PIDs (5219 5222) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 13:52:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050490 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 13:52:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050490 rh Waiting for PID 5286 of (5286 5289) to complete... Waiting for PID 5289 of (5286 5289) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050490 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-6.0.0/0050490/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... 18861 bright wm thresholded. 604 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.orig... computing class statistics... border white: 281912 voxels (1.68%) border gray 319696 voxels (1.91%) WM (96.0): 96.5 +- 9.0 [70.0 --> 110.0] GM (68.0) : 68.0 +- 10.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 52.8 (was 70) setting MAX_BORDER_WHITE to 110.0 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 42.5 (was 40) setting MAX_GRAY to 92.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.3 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-7.8, GM=63+-8.7 mean inside = 91.3, mean outside = 71.7 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.25 (0.03-->4.57) (max @ vno 108379 --> 108380) face area 0.34 +- 0.16 (0.00-->3.39) mean absolute distance = 0.53 +- 0.74 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 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 157 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown deleting segment 7 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown mean border=76.2, 35 (35) missing vertices, mean dist 0.3 [0.6 (%16.4)->0.5 (%83.6))] %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.11-->4.72) (max @ vno 108380 --> 108379) face area 0.34 +- 0.16 (0.00-->3.48) mean absolute distance = 0.33 +- 0.53 3795 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2568560.0, rms=7.898 001: dt: 0.5000, sse=1411311.5, rms=4.776 (39.529%) 002: dt: 0.5000, sse=1143989.6, rms=3.724 (22.026%) 003: dt: 0.5000, sse=1108550.8, rms=3.568 (4.177%) 004: dt: 0.5000, sse=1072233.8, rms=3.397 (4.807%) rms = 3.50, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=905890.7, rms=2.356 (30.627%) 006: dt: 0.2500, sse=848154.8, rms=1.850 (21.482%) 007: dt: 0.2500, sse=831939.7, rms=1.694 (8.435%) rms = 1.65, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=828308.0, rms=1.652 (2.475%) 009: dt: 0.1250, sse=822237.9, rms=1.586 (3.986%) rms = 1.58, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=821997.2, rms=1.577 (0.570%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 3 with 103 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 20 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown mean border=79.5, 54 (11) missing vertices, mean dist -0.2 [0.4 (%73.0)->0.2 (%27.0))] %80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.08-->5.07) (max @ vno 108380 --> 108379) face area 0.36 +- 0.17 (0.00-->4.11) mean absolute distance = 0.26 +- 0.40 4406 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1425067.8, rms=4.641 011: dt: 0.5000, sse=1071937.8, rms=3.064 (33.986%) rms = 3.24, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=947613.4, rms=2.277 (25.684%) 013: dt: 0.2500, sse=881596.7, rms=1.718 (24.548%) 014: dt: 0.2500, sse=859537.2, rms=1.469 (14.485%) 015: dt: 0.2500, sse=851964.0, rms=1.380 (6.076%) rms = 1.34, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=850602.8, rms=1.341 (2.854%) 017: dt: 0.1250, sse=844464.9, rms=1.282 (4.346%) rms = 1.28, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=844237.9, rms=1.281 (0.108%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 107 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 20 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown mean border=81.4, 67 (10) missing vertices, mean dist -0.1 [0.3 (%63.9)->0.2 (%36.1))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.25 (0.08-->5.05) (max @ vno 108380 --> 108379) face area 0.35 +- 0.16 (0.00-->4.19) mean absolute distance = 0.26 +- 0.36 4304 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=993206.5, rms=2.775 019: dt: 0.5000, sse=982003.6, rms=2.645 (4.673%) rms = 3.03, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=860322.1, rms=1.747 (33.944%) 021: dt: 0.2500, sse=823729.1, rms=1.350 (22.761%) 022: dt: 0.2500, sse=817866.4, rms=1.248 (7.543%) rms = 1.24, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=812990.2, rms=1.237 (0.880%) 024: dt: 0.1250, sse=808936.6, rms=1.172 (5.218%) rms = 1.18, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=808296.8, rms=1.176 (-0.272%) positioning took 1.2 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 removing 2 vertex label from ripped group deleting segment 3 with 102 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 20 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown mean border=82.2, 73 (8) missing vertices, mean dist -0.0 [0.3 (%54.7)->0.2 (%45.3))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=839374.1, rms=1.672 rms = 1.84, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=796976.4, rms=1.162 (30.487%) 027: dt: 0.2500, sse=780269.6, rms=0.887 (23.692%) rms = 0.89, time step reduction 2 of 3 to 0.125... rms = 0.88, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=779187.8, rms=0.883 (0.457%) positioning took 0.8 minutes generating cortex label... 8 non-cortical segments detected only using segment with 8328 vertices erasing segment 1 (vno[0] = 94701) erasing segment 2 (vno[0] = 104655) erasing segment 3 (vno[0] = 107495) erasing segment 4 (vno[0] = 108417) erasing segment 5 (vno[0] = 109348) erasing segment 6 (vno[0] = 111556) erasing segment 7 (vno[0] = 120208) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.area vertex spacing 0.90 +- 0.26 (0.03-->5.19) (max @ vno 108379 --> 108380) face area 0.34 +- 0.16 (0.00-->4.20) 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=51.3, 58 (58) missing vertices, mean dist 1.7 [0.2 (%0.0)->3.0 (%100.0))] %13 local maxima, %43 large gradients and %40 min vals, 686 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=29762172.0, rms=31.523 001: dt: 0.0500, sse=26197402.0, rms=29.523 (6.345%) 002: dt: 0.0500, sse=23621610.0, rms=27.989 (5.196%) 003: dt: 0.0500, sse=21639090.0, rms=26.748 (4.433%) 004: dt: 0.0500, sse=20031638.0, rms=25.698 (3.926%) 005: dt: 0.0500, sse=18679012.0, rms=24.780 (3.573%) 006: dt: 0.0500, sse=17509580.0, rms=23.958 (3.318%) 007: dt: 0.0500, sse=16477574.0, rms=23.208 (3.130%) 008: dt: 0.0500, sse=15552422.0, rms=22.514 (2.988%) 009: dt: 0.0500, sse=14712902.0, rms=21.866 (2.880%) 010: dt: 0.0500, sse=13946098.0, rms=21.256 (2.788%) positioning took 1.7 minutes mean border=51.1, 48 (33) missing vertices, mean dist 1.4 [0.0 (%0.0)->2.4 (%100.0))] %13 local maxima, %43 large gradients and %40 min vals, 643 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=14593958.0, rms=21.777 011: dt: 0.0500, sse=13886399.0, rms=21.213 (2.591%) 012: dt: 0.0500, sse=13233426.0, rms=20.678 (2.519%) 013: dt: 0.0500, sse=12628352.0, rms=20.170 (2.456%) 014: dt: 0.0500, sse=12067110.0, rms=19.687 (2.394%) 015: dt: 0.0500, sse=11546334.0, rms=19.228 (2.332%) 016: dt: 0.0500, sse=11061937.0, rms=18.791 (2.273%) 017: dt: 0.0500, sse=10611011.0, rms=18.375 (2.216%) 018: dt: 0.0500, sse=10191678.0, rms=17.979 (2.155%) 019: dt: 0.0500, sse=9801357.0, rms=17.602 (2.095%) 020: dt: 0.0500, sse=9437904.0, rms=17.244 (2.035%) positioning took 1.7 minutes mean border=51.0, 72 (28) missing vertices, mean dist 1.2 [0.1 (%0.8)->2.1 (%99.2))] %14 local maxima, %43 large gradients and %39 min vals, 599 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=9549234.0, rms=17.363 021: dt: 0.0500, sse=9205318.0, rms=17.019 (1.979%) 022: dt: 0.0500, sse=8885649.0, rms=16.693 (1.915%) 023: dt: 0.0500, sse=8586732.0, rms=16.382 (1.861%) 024: dt: 0.0500, sse=8308631.0, rms=16.088 (1.798%) 025: dt: 0.0500, sse=8049604.5, rms=15.809 (1.736%) 026: dt: 0.0500, sse=7807815.0, rms=15.543 (1.679%) 027: dt: 0.0500, sse=7580886.5, rms=15.290 (1.630%) 028: dt: 0.0500, sse=7366054.5, rms=15.046 (1.595%) 029: dt: 0.0500, sse=7162448.5, rms=14.811 (1.562%) 030: dt: 0.0500, sse=6969210.5, rms=14.584 (1.530%) positioning took 1.7 minutes mean border=51.0, 100 (25) missing vertices, mean dist 1.1 [0.1 (%7.6)->1.9 (%92.4))] %14 local maxima, %43 large gradients and %39 min vals, 566 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=7054325.0, rms=14.686 031: dt: 0.5000, sse=5695360.0, rms=12.994 (11.519%) 032: dt: 0.5000, sse=4759852.0, rms=11.680 (10.117%) 033: dt: 0.5000, sse=4037138.0, rms=10.554 (9.642%) 034: dt: 0.5000, sse=3461212.5, rms=9.555 (9.462%) 035: dt: 0.5000, sse=2991665.0, rms=8.658 (9.394%) 036: dt: 0.5000, sse=2602582.5, rms=7.834 (9.517%) 037: dt: 0.5000, sse=2276125.8, rms=7.073 (9.713%) 038: dt: 0.5000, sse=2023942.0, rms=6.419 (9.238%) 039: dt: 0.5000, sse=1823200.0, rms=5.853 (8.817%) 040: dt: 0.5000, sse=1683072.8, rms=5.419 (7.429%) 041: dt: 0.5000, sse=1578122.5, rms=5.073 (6.379%) 042: dt: 0.5000, sse=1513598.6, rms=4.842 (4.542%) 043: dt: 0.5000, sse=1466469.2, rms=4.674 (3.485%) 044: dt: 0.5000, sse=1441205.2, rms=4.575 (2.116%) 045: dt: 0.5000, sse=1422256.1, rms=4.505 (1.527%) rms = 4.46, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1410498.1, rms=4.456 (1.093%) 047: dt: 0.2500, sse=1342691.6, rms=4.134 (7.230%) 048: dt: 0.2500, sse=1325339.0, rms=4.058 (1.832%) rms = 4.05, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1325086.1, rms=4.054 (0.095%) rms = 4.02, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1317554.4, rms=4.017 (0.912%) positioning took 3.8 minutes mean border=50.0, 2327 (16) missing vertices, mean dist 0.1 [0.2 (%48.0)->0.6 (%52.0))] %25 local maxima, %35 large gradients and %34 min vals, 328 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=1581280.1, rms=4.218 051: dt: 0.5000, sse=1455028.8, rms=3.671 (12.966%) 052: dt: 0.5000, sse=1422030.5, rms=3.553 (3.198%) rms = 3.55, time step reduction 1 of 3 to 0.250... 