Sat Oct 7 16:58:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0051324 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_b/0051324/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0051324 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-900 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: 66074804 58473436 7601368 1735688 0 55859960 -/+ buffers/cache: 2613476 63461328 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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: 2017/10/07-14:58:33-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-900 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-6.0.0/0051324 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_b/0051324/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_b/0051324/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_b/0051324/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-6.0.0/0051324/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 16:58:35 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/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-6.0.0/0051324/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 16:58:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/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-900 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 16:58:43 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.26846 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26846/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.26846/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.26846/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 16:58:45 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.26846/nu0.mnc ./tmp.mri_nu_correct.mni.26846/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.26846/0/ -iterations 1000 -distance 50 [ntraut@tars-900:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/] [2017-10-07 16:58:45] 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.26846/0/ ./tmp.mri_nu_correct.mni.26846/nu0.mnc ./tmp.mri_nu_correct.mni.26846/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 Number of iterations: 33 CV of field change: 0.000946816 mri_convert ./tmp.mri_nu_correct.mni.26846/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.26846/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.26846/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sat Oct 7 16:59:44 CEST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Oct 7 16:59:44 CEST 2017 Ended at Sat Oct 7 17:00:21 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 17:00:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7047, 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-6.0.0/0051324/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/transforms/talairach_avi.log TalAviQA: 0.96159 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 17:00:23 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-6.0.0/0051324/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-900 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 17:00:23 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.27535 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27535/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27535/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.27535/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 17:00:25 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.27535/nu0.mnc ./tmp.mri_nu_correct.mni.27535/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27535/0/ [ntraut@tars-900:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/] [2017-10-07 17:00:25] 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.27535/0/ ./tmp.mri_nu_correct.mni.27535/nu0.mnc ./tmp.mri_nu_correct.mni.27535/nu1.imp Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00108467 -------------------------------------------------------- Iteration 2 Sat Oct 7 17:01:19 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.27535/nu1.mnc ./tmp.mri_nu_correct.mni.27535/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.27535/1/ [ntraut@tars-900:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/] [2017-10-07 17:01:19] 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.27535/1/ ./tmp.mri_nu_correct.mni.27535/nu1.mnc ./tmp.mri_nu_correct.mni.27535/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 21 CV of field change: 0.000960554 mri_binarize --i ./tmp.mri_nu_correct.mni.27535/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27535/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-6.0.0/0051324/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.27535/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27535/ones.mgz sysname Linux hostname tars-900 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.27535/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.27535/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.27535/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27535/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27535/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.27535/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27535/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27535/input.mean.dat sysname Linux hostname tars-900 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27535/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.27535/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27535/ones.mgz --i ./tmp.mri_nu_correct.mni.27535/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27535/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27535/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.27535/ones.mgz --i ./tmp.mri_nu_correct.mni.27535/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27535/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27535/output.mean.dat sysname Linux hostname tars-900 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27535/ones.mgz Loading ./tmp.mri_nu_correct.mni.27535/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.27535/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.27535/nu2.mnc ./tmp.mri_nu_correct.mni.27535/nu2.mnc mul 1.02495694377205172758 Saving result to './tmp.mri_nu_correct.mni.27535/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.27535/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.27535/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.27535/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 8 seconds. mapping (18, 140) to ( 3, 110) Sat Oct 7 17:02:31 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 17:02:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 1.05507 -0.00918 0.00220 -0.33511; 0.00261 1.03669 0.40109 -7.52888; -0.02010 -0.31960 1.12566 -8.27081; 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 = 18 Starting OpenSpline(): npoints = 18 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 64 (64), valley at 36 (36) csf peak at 33, setting threshold to 53 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 35 (35) 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 0 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 17:04:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (45, 69, 11) --> (210, 209, 194) using (100, 116, 103) as brain centroid... mean wm in atlas = 108, using box (80,99,80) --> (120, 133,125) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 103 +- 6.6 after smoothing, mri peak at 103, scaling input intensities by 1.049 scaling channel 0 by 1.04854 initial log_p = -4.739 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.567644 @ (-9.091, -27.273, -9.091) max log p = -4.443453 @ (4.545, 4.545, 4.545) max log p = -4.419755 @ (2.273, -2.273, -2.273) max log p = -4.400971 @ (1.136, 1.136, -1.136) max log p = -4.393530 @ (0.568, -0.568, 0.568) max log p = -4.393530 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -24.4, -7.4): log p = -4.394 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.147, old_max_log_p =-4.394 (thresh=-4.4) 1.07500 0.00000 0.00000 -9.97645; 0.00000 1.06246 0.44009 -86.90463; 0.00000 -0.40708 0.98278 62.47320; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.147, old_max_log_p =-4.147 (thresh=-4.1) 1.07500 0.00000 0.00000 -9.97645; 0.00000 1.06246 0.44009 -86.90463; 0.00000 -0.40708 0.98278 62.47320; 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=-4.047, old_max_log_p =-4.147 (thresh=-4.1) 1.05296 -0.04748 0.02088 -5.45843; 0.03384 1.13665 0.35779 -94.01412; -0.03385 -0.28687 0.98328 50.50199; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.047, old_max_log_p =-4.047 (thresh=-4.0) 1.05296 -0.04748 0.02088 -5.45843; 0.03384 1.13665 0.35779 -94.01412; -0.03385 -0.28687 0.98328 50.50199; 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=-4.012, old_max_log_p =-4.047 (thresh=-4.0) 1.05008 -0.02387 0.01096 -7.44278; 0.01592 1.13112 0.38215 -92.64061; -0.01736 -0.31651 0.97785 53.02369; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.003, old_max_log_p =-4.012 (thresh=-4.0) 1.04639 -0.02378 0.01092 -6.97796; 0.01592 1.13112 0.38215 -92.64061; -0.01736 -0.31651 0.97785 53.02369; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.994, old_max_log_p =-4.003 (thresh=-4.0) 1.04516 -0.02376 0.01091 -6.82307; 0.01592 1.13112 0.38215 -92.64061; -0.01736 -0.31651 0.97785 53.02369; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.994, old_max_log_p =-3.994 (thresh=-4.0) 1.04516 -0.02376 0.01091 -6.82307; 0.01592 1.13112 0.38215 -92.64061; -0.01736 -0.31651 0.97785 53.02369; 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 1.04516 -0.02376 0.01091 -6.82307; 0.01592 1.13112 0.38215 -92.64061; -0.01736 -0.31651 0.97785 53.02369; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.04516 -0.02376 0.01091 -6.82307; 0.01592 1.13112 0.38215 -92.64061; -0.01736 -0.31651 0.97785 53.02369; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.04516 -0.02376 0.01091 -6.82307; 0.01592 1.13112 0.38215 -92.64061; -0.01736 -0.31651 0.97785 53.02369; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.994 (old=-4.739) transform before final EM align: 1.04516 -0.02376 0.01091 -6.82307; 0.01592 1.13112 0.38215 -92.64061; -0.01736 -0.31651 0.97785 53.02369; 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 1.04516 -0.02376 0.01091 -6.82307; 0.01592 1.13112 0.38215 -92.64061; -0.01736 -0.31651 0.97785 53.02369; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.04516 -0.02376 0.01091 -6.82307; 0.01592 1.13112 0.38215 -92.64061; -0.01736 -0.31651 0.97785 53.02369; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.4 tol 0.000000 final transform: 1.04516 -0.02376 0.01091 -6.82307; 0.01592 1.13112 0.38215 -92.64061; -0.01736 -0.31651 0.97785 53.02369; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1350.507691 mri_em_register stimesec 1.503771 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 157581 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 148912 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 95 mri_em_register ru_nivcsw 5136 registration took 11 minutes and 43 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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=128 y=141 z=110 r=68 first estimation of the main basin volume: 1334373 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=150, y=136, z=77, 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=8825507198 voxels, voxel volume =1.000 = 8825507198 mmm3 = 8825506.816 cm3 done. PostAnalyze...Basin Prior 14 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=128,y=148, z=104, r=10158 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=47 , nb = 44360 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1035254719 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1046482004 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=50 , nb = 1051046757 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=51 , nb = 1058654546 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1077532074 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 47, 36, 27, 65 after analyzing : 26, 36, 36, 43 RIGHT_CER before analyzing : 3, 3, 21, 54 after analyzing : 3, 17, 25, 26 LEFT_CER before analyzing : 3, 3, 20, 55 after analyzing : 3, 17, 25, 26 RIGHT_BRAIN before analyzing : 50, 37, 28, 65 after analyzing : 28, 37, 37, 44 LEFT_BRAIN before analyzing : 51, 38, 27, 64 after analyzing : 30, 38, 38, 44 OTHER before analyzing : 3, 5, 71, 95 after analyzing : 3, 49, 71, 60 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...61 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 69.465, std = 7.014 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.08, sigma = 6.46 after rotation: sse = 4.08, sigma = 6.46 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.61, its var is 6.64 before Erosion-Dilatation 2.18% of inacurate vertices after Erosion-Dilatation 1.54% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1588383 voxels, voxel volume = 1.000 mm3 = 1588383 mmm3 = 1588.383 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 23.475431 mri_watershed stimesec 0.386941 mri_watershed ru_maxrss 820380 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212434 mri_watershed ru_majflt 2 mri_watershed ru_nswap 0 mri_watershed ru_inblock 13968 mri_watershed ru_oublock 2640 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1114 