053: dt: 0.5000, sse=1419740.2, rms=3.552 (0.035%) 054: dt: 0.2500, sse=1340842.5, rms=3.065 (13.706%) 055: dt: 0.2500, sse=1319575.1, rms=2.943 (3.996%) rms = 2.93, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1317783.6, rms=2.931 (0.408%) 057: dt: 0.1250, sse=1309214.0, rms=2.873 (1.985%) rms = 2.86, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1307431.9, rms=2.864 (0.313%) positioning took 1.4 minutes mean border=49.3, 2697 (15) missing vertices, mean dist 0.1 [0.2 (%49.4)->0.5 (%50.6))] %35 local maxima, %26 large gradients and %33 min vals, 362 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=1363939.2, rms=3.164 rms = 3.26, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1338844.4, rms=3.016 (4.664%) 060: dt: 0.2500, sse=1325213.6, rms=2.941 (2.503%) rms = 2.91, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1318807.9, rms=2.911 (0.999%) 062: dt: 0.1250, sse=1310227.8, rms=2.855 (1.926%) rms = 2.84, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1307132.4, rms=2.840 (0.533%) positioning took 1.1 minutes mean border=48.7, 4966 (15) missing vertices, mean dist 0.1 [0.2 (%48.6)->0.4 (%51.4))] %39 local maxima, %21 large gradients and %32 min vals, 362 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-6.0.0/0050490/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1333719.9, rms=2.982 rms = 3.08, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1318192.0, rms=2.888 (3.177%) 065: dt: 0.2500, sse=1304756.8, rms=2.822 (2.269%) rms = 2.79, time step reduction 2 of 3 to 0.125... 066: dt: 0.2500, sse=1297994.8, rms=2.790 (1.132%) 067: dt: 0.1250, sse=1288483.9, rms=2.728 (2.238%) rms = 2.71, time step reduction 3 of 3 to 0.062... 068: dt: 0.1250, sse=1284379.2, rms=2.707 (0.768%) positioning took 1.1 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.area.pial vertex spacing 1.03 +- 0.46 (0.07-->8.70) (max @ vno 104403 --> 104383) face area 0.42 +- 0.34 (0.00-->7.75) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 152526 vertices processed 25000 of 152526 vertices processed 50000 of 152526 vertices processed 75000 of 152526 vertices processed 100000 of 152526 vertices processed 125000 of 152526 vertices processed 150000 of 152526 vertices processed 0 of 152526 vertices processed 25000 of 152526 vertices processed 50000 of 152526 vertices processed 75000 of 152526 vertices processed 100000 of 152526 vertices processed 125000 of 152526 vertices processed 150000 of 152526 vertices processed thickness calculation complete, 709:1254 truncations. 28305 vertices at 0 distance 100548 vertices at 1 distance 97151 vertices at 2 distance 43359 vertices at 3 distance 14735 vertices at 4 distance 4848 vertices at 5 distance 1660 vertices at 6 distance 712 vertices at 7 distance 282 vertices at 8 distance 151 vertices at 9 distance 77 vertices at 10 distance 49 vertices at 11 distance 52 vertices at 12 distance 35 vertices at 13 distance 34 vertices at 14 distance 27 vertices at 15 distance 25 vertices at 16 distance 20 vertices at 17 distance 17 vertices at 18 distance 10 vertices at 19 distance 9 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.thickness positioning took 23.1 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050490 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-6.0.0/0050490/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... 18861 bright wm thresholded. 604 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.orig... computing class statistics... border white: 281912 voxels (1.68%) border gray 319696 voxels (1.91%) WM (96.0): 96.5 +- 9.0 [70.0 --> 110.0] GM (68.0) : 68.0 +- 10.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.8 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 65.0 (was 85) setting MAX_CSF to 44.5 (was 40) setting MAX_GRAY to 93.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.3 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-7.8, GM=65+-7.8 mean inside = 91.7, mean outside = 72.4 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.24 (0.02-->4.01) (max @ vno 24098 --> 25235) face area 0.34 +- 0.15 (0.00-->4.28) mean absolute distance = 0.53 +- 0.78 3586 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 237 points - only 0.00% unknown deleting segment 5 with 35 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown mean border=78.1, 63 (63) missing vertices, mean dist 0.3 [0.6 (%17.5)->0.5 (%82.5))] %69 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.05-->3.98) (max @ vno 123731 --> 123723) face area 0.34 +- 0.16 (0.00-->3.81) mean absolute distance = 0.33 +- 0.57 3741 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2379276.2, rms=7.415 001: dt: 0.5000, sse=1392713.5, rms=4.632 (37.528%) 002: dt: 0.5000, sse=1139185.1, rms=3.638 (21.465%) 003: dt: 0.5000, sse=1118103.0, rms=3.514 (3.419%) 004: dt: 0.5000, sse=1066665.0, rms=3.315 (5.660%) rms = 3.44, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=903378.0, rms=2.291 (30.880%) 006: dt: 0.2500, sse=847913.1, rms=1.800 (21.444%) 007: dt: 0.2500, sse=834445.1, rms=1.646 (8.535%) rms = 1.61, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=828903.8, rms=1.613 (2.046%) 009: dt: 0.1250, sse=823342.8, rms=1.547 (4.072%) rms = 1.54, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=822787.3, rms=1.539 (0.519%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 1 with 3 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 40 points - only 0.00% unknown deleting segment 4 with 38 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown mean border=81.1, 64 (10) missing vertices, mean dist -0.2 [0.4 (%70.9)->0.2 (%29.1))] %78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.07-->4.13) (max @ vno 55092 --> 55093) face area 0.36 +- 0.17 (0.00-->4.49) mean absolute distance = 0.28 +- 0.44 4038 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1354921.1, rms=4.343 011: dt: 0.5000, sse=1060712.9, rms=2.917 (32.823%) rms = 3.12, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=935119.1, rms=2.156 (26.107%) 013: dt: 0.2500, sse=876738.8, rms=1.643 (23.776%) 014: dt: 0.2500, sse=857526.8, rms=1.441 (12.328%) 015: dt: 0.2500, sse=853807.1, rms=1.371 (4.841%) rms = 1.34, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=849497.9, rms=1.342 (2.119%) 017: dt: 0.1250, sse=845816.0, rms=1.287 (4.059%) rms = 1.28, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=845187.2, rms=1.283 (0.346%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 51 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 39 points - only 0.00% unknown deleting segment 6 with 43 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown mean border=82.9, 77 (5) missing vertices, mean dist -0.1 [0.3 (%62.8)->0.2 (%37.2))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.07-->4.51) (max @ vno 111330 --> 110402) face area 0.34 +- 0.16 (0.00-->5.02) mean absolute distance = 0.26 +- 0.37 4165 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=996523.7, rms=2.757 019: dt: 0.5000, sse=968235.1, rms=2.546 (7.641%) rms = 2.93, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=861039.8, rms=1.717 (32.566%) 021: dt: 0.2500, sse=826542.8, rms=1.343 (21.765%) 022: dt: 0.2500, sse=818970.1, rms=1.251 (6.876%) rms = 1.24, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=817362.1, rms=1.236 (1.184%) 024: dt: 0.1250, sse=812619.4, rms=1.176 (4.904%) rms = 1.18, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=812121.3, rms=1.175 (0.027%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 99 points - only 0.00% unknown deleting segment 2 with 38 points - only 0.00% unknown deleting segment 3 with 45 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown mean border=83.6, 101 (4) missing vertices, mean dist -0.0 [0.3 (%54.0)->0.2 (%46.0))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=841924.2, rms=1.652 rms = 1.78, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=801637.6, rms=1.167 (29.348%) 027: dt: 0.2500, sse=787579.9, rms=0.892 (23.588%) rms = 0.90, time step reduction 2 of 3 to 0.125... rms = 0.89, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=784410.8, rms=0.888 (0.455%) positioning took 0.5 minutes generating cortex label... 7 non-cortical segments detected only using segment with 7688 vertices erasing segment 1 (vno[0] = 70657) erasing segment 2 (vno[0] = 96781) erasing segment 3 (vno[0] = 100810) erasing segment 4 (vno[0] = 117438) erasing segment 5 (vno[0] = 124558) erasing segment 6 (vno[0] = 154232) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.area vertex spacing 0.90 +- 0.25 (0.02-->4.59) (max @ vno 110402 --> 111330) face area 0.34 +- 0.16 (0.00-->5.04) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=53.6, 65 (65) missing vertices, mean dist 1.6 [1.9 (%0.0)->2.9 (%100.0))] %13 local maxima, %41 large gradients and %42 min vals, 738 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=28591284.0, rms=30.667 001: dt: 0.0500, sse=25126148.0, rms=28.695 (6.430%) 002: dt: 0.0500, sse=22636180.0, rms=27.190 (5.246%) 003: dt: 0.0500, sse=20726322.0, rms=25.976 (4.464%) 004: dt: 0.0500, sse=19182336.0, rms=24.952 (3.944%) 005: dt: 0.0500, sse=17887744.0, rms=24.059 (3.578%) 006: dt: 0.0500, sse=16771449.0, rms=23.262 (3.314%) 007: dt: 0.0500, sse=15788946.0, rms=22.537 (3.117%) 008: dt: 0.0500, sse=14910352.0, rms=21.868 (2.968%) 009: dt: 0.0500, sse=14115389.0, rms=21.244 (2.851%) 010: dt: 0.0500, sse=13390797.0, rms=20.660 (2.752%) positioning took 1.1 minutes mean border=53.5, 47 (28) missing vertices, mean dist 1.3 [0.7 (%0.0)->2.3 (%100.0))] %14 local maxima, %41 large gradients and %41 min vals, 700 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=14114317.0, rms=21.246 011: dt: 0.0500, sse=13446091.0, rms=20.708 (2.534%) 012: dt: 0.0500, sse=12830051.0, rms=20.199 (2.459%) 013: dt: 0.0500, sse=12260551.0, rms=19.716 (2.389%) 014: dt: 0.0500, sse=11732908.0, rms=19.258 (2.323%) 015: dt: 0.0500, sse=11243536.0, rms=18.824 (2.257%) 016: dt: 0.0500, sse=10788885.0, rms=18.410 (2.195%) 017: dt: 0.0500, sse=10366025.0, rms=18.017 (2.134%) 018: dt: 0.0500, sse=9972790.0, rms=17.644 (2.072%) 019: dt: 0.0500, sse=9606747.0, rms=17.289 (2.011%) 020: dt: 0.0500, sse=9265819.0, rms=16.952 (1.951%) positioning took 1.1 minutes mean border=53.3, 69 (18) missing vertices, mean dist 1.2 [0.1 (%1.1)->2.0 (%98.9))] %14 local maxima, %41 large gradients and %41 min vals, 690 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=9382395.0, rms=17.075 021: dt: 0.0500, sse=9057217.0, rms=16.749 (1.907%) 022: dt: 0.0500, sse=8754779.0, rms=16.441 (1.844%) 023: dt: 0.0500, sse=8471255.0, rms=16.146 (1.794%) 024: dt: 0.0500, sse=8207091.5, rms=15.866 (1.733%) 025: dt: 0.0500, sse=7960495.0, rms=15.600 (1.675%) 026: dt: 0.0500, sse=7729750.5, rms=15.347 (1.622%) 027: dt: 0.0500, sse=7512824.5, rms=15.105 (1.576%) 028: dt: 0.0500, sse=7307445.5, rms=14.873 (1.540%) 029: dt: 0.0500, sse=7112433.0, rms=14.648 (1.509%) 030: dt: 0.0500, sse=6927000.5, rms=14.431 (1.480%) positioning took 1.1 minutes mean border=53.3, 91 (17) missing vertices, mean dist 1.0 [0.1 (%9.9)->1.9 (%90.1))] %14 local maxima, %41 large gradients and %41 min vals, 661 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=7007615.0, rms=14.526 031: dt: 0.5000, sse=5685522.5, rms=12.889 (11.275%) 032: dt: 0.5000, sse=4774513.5, rms=11.618 (9.861%) 033: dt: 0.5000, sse=4069952.0, rms=10.530 (9.359%) 034: dt: 0.5000, sse=3506505.2, rms=9.566 (9.159%) 035: dt: 0.5000, sse=3032196.8, rms=8.673 (9.336%) 036: dt: 0.5000, sse=2642254.5, rms=7.861 (9.364%) 037: dt: 0.5000, sse=2315803.2, rms=7.114 (9.502%) 038: dt: 0.5000, sse=2057048.2, rms=6.459 (9.210%) 039: dt: 0.5000, sse=1861106.2, rms=5.916 (8.401%) 040: dt: 0.5000, sse=1721930.5, rms=5.496 (7.091%) 041: dt: 0.5000, sse=1619535.8, rms=5.168 (5.974%) 042: dt: 0.5000, sse=1551382.2, rms=4.933 (4.545%) 043: dt: 0.5000, sse=1501293.8, rms=4.757 (3.563%) 044: dt: 0.5000, sse=1469673.2, rms=4.639 (2.494%) 045: dt: 0.5000, sse=1447026.2, rms=4.555 (1.814%) 046: dt: 0.5000, sse=1431843.6, rms=4.495 (1.310%) rms = 4.46, time step reduction 1 of 3 to 0.250... 047: dt: 0.5000, sse=1421239.4, rms=4.455 (0.882%) 048: dt: 0.2500, sse=1356744.0, rms=4.149 (6.865%) 049: dt: 0.2500, sse=1338394.5, rms=4.072 (1.865%) rms = 4.07, time step reduction 2 of 3 to 0.125... rms = 4.05, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1334714.6, rms=4.054 (0.437%) positioning took 3.0 minutes mean border=52.2, 2709 (2) missing vertices, mean dist 0.2 [0.2 (%46.8)->0.7 (%53.2))] %25 local maxima, %33 large gradients and %36 min vals, 323 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=1646132.1, rms=4.453 051: dt: 0.5000, sse=1516327.1, rms=3.929 (11.773%) 052: dt: 0.5000, sse=1457182.1, rms=3.696 (5.927%) rms = 3.68, time step reduction 1 of 3 to 0.250... 053: dt: 0.5000, sse=1451123.4, rms=3.675 (0.554%) 054: dt: 0.2500, sse=1363523.4, rms=3.170 (13.762%) 055: dt: 0.2500, sse=1339227.8, rms=3.034 (4.269%) rms = 3.01, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1334617.8, rms=3.007 (0.908%) 057: dt: 0.1250, sse=1322336.6, rms=2.929 (2.594%) rms = 2.91, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1318630.8, rms=2.908 (0.714%) positioning took 1.4 minutes mean border=51.4, 2983 (2) missing vertices, mean dist 0.1 [0.2 (%46.6)->0.5 (%53.4))] %34 local maxima, %24 large gradients and %35 min vals, 366 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=1393568.2, rms=3.275 rms = 3.32, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1362484.8, rms=3.101 (5.307%) 060: dt: 0.2500, sse=1342400.1, rms=2.990 (3.593%) rms = 2.95, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1334520.8, rms=2.952 (1.272%) 062: dt: 0.1250, sse=1323991.2, rms=2.885 (2.278%) rms = 2.86, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1319919.6, rms=2.864 (0.723%) positioning took 1.1 minutes mean border=50.9, 5447 (2) missing vertices, mean dist 0.1 [0.2 (%45.6)->0.4 (%54.4))] %39 local maxima, %19 large gradients and %34 min vals, 371 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-6.0.0/0050490/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1349689.9, rms=3.016 rms = 3.11, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1331967.5, rms=2.910 (3.531%) 065: dt: 0.2500, sse=1317083.9, rms=2.834 (2.613%) rms = 2.81, time step reduction 2 of 3 to 0.125... 066: dt: 0.2500, sse=1310877.5, rms=2.807 (0.961%) 067: dt: 0.1250, sse=1299727.8, rms=2.735 (2.560%) rms = 2.71, time step reduction 3 of 3 to 0.062... 068: dt: 0.1250, sse=1295306.6, rms=2.712 (0.831%) positioning took 1.1 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.area.pial vertex spacing 1.03 +- 0.46 (0.04-->7.33) (max @ vno 106470 --> 105422) face area 0.42 +- 0.33 (0.00-->5.92) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 154525 vertices processed 25000 of 154525 vertices processed 50000 of 154525 vertices processed 75000 of 154525 vertices processed 100000 of 154525 vertices processed 125000 of 154525 vertices processed 150000 of 154525 vertices processed 0 of 154525 vertices processed 25000 of 154525 vertices processed 50000 of 154525 vertices processed 75000 of 154525 vertices processed 100000 of 154525 vertices processed 125000 of 154525 vertices processed 150000 of 154525 vertices processed thickness calculation complete, 734:1585 truncations. 31621 vertices at 0 distance 103576 vertices at 1 distance 95035 vertices at 2 distance 43210 vertices at 3 distance 14846 vertices at 4 distance 4800 vertices at 5 distance 1698 vertices at 6 distance 692 vertices at 7 distance 258 vertices at 8 distance 108 vertices at 9 distance 84 vertices at 10 distance 48 vertices at 11 distance 38 vertices at 12 distance 34 vertices at 13 distance 16 vertices at 14 distance 21 vertices at 15 distance 20 vertices at 16 distance 12 vertices at 17 distance 13 vertices at 18 distance 10 vertices at 19 distance 32 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.thickness positioning took 17.7 minutes PIDs (5286 5289) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 14:15:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label Total face volume 297729 Total vertex volume 293320 (mask=0) #@# 0050490 lh 293320 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 14:15:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label Total face volume 297991 Total vertex volume 293786 (mask=0) #@# 0050490 rh 293786 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 14:16:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 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 = 311 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/ribbon.mgz mris_volmask took 19.25 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 14:35:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 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 0050490 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 14:35:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 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 0050490 rh pial Waiting for PID 6925 of (6925 6929 6934 6937) to complete... Waiting for PID 6929 of (6925 6929 6934 6937) to complete... Waiting for PID 6934 of (6925 6929 6934 6937) to complete... Waiting for PID 6937 of (6925 6929 6934 6937) 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 0050490 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297729 Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 1452 1028 2661 2.640 0.489 0.110 0.025 10 1.3 bankssts 1130 742 2422 2.880 0.730 0.148 0.029 17 1.3 caudalanteriorcingulate 3987 2675 8257 2.798 0.629 0.123 0.036 45 6.4 caudalmiddlefrontal 2750 1882 3901 1.982 0.482 0.148 0.036 38 4.1 cuneus 527 361 1926 3.722 0.757 0.122 0.044 7 0.8 entorhinal 6037 4214 13566 2.775 0.717 0.124 0.032 72 8.0 fusiform 7306 5107 14077 2.448 0.647 0.130 0.028 93 8.9 inferiorparietal 5250 3743 14228 3.160 0.694 0.135 0.038 74 8.5 inferiortemporal 1625 1077 2893 2.389 0.953 0.133 0.037 23 2.1 isthmuscingulate 8572 5758 14417 2.165 0.614 0.141 0.036 115 11.9 lateraloccipital 4121 2871 8747 2.819 0.621 0.135 0.034 57 6.0 lateralorbitofrontal 5026 3521 7675 2.113 0.587 0.138 0.039 63 7.5 lingual 2518 1726 5388 2.614 0.821 0.132 0.035 42 3.5 medialorbitofrontal 4865 3382 11099 2.763 0.741 0.128 0.030 63 6.2 middletemporal 1080 714 2323 2.786 0.693 0.092 0.016 6 0.7 parahippocampal 2692 1803 5201 2.585 0.593 0.125 0.032 27 3.4 paracentral 2462 1711 5337 2.710 0.502 0.119 0.029 26 2.8 parsopercularis 1105 746 2897 2.829 0.617 0.134 0.044 17 1.8 parsorbitalis 1988 1334 4133 2.681 0.549 0.117 0.025 20 1.7 parstriangularis 1967 1360 1953 1.626 0.396 0.124 0.026 16 2.2 pericalcarine 6782 4518 11402 2.222 0.709 0.125 0.031 80 8.9 postcentral 2283 1560 4441 2.516 0.933 0.137 0.028 32 2.8 posteriorcingulate 7533 4881 14542 2.755 0.678 0.116 0.030 67 9.1 precentral 6155 4311 11223 2.453 0.594 0.134 0.033 73 8.3 precuneus 1364 933 3496 3.236 0.762 0.157 0.039 27 2.0 rostralanteriorcingulate 9697 6739 20612 2.573 0.626 0.138 0.036 156 14.1 rostralmiddlefrontal 13821 9483 32681 2.994 0.655 0.129 0.032 168 17.6 superiorfrontal 8771 5953 15975 2.371 0.615 0.130 0.031 103 10.3 superiorparietal 6992 4684 16370 3.002 0.714 0.111 0.025 72 6.9 superiortemporal 7552 5288 15015 2.530 0.621 0.128 0.030 91 9.1 supramarginal 468 316 1392 2.784 0.834 0.164 0.067 11 1.3 frontalpole 723 555 2833 3.643 0.897 0.132 0.026 10 0.9 temporalpole 833 537 1339 2.590 0.518 0.130 0.029 9 0.9 transversetemporal 4113 2847 8890 3.098 0.720 0.129 0.037 42 6.3 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050490 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297729 Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 1452 1003 2661 2.640 0.489 0.133 0.039 21 2.5 bankssts 1130 910 2422 2.880 0.730 0.157 0.039 39 1.6 caudalanteriorcingulate 3987 3193 8257 2.798 0.629 0.141 0.035 49 6.0 caudalmiddlefrontal 2750 2164 3901 1.982 0.482 0.143 0.035 42 4.4 cuneus 527 711 1926 3.722 0.757 0.212 0.052 6 1.2 entorhinal 6037 5415 13566 2.775 0.717 0.156 0.040 87 11.3 fusiform 7306 6359 14077 2.448 0.647 0.154 0.036 100 11.7 inferiorparietal 5250 4952 14228 3.160 0.694 0.164 0.043 93 10.3 inferiortemporal 1625 1304 2893 2.389 0.953 0.140 0.038 28 2.4 isthmuscingulate 8572 7293 14417 2.165 0.614 0.150 0.034 136 13.5 lateraloccipital 4121 3369 8747 2.819 0.621 0.147 0.038 65 7.1 lateralorbitofrontal 5026 4030 7675 2.113 0.587 0.141 0.036 74 8.2 lingual 2518 2321 5388 2.614 0.821 0.166 0.040 31 4.8 medialorbitofrontal 