mri_watershed ru_nivcsw 206 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Oct 7 17:16:38 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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=15.0 skull bounding box = (62, 82, 24) --> (197, 208, 191) using (107, 124, 108) as brain centroid... mean wm in atlas = 107, using box (90,109,87) --> (123, 139,128) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 6.4 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.544 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.118443 @ (-9.091, -27.273, -9.091) max log p = -3.964396 @ (4.545, -4.545, 4.545) max log p = -3.898541 @ (2.273, 2.273, 2.273) max log p = -3.895545 @ (1.136, 1.136, -1.136) max log p = -3.878737 @ (0.568, -1.705, -2.841) max log p = -3.878737 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -30.1, -6.3): log p = -3.879 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.720, old_max_log_p =-3.879 (thresh=-3.9) 1.00000 0.00000 0.00000 -0.56818; 0.00000 1.03837 0.27823 -63.59654; 0.00000 -0.25882 0.96593 43.21329; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.717, old_max_log_p =-3.720 (thresh=-3.7) 1.00000 0.00000 0.00000 -0.56818; 0.00000 0.99570 0.40193 -70.15472; 0.00000 -0.42155 0.99045 64.78014; 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=-3.587, old_max_log_p =-3.717 (thresh=-3.7) 1.00000 0.00000 0.00000 -0.56818; 0.00000 0.97703 0.39439 -68.40732; 0.00000 -0.39813 0.93543 68.84359; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.579, old_max_log_p =-3.587 (thresh=-3.6) 1.01820 -0.03337 -0.01108 1.40254; 0.03333 1.01920 0.33842 -71.34608; 0.00000 -0.33963 0.97721 55.73100; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.579, old_max_log_p =-3.579 (thresh=-3.6) 1.01820 -0.03337 -0.01108 1.40254; 0.03333 1.01920 0.33842 -71.34608; 0.00000 -0.33963 0.97721 55.73100; 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=-3.547, old_max_log_p =-3.579 (thresh=-3.6) 1.02179 -0.03348 -0.01112 0.96157; 0.03345 1.01997 0.34762 -71.47997; -0.00027 -0.34918 0.97783 57.13053; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.538, old_max_log_p =-3.547 (thresh=-3.5) 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92709; -0.00027 -0.34918 0.97783 57.13053; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.538, old_max_log_p =-3.538 (thresh=-3.5) 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92709; -0.00027 -0.34918 0.97783 57.13053; 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 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92709; -0.00027 -0.34918 0.97783 57.13053; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92709; -0.00027 -0.34918 0.97783 57.13053; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92709; -0.00027 -0.34918 0.97783 57.13053; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.538 (old=-4.544) transform before final EM align: 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92709; -0.00027 -0.34918 0.97783 57.13053; 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 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92709; -0.00027 -0.34918 0.97783 57.13053; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92709; -0.00027 -0.34918 0.97783 57.13053; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.0 tol 0.000000 final transform: 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92709; -0.00027 -0.34918 0.97783 57.13053; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1124.217093 mri_em_register stimesec 1.288804 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 158990 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 129 mri_em_register ru_nivcsw 3737 registration took 9 minutes and 39 seconds. #-------------------------------------- #@# CA Normalize Sat Oct 7 17:26:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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=15.0 skull bounding box = (62, 82, 24) --> (197, 208, 191) using (107, 124, 108) as brain centroid... mean wm in atlas = 107, using box (90,109,87) --> (123, 139,128) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 6.4 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 using 246344 sample points... INFO: compute sample coordinates transform 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92709; -0.00027 -0.34918 0.97783 57.13053; 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 (128, 86, 31) --> (194, 199, 188) Left_Cerebral_White_Matter: limiting intensities to 101.0 --> 132.0 2 of 31 (6.