4865 4403 11099 2.763 0.741 0.156 0.039 70 8.7 middletemporal 1080 996 2323 2.786 0.693 0.140 0.033 9 1.7 parahippocampal 2692 2168 5201 2.585 0.593 0.137 0.033 31 4.1 paracentral 2462 2186 5337 2.710 0.502 0.154 0.033 26 3.9 parsopercularis 1105 1187 2897 2.829 0.617 0.187 0.041 15 2.2 parsorbitalis 1988 1672 4133 2.681 0.549 0.153 0.035 25 3.2 parstriangularis 1967 1123 1953 1.626 0.396 0.115 0.028 21 2.6 pericalcarine 6782 5650 11402 2.222 0.709 0.140 0.032 77 10.1 postcentral 2283 1905 4441 2.516 0.933 0.157 0.041 83 4.1 posteriorcingulate 7533 5488 14542 2.755 0.678 0.115 0.028 83 9.4 precentral 6155 4731 11223 2.453 0.594 0.148 0.040 113 11.1 precuneus 1364 1236 3496 3.236 0.762 0.171 0.049 33 2.9 rostralanteriorcingulate 9697 8887 20612 2.573 0.626 0.171 0.039 153 17.5 rostralmiddlefrontal 13821 11893 32681 2.994 0.655 0.152 0.039 216 24.2 superiorfrontal 8771 7229 15975 2.371 0.615 0.148 0.036 121 14.1 superiorparietal 6992 5936 16370 3.002 0.714 0.136 0.030 71 9.2 superiortemporal 7552 6549 15015 2.530 0.621 0.154 0.037 113 12.9 supramarginal 468 613 1392 2.784 0.834 0.242 0.059 8 1.4 frontalpole 723 988 2833 3.643 0.897 0.205 0.038 9 1.4 temporalpole 833 523 1339 2.590 0.518 0.108 0.028 7 1.0 transversetemporal 4113 2707 8890 3.098 0.720 0.138 0.043 79 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 0050490 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297991 Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 1359 1001 2708 2.833 0.532 0.109 0.018 10 1.0 bankssts 1530 1019 3131 2.595 0.732 0.134 0.025 25 1.5 caudalanteriorcingulate 3447 2402 7266 2.704 0.639 0.125 0.027 36 3.8 caudalmiddlefrontal 2755 1846 3927 2.065 0.530 0.152 0.040 37 4.6 cuneus 751 478 2815 3.328 1.029 0.130 0.051 11 1.7 entorhinal 5943 4104 14178 2.905 0.792 0.132 0.036 79 8.2 fusiform 10788 7450 21775 2.585 0.647 0.128 0.030 127 12.8 inferiorparietal 5597 3803 13810 3.081 0.844 0.124 0.034 63 7.0 inferiortemporal 1375 911 2858 2.659 1.074 0.137 0.038 21 1.9 isthmuscingulate 9417 6261 15954 2.365 0.633 0.142 0.037 125 13.5 lateraloccipital 4059 2763 8200 2.645 0.626 0.130 0.035 60 5.3 lateralorbitofrontal 4842 3413 7321 2.031 0.608 0.142 0.038 64 7.6 lingual 2960 2070 6043 2.429 0.785 0.135 0.039 52 4.5 medialorbitofrontal 5427 3778 13797 3.042 0.646 0.119 0.027 66 5.6 middletemporal 1221 803 2591 2.817 0.646 0.109 0.024 10 1.1 parahippocampal 2458 1655 4340 2.473 0.492 0.111 0.030 21 2.8 paracentral 1717 1199 3677 2.733 0.561 0.109 0.020 18 1.3 parsopercularis 1340 945 3241 2.677 0.786 0.142 0.033 23 1.7 parsorbitalis 1923 1356 3861 2.403 0.563 0.124 0.025 25 1.8 parstriangularis 2217 1520 2262 1.698 0.464 0.125 0.027 23 2.4 pericalcarine 5982 3857 9758 2.277 0.724 0.116 0.026 60 6.2 postcentral 1900 1305 3423 2.369 0.730 0.147 0.037 30 2.8 posteriorcingulate 8693 5674 16188 2.650 0.685 0.113 0.026 74 9.2 precentral 6796 4767 12237 2.464 0.602 0.131 0.033 85 9.0 precuneus 1213 834 2865 2.834 0.661 0.128 0.032 17 1.6 rostralanteriorcingulate 9558 6521 18653 2.312 0.671 0.134 0.037 184 14.0 rostralmiddlefrontal 13200 8958 29919 2.788 0.715 0.130 0.033 207 17.4 superiorfrontal 9310 6213 16864 2.369 0.635 0.130 0.034 113 13.1 superiorparietal 6018 4002 13607 2.963 0.641 0.107 0.027 61 6.0 superiortemporal 6437 4324 12621 2.676 0.555 0.121 0.031 70 7.8 supramarginal 573 379 1752 2.987 0.695 0.179 0.071 23 1.8 frontalpole 686 520 2652 3.467 0.838 0.154 0.042 15 1.2 temporalpole 566 329 1082 3.080 0.574 0.110 0.033 6 0.8 transversetemporal 3990 2677 8366 3.154 0.773 0.126 0.034 52 5.4 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050490 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297991 Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 1359 929 2708 2.833 0.532 0.129 0.036 20 2.0 bankssts 1530 1303 3131 2.595 0.732 0.146 0.036 28 2.2 caudalanteriorcingulate 3447 2793 7266 2.704 0.639 0.142 0.033 41 5.2 caudalmiddlefrontal 2755 2109 3927 2.065 0.530 0.137 0.034 42 4.1 cuneus 751 1002 2815 3.328 1.029 0.193 0.042 8 1.5 entorhinal 5943 5499 14178 2.905 0.792 0.155 0.038 88 10.2 fusiform 10788 8967 21775 2.585 0.647 0.141 0.032 152 15.5 inferiorparietal 5597 4875 13810 3.081 0.844 0.149 0.039 88 9.9 inferiortemporal 1375 1171 2858 2.659 1.074 0.161 0.040 31 2.4 isthmuscingulate 9417 7273 15954 2.365 0.633 0.137 0.037 132 15.6 lateraloccipital 4059 3491 8200 2.645 0.626 0.169 0.043 66 8.1 lateralorbitofrontal 4842 3899 7321 2.031 0.608 0.140 0.035 61 7.5 lingual 2960 2774 6043 2.429 0.785 0.175 0.043 44 5.8 medialorbitofrontal 5427 5209 13797 3.042 0.646 0.157 0.033 72 8.6 middletemporal 1221 1032 2591 2.817 0.646 0.137 0.030 15 1.8 parahippocampal 2458 1841 4340 2.473 0.492 0.122 0.027 31 3.0 paracentral 1717 1516 3677 2.733 0.561 0.152 0.032 22 2.5 parsopercularis 1340 1433 3241 2.677 0.786 0.193 0.042 21 2.6 parsorbitalis 1923 1821 3861 2.403 0.563 0.165 0.035 24 3.1 parstriangularis 2217 1296 2262 1.698 0.464 0.119 0.033 29 3.2 pericalcarine 5982 4681 9758 2.277 0.724 0.127 0.030 53 7.8 postcentral 1900 1535 3423 2.369 0.730 0.160 0.044 41 3.7 posteriorcingulate 8693 6265 16188 2.650 0.685 0.113 0.025 91 10.0 precentral 6796 5168 12237 2.464 0.602 0.146 0.039 104 11.8 precuneus 1213 1143 2865 2.834 0.661 0.164 0.040 13 2.1 rostralanteriorcingulate 9558 9130 18653 2.312 0.671 0.181 0.044 140 19.8 rostralmiddlefrontal 13200 11970 29919 2.788 0.715 0.164 0.041 195 24.3 superiorfrontal 9310 7647 16864 2.369 0.635 0.143 0.034 117 14.1 superiorparietal 6018 5043 13607 2.963 0.641 0.140 0.032 77 8.7 superiortemporal 6437 4970 12621 2.676 0.555 0.136 0.034 77 9.7 supramarginal 573 790 1752 2.987 0.695 0.236 0.049 7 1.6 frontalpole 686 996 2652 3.467 0.838 0.241 0.048 8 1.7 temporalpole 566 388 1082 3.080 0.574 0.101 0.024 3 0.6 transversetemporal 3990 2454 8366 3.154 0.773 0.132 0.038 83 6.1 insula PIDs (6925 6929 6934 6937) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 14:37:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 14:37:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 7046 of (7046 7049) to complete... Waiting for PID 7049 of (7046 7049) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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... 7 labels changed using aseg relabeling using gibbs priors... 000: 9715 changed, 152526 examined... 001: 2311 changed, 38077 examined... 002: 662 changed, 11921 examined... 003: 253 changed, 3765 examined... 004: 130 changed, 1497 examined... 005: 62 changed, 723 examined... 006: 37 changed, 362 examined... 007: 23 changed, 212 examined... 008: 14 changed, 119 examined... 009: 4 changed, 69 examined... 010: 2 changed, 22 examined... 011: 0 changed, 14 examined... 0 labels changed using aseg 000: 283 total segments, 194 labels (2687 vertices) changed 001: 94 total segments, 6 labels (27 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 29 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 662 vertices marked for relabeling... 662 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 20 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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... 0 labels changed using aseg relabeling using gibbs priors... 000: 9915 changed, 154525 examined... 001: 2243 changed, 39162 examined... 002: 642 changed, 11781 examined... 003: 291 changed, 3635 examined... 004: 149 changed, 1654 examined... 005: 90 changed, 838 examined... 006: 40 changed, 487 examined... 007: 11 changed, 212 examined... 008: 4 changed, 71 examined... 009: 3 changed, 22 examined... 010: 0 changed, 19 examined... 1 labels changed using aseg 000: 275 total segments, 188 labels (2584 vertices) changed 001: 97 total segments, 10 labels (25 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 50 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1098 vertices marked for relabeling... 1098 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 36 seconds. PIDs (7046 7049) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 14:38:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 14:38:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 rh white Waiting for PID 7125 of (7125 7128) to complete... Waiting for PID 7128 of (7125 7128) 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 0050490 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297729 Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 1566 1101 3361 2.448 0.695 0.145 0.042 28 2.7 G&S_frontomargin 2008 1429 4160 2.425 0.664 0.142 0.034 25 2.7 G&S_occipital_inf 1977 1282 3753 2.413 0.552 0.136 0.047 28 4.0 G&S_paracentral 1795 1203 4090 2.933 0.635 0.126 0.027 19 2.0 G&S_subcentral 1019 698 2831 2.723 0.772 0.154 0.051 21 2.1 G&S_transv_frontopol 2761 1910 6184 2.969 0.662 0.132 0.031 38 3.5 G&S_cingul-Ant 1635 1142 3549 2.937 0.538 0.130 0.026 16 1.9 G&S_cingul-Mid-Ant 1696 1176 3317 2.726 0.717 0.127 0.027 17 1.8 G&S_cingul-Mid-Post 759 529 2148 3.175 0.857 0.155 0.042 13 1.2 G_cingul-Post-dorsal 307 194 751 2.943 0.800 0.138 0.046 4 0.5 G_cingul-Post-ventral 2467 1695 3778 1.980 0.542 0.154 0.037 37 3.7 G_cuneus 1452 971 3707 2.885 0.495 0.138 0.040 22 2.3 G_front_inf-Opercular 439 289 1002 2.505 0.489 0.135 0.058 9 0.8 G_front_inf-Orbital 1212 780 3197 2.869 0.575 0.125 0.030 17 1.3 G_front_inf-Triangul 5307 3589 13466 2.801 0.647 0.153 0.049 115 11.1 G_front_middle 9689 6544 25607 3.070 0.690 0.137 0.037 143 14.0 G_front_sup 883 621 2070 3.095 0.873 0.159 0.059 15 2.2 G_Ins_lg&S_cent_ins 978 691 3223 3.603 0.744 0.150 0.047 15 1.9 G_insular_short 2611 1733 5689 2.445 0.715 0.145 0.039 43 3.8 G_occipital_middle 1861 1234 3188 2.212 0.556 0.141 0.032 25 2.3 G_occipital_sup 2642 1793 6850 2.937 0.799 0.139 0.039 43 4.2 G_oc-temp_lat-fusifor 3428 2411 5622 2.055 0.611 0.148 0.047 50 6.1 G_oc-temp_med-Lingual 1243 804 3536 3.202 0.810 0.101 0.023 10 1.1 G_oc-temp_med-Parahip 2707 1900 7468 2.951 0.679 0.143 0.040 47 4.4 G_orbital 3150 2211 8185 2.759 0.713 0.148 0.038 60 4.9 G_pariet_inf-Angular 3910 2738 8759 2.546 0.655 0.133 0.033 55 5.2 G_pariet_inf-Supramar 3468 2321 7344 2.485 0.694 0.139 0.036 54 4.7 G_parietal_sup 2515 1608 4529 2.267 0.660 0.138 0.038 38 3.7 G_postcentral 2701 1668 6887 3.056 0.649 0.120 0.038 33 3.7 G_precentral 2841 2062 6700 2.511 0.681 0.152 0.043 47 4.9 G_precuneus 940 643 2473 2.746 0.776 0.165 0.059 23 2.4 G_rectus 172 119 399 3.772 0.579 0.078 0.017 1 0.1 G_subcallosal 606 343 1072 2.664 0.572 0.117 0.031 7 0.7 G_temp_sup-G_T_transv 2298 1491 7795 3.422 0.690 0.137 0.038 41 3.0 G_temp_sup-Lateral 1053 709 2829 3.536 0.704 0.074 0.016 4 0.7 G_temp_sup-Plan_polar 1305 941 2614 2.498 0.705 0.128 0.029 17 1.6 G_temp_sup-Plan_tempo 2672 1889 8494 3.287 0.747 0.151 0.049 49 5.5 G_temporal_inf 2424 1711 6910 2.916 0.777 0.147 0.040 44 4.2 G_temporal_middle 363 245 533 2.514 0.372 0.094 0.015 2 0.2 Lat_Fis-ant-Horizont 315 236 532 2.555 0.495 0.110 0.016 2 0.2 Lat_Fis-ant-Vertical 1255 853 1691 2.555 0.589 0.115 0.024 9 1.2 Lat_Fis-post 2455 1549 3480 2.027 0.505 0.148 0.042 39 4.1 Pole_occipital 1752 1314 6109 3.268 0.766 0.151 0.040 32 3.0 Pole_temporal 2388 1661 2732 1.916 0.658 0.121 0.027 18 2.8 S_calcarine 3456 2289 4041 2.036 0.637 0.106 0.024 21 3.4 S_central 1210 835 1779 2.357 0.559 0.123 0.024 10 1.3 S_cingul-Marginalis 509 352 853 3.013 0.349 0.100 0.020 2 0.4 S_circular_insula_ant 1687 1171 2747 2.925 0.472 0.089 0.015 7 1.1 S_circular_insula_inf 1943 1327 2933 2.846 0.520 0.106 0.021 9 1.8 S_circular_insula_sup 1251 858 2586 3.000 0.523 0.104 0.022 10 1.2 S_collat_transv_ant 517 355 619 2.015 0.395 0.125 0.025 4 0.5 S_collat_transv_post 2205 1549 3299 2.236 0.506 0.103 0.018 16 1.5 S_front_inf 1911 1302 2934 2.475 0.463 0.111 0.021 12 1.7 S_front_middle 3675 2594 6929 2.800 0.522 0.119 0.028 29 4.0 S_front_sup 648 456 931 2.484 0.393 0.106 0.018 4 0.5 S_interm_prim-Jensen 3334 2357 5226 2.386 0.462 0.124 0.024 28 3.3 S_intrapariet&P_trans 1048 728 1191 1.899 0.476 0.127 0.025 9 1.1 S_oc_middle&Lunatus 1536 1039 1982 2.046 0.430 0.111 0.020 10 1.2 S_oc_sup&transversal 768 542 1170 2.228 0.562 0.112 0.034 6 0.9 S_occipital_ant 1370 965 2197 2.683 0.482 0.098 0.016 8 1.0 S_oc-temp_lat 2774 1967 4116 2.358 0.486 0.110 0.022 19 2.4 S_oc-temp_med&Lingual 451 312 623 2.286 0.422 0.118 0.019 3 0.4 S_orbital_lateral 520 392 974 2.722 0.661 0.126 0.019 4 0.4 S_orbital_med-olfact 1488 1038 2748 2.714 0.617 0.124 0.028 14 1.8 S_orbital-H_Shaped 2399 1651 3502 2.325 0.512 0.113 0.025 18 2.4 S_parieto_occipital 1590 948 1450 1.980 0.951 0.129 0.022 27 1.2 S_pericallosal 3041 2075 4351 2.273 0.542 0.120 0.028 25 3.3 S_postcentral 1963 1358 3232 2.626 0.495 0.113 0.021 13 1.8 S_precentral-inf-part 1117 791 1718 2.484 0.606 0.110 0.021 7 1.0 S_precentral-sup-part 784 542 1304 2.452 0.859 0.124 0.024 8 0.7 S_suborbital 1189 831 1656 2.400 0.507 0.124 0.027 10 1.3 S_subparietal 1490 1077 2836 2.761 0.733 0.113 0.024 9 1.5 S_temporal_inf 6360 4427 10353 2.476 0.587 0.109 0.021 48 5.7 S_temporal_sup 292 203 424 2.537 0.477 0.117 0.018 3 0.2 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050490 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297991 Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 1304 853 2188 2.086 0.730 0.151 0.051 43 3.2 G&S_frontomargin 1889 1295 3781 2.645 0.542 0.140 0.039 25 2.8 G&S_occipital_inf 1509 940 2648 2.368 0.608 0.119 0.035 15 2.1 G&S_paracentral 1305 846 3168 3.147 0.522 0.126 0.028 15 1.4 G&S_subcentral 1591 1071 3889 2.593 0.700 0.140 0.038 32 2.5 G&S_transv_frontopol 3491 2405 7049 2.565 0.655 0.130 0.031 47 4.5 G&S_cingul-Ant 1636 1151 3547 2.944 0.495 0.113 0.022 16 1.4 G&S_cingul-Mid-Ant 1599 1101 3106 2.654 0.589 0.132 0.036 17 2.2 G&S_cingul-Mid-Post 546 361 1523 3.066 0.923 0.167 0.050 12 1.0 G_cingul-Post-dorsal 346 238 784 2.529 0.727 0.160 0.050 7 0.7 G_cingul-Post-ventral 2454 1635 3572 2.012 0.557 0.152 0.040 36 3.9 G_cuneus 1228 831 3237 2.894 0.529 0.125 0.024 19 1.2 G_front_inf-Opercular 431 288 1190 2.856 0.490 0.145 0.031 9 0.6 G_front_inf-Orbital 751 534 1867 2.589 0.478 0.129 0.029 12 0.8 G_front_inf-Triangul 4543 3081 12387 2.810 0.678 0.151 0.046 111 8.1 G_front_middle 8770 5905 22615 2.903 0.747 0.141 0.041 181 14.4 G_front_sup 758 515 1700 3.147 0.952 0.139 0.043 10 1.1 G_Ins_lg&S_cent_ins 858 560 2523 3.460 0.870 0.148 0.051 15 1.7 G_insular_short 3032 2005 6716 2.700 0.730 0.149 0.041 47 4.7 G_occipital_middle 1968 1256 3650 2.363 0.620 0.152 0.054 35 4.8 G_occipital_sup 2942 1978 7820 3.002 0.801 0.150 0.046 53 5.0 G_oc-temp_lat-fusifor 3276 2294 5247 1.995 0.639 0.142 0.039 45 5.0 G_oc-temp_med-Lingual 1402 875 4200 3.156 0.806 0.116 0.039 15 2.2 G_oc-temp_med-Parahip 3003 2030 7863 2.776 0.705 0.146 0.043 70 4.7 G_orbital 4637 3087 11324 2.803 0.678 0.138 0.037 71 6.6 G_pariet_inf-Angular 2925 1881 6668 2.795 0.601 0.132 0.041 44 4.6 G_pariet_inf-Supramar 2810 1852 6706 2.610 0.746 0.133 0.037 40 4.0 G_parietal_sup 2146 1298 3804 2.276 0.640 0.122 0.031 28 2.6 G_postcentral 3587 2256 8378 2.780 0.785 0.118 0.032 40 4.6 G_precentral 2851 1999 6357 2.558 0.597 0.147 0.040 52 4.6 G_precuneus 873 608 2429 2.628 0.764 0.154 0.056 28 1.9 G_rectus 145 111 402 3.441 0.671 0.121 0.025 1 0.1 G_subcallosal 538 290 1075 2.923 0.514 0.090 0.033 5 0.7 G_temp_sup-G_T_transv 1975 1322 5939 3.232 0.655 0.137 0.041 35 3.1 G_temp_sup-Lateral 684 503 1964 3.357 0.667 0.094 0.019 4 0.6 G_temp_sup-Plan_polar 929 646 2021 2.826 0.524 0.100 0.023 6 0.8 G_temp_sup-Plan_tempo 2883 1930 9151 3.311 0.872 0.138 0.044 44 4.5 G_temporal_inf 3255 2215 9844 3.202 0.651 0.128 0.031 49 3.9 G_temporal_middle 362 255 433 2.030 0.567 0.097 0.012 2 0.1 Lat_Fis-ant-Horizont 242 184 356 2.104 0.432 0.102 0.016 1 0.1 Lat_Fis-ant-Vertical 1487 1016 2372 2.923 0.619 0.101 0.021 7 1.2 Lat_Fis-post 4202 2724 6171 2.031 0.530 0.143 0.038 57 6.6 Pole_occipital 2055 1458 6898 3.169 0.763 0.141 0.045 41 3.5 Pole_temporal 2295 1569 2815 2.106 0.747 0.124 0.027 21 2.6 S_calcarine 3571 2427 4159 2.011 0.539 0.106 0.021 23 3.1 S_central 1460 993 2211 2.305 0.487 0.108 0.027 12 1.4 S_cingul-Marginalis 748 519 1218 2.869 0.432 0.109 0.023 3 0.8 S_circular_insula_ant 1603 1058 2357 2.718 0.586 0.081 0.014 6 1.0 S_circular_insula_inf 1481 1007 2493 2.908 0.580 0.110 0.022 8 1.4 S_circular_insula_sup 1159 798 2561 3.172 0.779 0.100 0.021 7 0.9 S_collat_transv_ant 655 448 780 2.394 0.547 0.147 0.035 7 0.8 S_collat_transv_post 1690 1178 2545 2.231 0.499 0.120 0.027 17 1.7 S_front_inf 2678 1873 3635 1.988 0.486 0.108 0.021 19 2.1 S_front_middle 3124 2174 5185 2.400 0.553 0.119 0.024 26 3.2 S_front_sup 797 547 1061 2.459 0.392 0.092 0.015 3 0.6 S_interm_prim-Jensen 4411 3047 6130 2.225 0.499 0.116 0.024 36 4.2 S_intrapariet&P_trans 1070 763 1404 2.190 0.378 0.126 0.028 8 1.1 S_oc_middle&Lunatus 1622 1150 2103 2.108 0.392 0.127 0.024 14 1.6 S_oc_sup&transversal 920 631 1402 2.505 0.513 0.125 0.025 7 1.0 S_occipital_ant 1756 1217 2890 2.648 0.602 0.101 0.022 10 1.6 S_oc-temp_lat 2310 1680 3390 2.345 0.619 0.118 0.022 19 2.1 S_oc-temp_med&Lingual 548 366 654 1.931 0.471 0.133 0.025 6 0.6 S_orbital_lateral 682 475 1088 2.566 0.852 0.124 0.040 10 1.0 S_orbital_med-olfact 1515 1065 2532 2.350 0.485 0.125 0.025 18 1.5 S_orbital-H_Shaped 2457 1715 3419 2.312 0.521 0.113 0.024 19 2.6 S_parieto_occipital 1723 1103 1651 1.894 0.732 0.125 0.019 24 1.1 S_pericallosal 2406 1622 3265 2.248 0.474 0.129 0.028 24 2.7 S_postcentral 1522 1071 2636 2.772 0.477 0.102 0.018 9 1.0 S_precentral-inf-part 1791 1262 2842 2.723 0.443 0.095 0.016 7 1.3 S_precentral-sup-part 508 351 667 2.218 0.802 0.115 0.016 4 0.3 S_suborbital 1680 1209 3067 2.629 0.691 0.137 0.031 18 2.2 S_subparietal 1273 895 2126 2.788 0.789 0.108 0.019 8 1.0 S_temporal_inf 7181 5104 12593 2.679 0.598 0.109 0.020 53 5.8 S_temporal_sup 221 147 345 3.032 0.567 0.166 0.030 4 0.3 S_temporal_transverse PIDs (7125 7128) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 14:39:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 14:39:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 7203 of (7203 7206) to complete... Waiting for PID 7206 of (7203 7206) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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... 1281 labels changed using aseg relabeling using gibbs priors... 000: 2119 changed, 152526 examined... 001: 464 changed, 9900 examined... 002: 125 changed, 2681 examined... 003: 44 changed, 734 examined... 004: 19 changed, 267 examined... 005: 19 changed, 110 examined... 006: 12 changed, 99 examined... 007: 14 changed, 72 examined... 008: 12 changed, 77 examined... 009: 9 changed, 47 examined... 010: 10 changed, 50 examined... 011: 11 changed, 57 examined... 012: 7 changed, 53 examined... 013: 5 changed, 34 examined... 014: 3 changed, 27 examined... 015: 2 changed, 18 examined... 016: 1 changed, 12 examined... 017: 3 changed, 10 examined... 018: 1 changed, 9 examined... 019: 1 changed, 7 examined... 020: 0 changed, 9 examined... 236 labels changed using aseg 000: 56 total segments, 23 labels (143 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 10 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 578 vertices marked for relabeling... 578 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 31 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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... 1246 labels changed using aseg relabeling using gibbs priors... 000: 2119 changed, 154525 examined... 001: 522 changed, 9999 examined... 002: 143 changed, 2839 examined... 003: 66 changed, 886 examined... 004: 28 changed, 374 examined... 005: 18 changed, 158 examined... 006: 11 changed, 97 examined... 007: 6 changed, 57 examined... 008: 4 changed, 40 examined... 009: 8 changed, 22 examined... 010: 8 changed, 33 examined... 011: 4 changed, 34 examined... 012: 5 changed, 25 examined... 013: 4 changed, 29 examined... 014: 7 changed, 26 examined... 015: 1 changed, 35 examined... 016: 0 changed, 7 examined... 223 labels changed using aseg 000: 54 total segments, 21 labels (742 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 347 vertices marked for relabeling... 347 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. PIDs (7203 7206) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 14:40:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 14:40:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 rh white Waiting for PID 7288 of (7288 7291) to complete... Waiting for PID 7291 of (7288 7291) 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 0050490 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297729 Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 1944 1287 4067 2.912 0.665 0.135 0.026 24 2.1 caudalanteriorcingulate 4290 2882 8854 2.783 0.627 0.123 0.035 48 6.7 caudalmiddlefrontal 3586 2446 5233 2.074 0.531 0.139 0.033 45 4.6 cuneus 530 351 1805 3.603 0.784 0.118 0.039 6 0.8 entorhinal 5500 3840 11951 2.739 0.707 0.123 0.030 63 6.8 fusiform 7364 5173 14392 2.455 0.661 0.129 0.029 91 8.8 inferiorparietal 5364 3817 14686 3.159 0.707 0.134 0.038 76 8.5 inferiortemporal 1577 1059 2881 2.436 0.946 0.136 0.038 23 2.1 isthmuscingulate 8724 5826 14688 2.169 0.621 0.140 0.035 115 11.9 lateraloccipital 4470 3165 10463 2.861 0.704 0.145 0.041 73 7.8 lateralorbitofrontal 5107 3568 7778 2.110 0.585 0.138 0.039 65 7.8 lingual 1978 1379 4382 2.647 0.856 0.142 0.040 34 3.2 medialorbitofrontal 6257 4367 13832 2.768 0.709 0.127 0.030 77 8.1 middletemporal 1163 773 2466 2.764 0.694 0.094 0.016 7 0.7 parahippocampal 3240 2158 6245 2.609 0.591 0.123 0.031 31 3.9 paracentral 2284 1590 4809 2.714 0.495 0.122 0.030 25 2.7 parsopercularis 1109 740 2133 2.541 0.495 0.117 0.033 12 1.4 parsorbitalis 2412 1613 5094 2.647 0.561 0.110 0.023 23 2.0 parstriangularis 2016 1393 2026 1.629 0.397 0.125 0.026 17 2.3 pericalcarine 7709 5125 12867 2.243 0.703 0.123 0.031 89 9.8 postcentral 2488 1685 4731 2.533 0.923 0.135 0.028 34 3.0 posteriorcingulate 7444 4788 14391 2.779 0.673 0.115 0.030 66 9.1 precentral 5979 4214 11418 2.469 0.605 0.137 0.034 74 8.3 precuneus 1826 1239 4301 3.164 0.768 0.145 0.037 31 2.5 rostralanteriorcingulate 6509 4523 13797 2.583 0.623 0.139 0.036 98 9.1 rostralmiddlefrontal 15443 10625 36838 2.910 0.681 0.132 0.034 217 21.3 superiorfrontal 7019 4780 12710 2.378 0.609 0.130 0.031 82 8.5 superiorparietal 8920 6088 21925 3.018 0.746 0.115 0.027 98 9.5 superiortemporal 6960 4879 13404 2.502 0.605 0.129 0.030 83 8.4 supramarginal 802 510 1282 2.597 0.510 0.129 0.029 9 0.9 transversetemporal 3537 2479 7869 3.129 0.687 0.127 0.033 32 4.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050490 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297991 Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 1618 1085 3296 2.588 0.724 0.135 0.025 26 1.6 caudalanteriorcingulate 3635 2522 7603 2.700 0.632 0.125 0.028 38 4.1 caudalmiddlefrontal 3262 2196 4950 2.132 0.564 0.147 0.037 41 5.2 cuneus 699 448 2553 3.259 1.062 0.124 0.046 9 1.4 entorhinal 5507 3802 12583 2.877 0.782 0.129 0.035 69 7.4 fusiform 10802 7444 21968 2.587 0.644 0.129 0.030 129 13.0 inferiorparietal 6139 4185 15589 3.075 0.848 0.126 0.035 73 8.0 inferiortemporal 1366 910 2896 2.681 1.061 0.140 0.040 22 1.9 isthmuscingulate 9492 6286 16217 2.358 0.640 0.143 0.038 128 13.8 lateraloccipital 4595 3115 9287 2.534 0.706 0.140 0.041 90 7.5 lateralorbitofrontal 4790 3386 7273 2.034 0.602 0.143 0.038 63 7.6 lingual 1857 1318 4273 2.542 0.849 0.134 0.040 37 2.7 medialorbitofrontal 6593 4615 16177 3.023 0.637 0.119 0.026 77 6.6 middletemporal 1246 819 2592 2.812 0.633 0.111 0.024 11 1.1 parahippocampal 2639 1752 4841 2.517 0.516 0.114 0.031 23 3.0 paracentral 1962 1362 4040 2.675 0.554 0.112 0.021 21 1.6 parsopercularis 1188 814 2788 2.831 0.670 0.125 0.027 18 1.4 parsorbitalis 1900 1332 3624 2.343 0.577 0.126 0.025 24 1.8 parstriangularis 2184 1493 2215 1.697 0.467 0.123 0.027 22 2.3 pericalcarine 6540 4234 10740 2.289 0.719 0.118 0.027 66 7.0 postcentral 1961 1343 3516 2.386 0.744 0.147 0.038 31 3.0 posteriorcingulate 8233 5353 15467 2.661 0.692 0.112 0.025 70 8.5 precentral 6932 4876 12631 2.464 0.602 0.132 0.033 88 9.2 precuneus 1477 1015 3276 2.785 0.664 0.129 0.030 20 1.8 rostralanteriorcingulate 6323 4352 12252 2.303 0.651 0.135 0.037 114 8.8 rostralmiddlefrontal 17338 11782 38512 2.701 0.729 0.131 0.035 297 24.6 superiorfrontal 7874 5231 13908 2.348 0.632 0.129 0.034 97 11.1 superiorparietal 7737 5249 18232 2.986 0.670 0.113 0.028 85 8.5 superiortemporal 6005 4033 11604 2.676 0.559 0.117 0.029 62 6.9 supramarginal 559 328 1081 3.074 0.561 0.107 0.032 6 0.8 transversetemporal 3622 2465 7801 3.194 0.765 0.125 0.033 36 4.5 insula PIDs (7288 7291) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 14:41:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts pctsurfcon --s 0050490 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 14:41:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts pctsurfcon --s 0050490 --rh-only Waiting for PID 7371 of (7371 7375) to complete... Waiting for PID 7375 of (7371 7375) to complete... pctsurfcon --s 0050490 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts/pctsurfcon.log Sun Oct 8 14:41:52 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-6.0.0/0050490/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-114 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-6.0.0/0050490/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.wm.mgh --regheader 0050490 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 119280 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.wm.mgh Dim: 152526 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.gm.mgh --projfrac 0.3 --regheader 0050490 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 134998 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.gm.mgh Dim: 152526 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.w-g.pct.mgh --annot 0050490 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/lh.w-g.pct.mgh --annot 0050490 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-114 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/lh.w-g.pct.mgh Vertex Area is 0.683006 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 0050490 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts/pctsurfcon.log Sun Oct 8 14:41:52 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-6.0.0/0050490/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-114 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-6.0.0/0050490/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.wm.mgh --regheader 0050490 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 120584 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.wm.mgh Dim: 154525 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.gm.mgh --projfrac 0.3 --regheader 0050490 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 136544 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.gm.mgh Dim: 154525 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.w-g.pct.mgh --annot 0050490 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.w-g.pct.mgh --annot 0050490 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-114 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.w-g.pct.mgh Vertex Area is 0.677396 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 (7371 7375) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 14:42:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1289 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1862 voxels changed to hypointensity... 3168 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 14:43:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490 mri_aparc2aseg --s 0050490 --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 14:43:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490 mri_aparc2aseg --s 0050490 --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 14:43:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490 mri_aparc2aseg --s 0050490 --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 7574 of (7574 7577 7580) to complete... Waiting for PID 7577 of (7574 7577 7580) to complete... Waiting for PID 7580 of (7574 7577 7580) to complete... mri_aparc2aseg --s 0050490 --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 0050490 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.14 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 57 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 28 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 58 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 66 rescaling Left_Putamen from 80 --> 81 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 27 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 60 rescaling Left_Amygdala from 56 --> 63 rescaling CSF from 32 --> 37 rescaling Left_Accumbens_area from 62 --> 60 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 59 rescaling Right_Lateral_Ventricle from 13 --> 16 rescaling Right_Inf_Lat_Vent from 25 --> 25 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 59 rescaling Right_Thalamus_Proper from 85 --> 92 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 59 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 96 rescaling Fifth_Ventricle from 40 --> 33 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 582624 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 122 changed. pass 2: 9 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aparc+aseg.mgz mri_aparc2aseg --s 0050490 --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 0050490 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.14 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 57 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 28 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 58 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 66 rescaling Left_Putamen from 80 --> 81 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 27 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 60 rescaling Left_Amygdala from 56 --> 63 rescaling CSF from 32 --> 37 rescaling Left_Accumbens_area from 62 --> 60 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 59 rescaling Right_Lateral_Ventricle from 13 --> 16 rescaling Right_Inf_Lat_Vent from 25 --> 25 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 59 rescaling Right_Thalamus_Proper from 85 --> 92 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 59 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 96 rescaling Fifth_Ventricle from 40 --> 33 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 582670 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 122 changed. pass 2: 9 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0050490 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050490 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.14 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 57 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 28 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 58 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 66 rescaling Left_Putamen from 80 --> 81 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 27 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 60 rescaling Left_Amygdala from 56 --> 63 rescaling CSF from 32 --> 37 rescaling Left_Accumbens_area from 62 --> 60 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 59 rescaling Right_Lateral_Ventricle from 13 --> 16 rescaling Right_Inf_Lat_Vent from 25 --> 25 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 59 rescaling Right_Thalamus_Proper from 85 --> 92 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 59 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 96 rescaling Fifth_Ventricle from 40 --> 33 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 582670 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 122 changed. pass 2: 9 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (7574 7577 7580) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 14:52:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 14:52:35 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-6.0.0/0050490/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-114 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-6.0.0/0050490/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-114 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 14:52:35 CEST 2017 Ended at Sun Oct 8 14:52:48 CEST 2017 Apas2aseg-Run-Time-Sec 13 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 14:52:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490 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 0050490 $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 0050490 sysname Linux hostname tars-114 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1695813 mm^3 (det: 1.148774 ) Computing euler number orig.nofix lheno = -68, rheno = -66 orig.nofix lhholes = 35, rhholes = 34 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 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 14:56:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490 mri_aparc2aseg --s 0050490 --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 0050490 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-6.0.0/0050490/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8979 vertices from left hemi Ripped 8477 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-6.0.0/0050490/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 1084513 Used brute-force search on 544 voxels Fixing Parahip LH WM Found 7 clusters 0 k 1.000000 1 k 1515.000000 2 k 1.000000 3 k 1.000000 4 k 11.000000 5 k 1.000000 6 k 4.000000 Fixing Parahip RH WM Found 12 clusters 0 k 5.000000 1 k 2.000000 2 k 1.000000 3 k 1785.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 12.000000 8 k 1.000000 9 k 1.000000 10 k 2.000000 11 k 1.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050490 --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 0050490 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-114 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1695813 mm^3 (det: 1.148774 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 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-6.0.0/0050490/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 15:17:50 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 9004 of (9004 9010 9016 9022 9027) to complete... Waiting for PID 9010 of (9004 9010 9016 9022 9027) to complete... Waiting for PID 9016 of (9004 9010 9016 9022 9027) to complete... Waiting for PID 9022 of (9004 9010 9016 9022 9027) to complete... Waiting for PID 9027 of (9004 9010 9016 9022 9027) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 382 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4511 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 630 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8539 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 208 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4285 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 525 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6508 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 645 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6429 mri_label2label: Done PIDs (9004 9010 9016 9022 9027) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 9088 of (9088 9094 9100 9106) to complete... Waiting for PID 9094 of (9088 9094 9100 9106) to complete... Waiting for PID 9100 of (9088 9094 9100 9106) to complete... Waiting for PID 9106 of (9088 9094 9100 9106) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 263 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4333 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 2103 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15692 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 324 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4505 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 522 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3944 mri_label2label: Done PIDs (9088 9094 9100 9106) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 9146 of (9146 9152 9156 9163 9169) to complete... Waiting for PID 9152 of (9146 9152 9156 9163 9169) to complete... Waiting for PID 9156 of (9146 9152 9156 9163 9169) to complete... Waiting for PID 9163 of (9146 9152 9156 9163 9169) to complete... Waiting for PID 9169 of (9146 9152 9156 9163 9169) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 1479 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6120 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 3642 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11756 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 509 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2527 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1397 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 83 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1282 mri_label2label: Done PIDs (9146 9152 9156 9163 9169) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 9235 of (9235 9241 9247 9253 9257) to complete... Waiting for PID 9241 of (9235 9241 9247 9253 9257) to complete... Waiting for PID 9247 of (9235 9241 9247 9253 9257) to complete... Waiting for PID 9253 of (9235 9241 9247 9253 9257) to complete... Waiting for PID 9257 of (9235 9241 9247 9253 9257) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1095 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2275 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1548 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 193 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2189 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 313 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2632 mri_label2label: Done PIDs (9235 9241 9247 9253 9257) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 9300 of (9300 9306 9312 9320) to complete... Waiting for PID 9306 of (9300 9306 9312 9320) to complete... Waiting for PID 9312 of (9300 9306 9312 9320) to complete... Waiting for PID 9320 of (9300 9306 9312 9320) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1669 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 1039 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8074 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2043 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 241 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1392 mri_label2label: Done PIDs (9300 9306 9312 9320) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 9379 of (9379 9385 9391 9397 9401) to complete... Waiting for PID 9385 of (9379 9385 9391 9397 9401) to complete... Waiting for PID 9391 of (9379 9385 9391 9397 9401) to complete... Waiting for PID 9397 of (9379 9385 9391 9397 9401) to complete... Waiting for PID 9401 of (9379 9385 9391 9397 9401) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 1035 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4440 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 1605 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4939 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 641 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 499 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 470 mri_label2label: Done PIDs (9379 9385 9391 9397 9401) completed and logs appended. mris_label2annot --s 0050490 --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-6.0.0/0050490/label cmdline mris_label2annot --s 0050490 --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-114 machine x86_64 user ntraut subject 0050490 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-6.0.0/0050490/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 107137 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.BA_exvivo.annot mris_label2annot --s 0050490 --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-6.0.0/0050490/label cmdline mris_label2annot --s 0050490 --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-114 machine x86_64 user ntraut subject 0050490 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-6.0.0/0050490/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 125920 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 297729 Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 1194 748 2269 2.363 0.572 0.147 0.045 21 2.0 BA1_exvivo 4295 2898 7035 2.317 0.592 0.123 0.028 42 4.7 BA2_exvivo 1110 750 1165 1.904 0.460 0.120 0.026 8 1.2 BA3a_exvivo 2670 1790 3991 1.980 0.728 0.117 0.031 31 3.6 BA3b_exvivo 2027 1262 3877 2.689 0.571 0.123 0.037 20 3.2 BA4a_exvivo 1451 894 2278 2.672 0.550 0.102 0.033 9 2.0 BA4p_exvivo 10985 7427 26094 2.961 0.667 0.119 0.029 114 12.3 BA6_exvivo 2346 1606 4827 2.765 0.521 0.127 0.030 25 2.8 BA44_exvivo 2870 1982 6426 2.602 0.615 0.123 0.026 37 2.7 BA45_exvivo 3684 2528 4362 1.710 0.467 0.134 0.032 43 5.0 V1_exvivo 9362 6361 14104 2.082 0.533 0.145 0.039 128 13.8 V2_exvivo 2125 1492 4515 2.502 0.747 0.127 0.032 21 2.7 MT_exvivo 609 386 1818 3.534 0.723 0.124 0.038 7 0.9 perirhinal_exvivo 661 478 1633 2.946 0.838 0.120 0.038 8 1.1 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 0050490 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 297729 Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 760 473 1376 2.304 0.577 0.147 0.044 14 1.3 BA1_exvivo 1630 1106 2849 2.342 0.552 0.128 0.032 18 2.0 BA2_exvivo 918 611 860 1.839 0.407 0.127 0.028 7 1.1 BA3a_exvivo 1613 1066 1729 1.581 0.385 0.108 0.032 18 2.3 BA3b_exvivo 1966 1189 3509 2.697 0.582 0.118 0.037 19 3.1 BA4a_exvivo 1174 735 1752 2.541 0.509 0.109 0.038 8 1.8 BA4p_exvivo 6113 4075 14349 2.904 0.672 0.116 0.028 61 6.7 BA6_exvivo 1473 1014 3183 2.752 0.464 0.143 0.037 21 2.2 BA44_exvivo 1224 817 3319 2.812 0.619 0.129 0.032 17 1.3 BA45_exvivo 3931 2692 4709 1.719 0.465 0.135 0.034 47 5.5 V1_exvivo 4608 3128 6182 1.961 0.472 0.149 0.040 64 7.1 V2_exvivo 576 411 1602 2.826 0.871 0.134 0.043 7 1.0 MT_exvivo 292 190 1167 3.893 0.596 0.094 0.018 2 0.2 perirhinal_exvivo 328 224 829 3.104 0.827 0.086 0.018 2 0.3 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 15:22:07 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 9542 of (9542 9548 9554 9560 9565) to complete... Waiting for PID 9548 of (9542 9548 9554 9560 9565) to complete... Waiting for PID 9554 of (9542 9548 9554 9560 9565) to complete... Waiting for PID 9560 of (9542 9548 9554 9560 9565) to complete... Waiting for PID 9565 of (9542 9548 9554 9560 9565) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 292 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4254 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 344 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7031 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 214 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4194 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 296 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4818 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 877 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6624 mri_label2label: Done PIDs (9542 9548 9554 9560 9565) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 9756 of (9756 9762 9768 9774) to complete... Waiting for PID 9762 of (9756 9762 9768 9774) to complete... Waiting for PID 9768 of (9756 9762 9768 9774) to complete... Waiting for PID 9774 of (9756 9762 9768 9774) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 469 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4942 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 2119 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 14375 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 354 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7266 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 557 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5912 mri_label2label: Done PIDs (9756 9762 9768 9774) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 9864 of (9864 9870 9876 9882 9888) to complete... Waiting for PID 9870 of (9864 9870 9876 9882 9888) to complete... Waiting for PID 9876 of (9864 9870 9876 9882 9888) to complete... Waiting for PID 9882 of (9864 9870 9876 9882 9888) to complete... Waiting for PID 9888 of (9864 9870 9876 9882 9888) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 1731 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6458 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 3809 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11825 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 816 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2748 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 189 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1227 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 881 mri_label2label: Done PIDs (9864 9870 9876 9882 9888) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 9949 of (9949 9955 9961 9966 9973) to complete... Waiting for PID 9955 of (9949 9955 9961 9966 9973) to complete... Waiting for PID 9961 of (9949 9955 9961 9966 9973) to complete... Waiting for PID 9966 of (9949 9955 9961 9966 9973) to complete... Waiting for PID 9973 of (9949 9955 9961 9966 9973) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 66 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 942 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2764 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1775 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2324 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 167 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1555 mri_label2label: Done PIDs (9949 9955 9961 9966 9973) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 10019 of (10019 10025 10031 10037) to complete... Waiting for PID 10025 of (10019 10025 10031 10037) to complete... Waiting for PID 10031 of (10019 10025 10031 10037) to complete... Waiting for PID 10037 of (10019 10025 10031 10037) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 184 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1673 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 1306 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 8265 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1089 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1263 mri_label2label: Done PIDs (10019 10025 10031 10037) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 10092 of (10092 10098 10104 10110 10114) to complete... Waiting for PID 10098 of (10092 10098 10104 10110 10114) to complete... Waiting for PID 10104 of (10092 10098 10104 10110 10114) to complete... Waiting for PID 10110 of (10092 10098 10104 10110 10114) to complete... Waiting for PID 10114 of (10092 10098 10104 10110 10114) 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 1061 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4293 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 1719 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5156 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 108 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 376 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 815 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 0050490 --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 = 0050490 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-6.0.0/0050490/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 324 mri_label2label: Done PIDs (10092 10098 10104 10110 10114) completed and logs appended. mris_label2annot --s 0050490 --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-6.0.0/0050490/label cmdline mris_label2annot --s 0050490 --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-114 machine x86_64 user ntraut subject 0050490 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-6.0.0/0050490/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 109634 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.BA_exvivo.annot mris_label2annot --s 0050490 --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-6.0.0/0050490/label cmdline mris_label2annot --s 0050490 --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-114 machine x86_64 user ntraut subject 0050490 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-6.0.0/0050490/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 128814 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 297991 Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 968 538 1898 2.469 0.628 0.121 0.036 13 1.3 BA1_exvivo 2850 1900 4708 2.380 0.548 0.132 0.031 33 3.3 BA2_exvivo 1204 807 1145 1.887 0.456 0.130 0.030 11 1.4 BA3a_exvivo 2076 1385 2804 1.830 0.554 0.105 0.022 18 1.9 BA3b_exvivo 1893 1192 3318 2.494 0.686 0.107 0.029 17 2.1 BA4a_exvivo 1588 1040 2307 2.327 0.552 0.107 0.026 10 1.8 BA4p_exvivo 10423 6999 24281 2.905 0.689 0.122 0.031 142 13.4 BA6_exvivo 3133 2165 6658 2.815 0.538 0.113 0.021 30 2.5 BA44_exvivo 3604 2505 7310 2.447 0.668 0.130 0.027 52 3.9 BA45_exvivo 4026 2726 5233 1.805 0.517 0.135 0.034 48 5.7 V1_exvivo 9382 6276 13978 2.117 0.575 0.144 0.038 123 14.1 V2_exvivo 2604 1800 4558 2.504 0.509 0.133 0.030 27 2.9 MT_exvivo 709 449 2716 3.430 0.947 0.128 0.048 11 1.4 perirhinal_exvivo 431 297 1095 2.890 0.667 0.099 0.025 3 0.5 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 0050490 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 297991 Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 ) lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151 rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100 lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214 rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252 SubCortGMVol 65030.000 SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202 SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205 BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215 BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052 BrainSegVolNotVent 1309200.000 CerebellumVol 156481.000 VentChorVol 16563.000 3rd4th5thCSF 4491.000 CSFVol 1635.000, OptChiasmVol 245.000 MaskVol 1762497.000 597 359 1164 2.376 0.569 0.112 0.032 6 0.7 BA1_exvivo 1597 1030 2861 2.475 0.546 0.122 0.029 18 1.8 BA2_exvivo 1103 739 945 1.851 0.416 0.137 0.030 10 1.4 BA3a_exvivo 1650 1141 1903 1.667 0.366 0.098 0.018 11 1.2 BA3b_exvivo 1122 722 1876 2.341 0.664 0.134 0.043 15 1.9 BA4a_exvivo 1295 870 1856 2.331 0.578 0.109 0.026 8 1.4 BA4p_exvivo 6908 4578 15248 2.821 0.668 0.116 0.030 102 8.5 BA6_exvivo 816 559 2178 2.959 0.480 0.119 0.021 11 0.7 BA44_exvivo 888 645 2187 2.515 0.512 0.139 0.031 16 1.1 BA45_exvivo 3796 2578 4902 1.807 0.533 0.134 0.033 44 5.2 V1_exvivo 4862 3257 6697 1.979 0.544 0.145 0.037 65 7.3 V2_exvivo 360 254 697 2.530 0.459 0.146 0.034 4 0.5 MT_exvivo 438 266 1614 3.342 0.954 0.132 0.050 7 1.0 perirhinal_exvivo 279 188 707 2.958 0.565 0.081 0.020 1 0.2 entorhinal_exvivo Started at Sun Oct 8 01:15:11 CEST 2017 Ended at Sun Oct 8 15:26:14 CEST 2017 #@#%# recon-all-run-time-hours 14.184 recon-all -s 0050490 finished without error at Sun Oct 8 15:26:14 CEST 2017