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 86, 30) --> (130, 192, 188) Right_Cerebral_White_Matter: limiting intensities to 100.0 --> 132.0 0 of 42 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 174, 62) --> (179, 213, 114) Left_Cerebellum_White_Matter: limiting intensities to 118.0 --> 132.0 7 of 17 (41.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 174, 60) --> (130, 213, 114) Right_Cerebellum_White_Matter: limiting intensities to 124.0 --> 132.0 3 of 4 (75.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 158, 94) --> (147, 223, 124) Brain_Stem: limiting intensities to 98.0 --> 132.0 0 of 20 (0.0%) samples deleted using 114 total control points for intensity normalization... bias field = 0.881 +- 0.105 0 of 102 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 86, 31) --> (194, 199, 188) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 121 (0.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 86, 30) --> (130, 192, 188) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 149 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 174, 62) --> (179, 213, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 41 of 49 (83.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 174, 60) --> (130, 213, 114) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 20 of 55 (36.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 158, 94) --> (147, 223, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 50 of 96 (52.1%) samples deleted using 470 total control points for intensity normalization... bias field = 0.992 +- 0.065 0 of 355 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 86, 31) --> (194, 199, 188) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 205 (2.9%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 86, 30) --> (130, 192, 188) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 210 (1.9%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 174, 62) --> (179, 213, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 29 of 74 (39.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 174, 60) --> (130, 213, 114) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 46 of 60 (76.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 158, 94) --> (147, 223, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 121 of 183 (66.1%) samples deleted using 732 total control points for intensity normalization... bias field = 0.998 +- 0.057 0 of 519 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 46 seconds. #-------------------------------------- #@# CA Reg Sat Oct 7 17:28:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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) = 1.15 (predicted orig area = 7.0) 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=0.934, neg=0, invalid=762 0001: dt=221.952000, rms=0.858 (8.161%), neg=0, invalid=762 0002: dt=363.011806, rms=0.821 (4.260%), neg=0, invalid=762 0003: dt=159.853211, rms=0.800 (2.581%), neg=0, invalid=762 0004: dt=335.323944, rms=0.785 (1.894%), neg=0, invalid=762 0005: dt=177.012658, rms=0.774 (1.311%), neg=0, invalid=762 0006: dt=149.333333, rms=0.769 (0.720%), neg=0, invalid=762 0007: dt=517.888000, rms=0.759 (1.220%), neg=0, invalid=762 0008: dt=110.976000, rms=0.756 (0.518%), neg=0, invalid=762 0009: dt=1775.616000, rms=0.744 (1.555%), neg=0, invalid=762 0010: dt=295.936000, rms=0.736 (1.045%), neg=0, invalid=762 0011: dt=32.368000, rms=0.736 (0.018%), neg=0, invalid=762 0012: dt=32.368000, rms=0.736 (0.015%), neg=0, invalid=762 0013: dt=32.368000, rms=0.736 (-0.029%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.736, neg=0, invalid=762 0014: dt=129.472000, rms=0.735 (0.153%), neg=0, invalid=762 0015: dt=517.888000, rms=0.733 (0.271%), neg=0, invalid=762 0016: dt=517.888000, rms=0.731 (0.286%), neg=0, invalid=762 0017: dt=129.472000, rms=0.731 (0.025%), neg=0, invalid=762 0018: dt=129.472000, rms=0.730 (0.055%), neg=0, invalid=762 0019: dt=129.472000, rms=0.730 (0.091%), neg=0, invalid=762 0020: dt=129.472000, rms=0.729 (0.131%), neg=0, invalid=762 0021: dt=129.472000, rms=0.727 (0.166%), neg=0, invalid=762 0022: dt=129.472000, rms=0.726 (0.189%), neg=0, invalid=762 0023: dt=129.472000, rms=0.725 (0.207%), neg=0, invalid=762 0024: dt=129.472000, rms=0.723 (0.216%), neg=0, invalid=762 0025: dt=129.472000, rms=0.721 (0.221%), neg=0, invalid=762 0026: dt=129.472000, rms=0.720 (0.225%), neg=0, invalid=762 0027: dt=129.472000, rms=0.718 (0.207%), neg=0, invalid=762 0028: dt=129.472000, rms=0.717 (0.195%), neg=0, invalid=762 0029: dt=129.472000, rms=0.716 (0.158%), neg=0, invalid=762 0030: dt=129.472000, rms=0.715 (0.152%), neg=0, invalid=762 0031: dt=129.472000, rms=0.714 (0.157%), neg=0, invalid=762 0032: dt=129.472000, rms=0.713 (0.142%), neg=0, invalid=762 0033: dt=129.472000, rms=0.711 (0.145%), neg=0, invalid=762 0034: dt=129.472000, rms=0.711 (0.133%), neg=0, invalid=762 0035: dt=129.472000, rms=0.710 (0.140%), neg=0, invalid=762 0036: dt=129.472000, rms=0.709 (0.144%), neg=0, invalid=762 0037: dt=129.472000, rms=0.708 (0.115%), neg=0, invalid=762 0038: dt=129.472000, rms=0.707 (0.100%), neg=0, invalid=762 0039: dt=517.888000, rms=0.707 (0.027%), neg=0, invalid=762 0040: dt=517.888000, rms=0.706 (0.050%), neg=0, invalid=762 0041: dt=517.888000, rms=0.707 (-0.374%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.714, neg=0, invalid=762 0042: dt=36.288000, rms=0.712 (0.283%), neg=0, invalid=762 0043: dt=145.152000, rms=0.702 (1.496%), neg=0, invalid=762 0044: dt=145.152000, rms=0.696 (0.766%), neg=0, invalid=762 0045: dt=81.777778, rms=0.692 (0.560%), neg=0, invalid=762 0046: dt=45.891473, rms=0.688 (0.579%), neg=0, invalid=762 0047: dt=99.855422, rms=0.685 (0.453%), neg=0, invalid=762 0048: dt=36.288000, rms=0.683 (0.313%), neg=0, invalid=762 0049: dt=248.832000, rms=0.680 (0.452%), neg=0, invalid=762 0050: dt=62.208000, rms=0.673 (1.034%), neg=0, invalid=762 0051: dt=6.480000, rms=0.673 (0.010%), neg=0, invalid=762 0052: dt=6.480000, rms=0.673 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.673, neg=0, invalid=762 0053: dt=9.072000, rms=0.673 (0.080%), neg=0, invalid=762 0054: dt=9.072000, rms=0.673 (0.004%), neg=0, invalid=762 0055: dt=9.072000, rms=0.673 (0.002%), neg=0, invalid=762 0056: dt=9.072000, rms=0.673 (-0.013%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.700, neg=0, invalid=762 0057: dt=9.600000, rms=0.698 (0.228%), neg=0, invalid=762 0058: dt=32.000000, rms=0.691 (1.077%), neg=0, invalid=762 0059: dt=44.800000, rms=0.686 (0.760%), neg=0, invalid=762 0060: dt=11.200000, rms=0.684 (0.267%), neg=0, invalid=762 0061: dt=11.200000, rms=0.681 (0.319%), neg=0, invalid=762 0062: dt=32.000000, rms=0.678 (0.471%), neg=0, invalid=762 0063: dt=44.800000, rms=0.678 (0.064%), neg=0, invalid=762 0064: dt=22.400000, rms=0.677 (0.198%), neg=0, invalid=762 0065: dt=22.400000, rms=0.674 (0.354%), neg=0, invalid=762 0066: dt=22.400000, rms=0.673 (0.125%), neg=0, invalid=762 0067: dt=22.400000, rms=0.673 (-0.075%), neg=0, invalid=762 0068: dt=0.700000, rms=0.673 (0.000%), neg=0, invalid=762 0069: dt=1.600000, rms=0.673 (0.000%), neg=0, invalid=762 0070: dt=2.800000, rms=0.673 (0.003%), neg=0, invalid=762 0071: dt=11.200000, rms=0.673 (0.014%), neg=0, invalid=762 0072: dt=44.800000, rms=0.672 (0.229%), neg=0, invalid=762 0073: dt=0.000000, rms=0.672 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.672, neg=0, invalid=762 0074: dt=0.000000, rms=0.672 (0.062%), neg=0, invalid=762 0075: dt=0.000000, rms=0.672 (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=0.727, neg=0, invalid=762 0076: dt=0.000000, rms=0.727 (0.053%), neg=0, invalid=762 0077: dt=0.000000, rms=0.727 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.727, neg=0, invalid=762 0078: dt=0.000000, rms=0.727 (0.053%), neg=0, invalid=762 0079: dt=0.000000, rms=0.727 (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=0.833, neg=0, invalid=762 0080: dt=1.029777, rms=0.825 (0.900%), neg=0, invalid=762 0081: dt=0.448000, rms=0.825 (0.071%), neg=0, invalid=762 0082: dt=0.448000, rms=0.825 (0.010%), neg=0, invalid=762 0083: dt=0.448000, rms=0.825 (-0.145%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.825, neg=0, invalid=762 0084: dt=0.448000, rms=0.825 (0.073%), neg=0, invalid=762 0085: dt=0.112000, rms=0.824 (0.002%), neg=0, invalid=762 0086: dt=0.112000, rms=0.824 (0.002%), neg=0, invalid=762 0087: dt=0.112000, rms=0.824 (-0.004%), 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=0.694, neg=0, invalid=762 0088: dt=0.957642, rms=0.671 (3.365%), neg=0, invalid=762 0089: dt=0.096000, rms=0.670 (0.190%), neg=0, invalid=762 0090: dt=0.096000, rms=0.670 (-0.120%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.670, neg=0, invalid=762 0091: dt=0.028000, rms=0.669 (0.078%), neg=0, invalid=762 0092: dt=0.001500, rms=0.669 (0.001%), neg=0, invalid=762 0093: dt=0.001500, rms=0.669 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.10100 (14) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (2194 voxels, overlap=0.515) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (2194 voxels, peak = 14), gca=13.7 gca peak = 0.15565 (16) mri peak = 0.11082 (16) Right_Lateral_Ventricle (43): linear fit = 0.86 x + 0.0 (2116 voxels, overlap=0.821) Right_Lateral_Ventricle (43): linear fit = 0.86 x + 0.0 (2116 voxels, peak = 14), gca=13.7 gca peak = 0.26829 (96) mri peak = 0.08588 (99) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (885 voxels, overlap=1.003) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (885 voxels, peak = 100), gca=100.3 gca peak = 0.20183 (93) mri peak = 0.08026 (102) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (760 voxels, overlap=0.983) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (760 voxels, peak = 99), gca=99.0 gca peak = 0.21683 (55) mri peak = 0.09651 (65) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (744 voxels, overlap=0.849) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (744 voxels, peak = 64), gca=63.5 gca peak = 0.30730 (58) mri peak = 0.06897 (67) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (382 voxels, overlap=0.838) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (382 voxels, peak = 65), gca=64.7 gca peak = 0.11430 (101) mri peak = 0.07325 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (59344 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (59344 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.06508 (108) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (56534 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (56534 voxels, peak = 109), gca=108.6 gca peak = 0.14995 (59) mri peak = 0.02788 (56) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19929 voxels, overlap=0.824) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19929 voxels, peak = 60), gca=60.5 gca peak = 0.15082 (58) mri peak = 0.03290 (63) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (20759 voxels, overlap=0.536) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (20759 voxels, peak = 64), gca=63.5 gca peak = 0.14161 (67) mri peak = 0.09865 (74) Right_Caudate (50): linear fit = 1.09 x + 0.0 (619 voxels, overlap=0.615) Right_Caudate (50): linear fit = 1.09 x + 0.0 (619 voxels, peak = 73), gca=72.7 gca peak = 0.15243 (71) mri peak = 0.07906 (74) Left_Caudate (11): linear fit = 1.03 x + 0.0 (895 voxels, overlap=0.907) Left_Caudate (11): linear fit = 1.03 x + 0.0 (895 voxels, peak = 73), gca=73.5 gca peak = 0.13336 (57) mri peak = 0.02088 (42) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (10439 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (10439 voxels, peak = 64), gca=63.6 gca peak = 0.13252 (56) mri peak = 0.03113 (63) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (11979 voxels, overlap=0.181) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (11979 voxels, peak = 62), gca=62.4 gca peak = 0.18181 (84) mri peak = 0.04170 (65) Left_Cerebellum_White_Matter (7): linear fit = 0.79 x + 0.0 (7082 voxels, overlap=0.016) Left_Cerebellum_White_Matter (7): linear fit = 0.79 x + 0.0 (7082 voxels, peak = 66), gca=65.9 gca peak = 0.20573 (83) mri peak = 0.04258 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6299 voxels, overlap=0.901) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6299 voxels, peak = 84), gca=84.2 gca peak = 0.21969 (57) mri peak = 0.08629 (65) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (398 voxels, overlap=0.553) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (398 voxels, peak = 66), gca=66.4 gca peak = 0.39313 (56) mri peak = 0.08907 (67) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (495 voxels, overlap=0.771) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (495 voxels, peak = 64), gca=63.6 gca peak = 0.14181 (85) mri peak = 0.05725 (93) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4319 voxels, overlap=0.852) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4319 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.07287 (87) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3595 voxels, overlap=0.805) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3595 voxels, peak = 88), gca=87.6 gca peak = 0.13399 (79) mri peak = 0.05567 (86) Left_Putamen (12): linear fit = 1.09 x + 0.0 (2031 voxels, overlap=0.867) Left_Putamen (12): linear fit = 1.09 x + 0.0 (2031 voxels, peak = 86), gca=85.7 gca peak = 0.14159 (79) mri peak = 0.05243 (84) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2309 voxels, overlap=0.999) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2309 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.08980 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10310 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10310 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.06849 (98) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1202 voxels, overlap=0.277) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1202 voxels, peak = 96), gca=95.9 gca peak = 0.12801 (89) mri peak = 0.07561 (96) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1481 voxels, overlap=0.540) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1481 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.11852 (21) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (133 voxels, overlap=0.544) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (133 voxels, peak = 17), gca=17.4 gca peak = 0.15061 (21) mri peak = 0.09176 (16) Fourth_Ventricle (15): linear fit = 0.86 x + 0.0 (363 voxels, overlap=0.786) Fourth_Ventricle (15): linear fit = 0.86 x + 0.0 (363 voxels, peak = 18), gca=18.0 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) 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 1.11 x + 0.0 estimating mean wm scale to be 1.06 x + 0.0 estimating mean csf scale to be 0.79 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=0.696, neg=0, invalid=762 0094: dt=116.286472, rms=0.684 (1.658%), neg=0, invalid=762 0095: dt=369.920000, rms=0.679 (0.737%), neg=0, invalid=762 0096: dt=129.472000, rms=0.677 (0.379%), neg=0, invalid=762 0097: dt=129.472000, rms=0.676 (0.120%), neg=0, invalid=762 0098: dt=443.904000, rms=0.674 (0.305%), neg=0, invalid=762 0099: dt=73.984000, rms=0.673 (0.127%), neg=0, invalid=762 0100: dt=369.920000, rms=0.672 (0.107%), neg=0, invalid=762 0101: dt=129.472000, rms=0.671 (0.163%), neg=0, invalid=762 0102: dt=110.976000, rms=0.671 (0.018%), neg=0, invalid=762 0103: dt=110.976000, rms=0.670 (0.063%), neg=0, invalid=762 0104: dt=110.976000, rms=0.670 (0.089%), neg=0, invalid=762 0105: dt=110.976000, rms=0.669 (0.101%), neg=0, invalid=762 0106: dt=110.976000, rms=0.668 (0.114%), neg=0, invalid=762 0107: dt=110.976000, rms=0.668 (0.138%), neg=0, invalid=762 0108: dt=110.976000, rms=0.666 (0.153%), neg=0, invalid=762 0109: dt=110.976000, rms=0.666 (0.141%), neg=0, invalid=762 0110: dt=110.976000, rms=0.665 (0.124%), neg=0, invalid=762 0111: dt=110.976000, rms=0.664 (0.112%), neg=0, invalid=762 0112: dt=110.976000, rms=0.663 (0.106%), neg=0, invalid=762 0113: dt=110.976000, rms=0.663 (0.102%), neg=0, invalid=762 0114: dt=110.976000, rms=0.662 (0.082%), neg=0, invalid=762 0115: dt=110.976000, rms=0.662 (0.074%), neg=0, invalid=762 0116: dt=110.976000, rms=0.661 (0.069%), neg=0, invalid=762 0117: dt=110.976000, rms=0.661 (0.066%), neg=0, invalid=762 0118: dt=110.976000, rms=0.660 (0.064%), neg=0, invalid=762 0119: dt=110.976000, rms=0.660 (0.061%), neg=0, invalid=762 0120: dt=110.976000, rms=0.659 (0.057%), neg=0, invalid=762 0121: dt=110.976000, rms=0.659 (0.065%), neg=0, invalid=762 0122: dt=110.976000, rms=0.659 (0.074%), neg=0, invalid=762 0123: dt=110.976000, rms=0.658 (0.078%), neg=0, invalid=762 0124: dt=110.976000, rms=0.658 (0.073%), neg=0, invalid=762 0125: dt=110.976000, rms=0.657 (0.066%), neg=0, invalid=762 0126: dt=110.976000, rms=0.657 (0.058%), neg=0, invalid=762 0127: dt=110.976000, rms=0.656 (0.064%), neg=0, invalid=762 0128: dt=110.976000, rms=0.656 (0.067%), neg=0, invalid=762 0129: dt=110.976000, rms=0.655 (0.072%), neg=0, invalid=762 0130: dt=110.976000, rms=0.655 (0.069%), neg=0, invalid=762 0131: dt=110.976000, rms=0.655 (0.061%), neg=0, invalid=762 0132: dt=110.976000, rms=0.654 (0.056%), neg=0, invalid=762 0133: dt=110.976000, rms=0.654 (0.055%), neg=0, invalid=762 0134: dt=110.976000, rms=0.653 (0.054%), neg=0, invalid=762 0135: dt=110.976000, rms=0.653 (0.049%), neg=0, invalid=762 0136: dt=110.976000, rms=0.653 (0.049%), neg=0, invalid=762 0137: dt=110.976000, rms=0.653 (0.046%), neg=0, invalid=762 0138: dt=110.976000, rms=0.652 (0.046%), neg=0, invalid=762 0139: dt=110.976000, rms=0.652 (0.046%), neg=0, invalid=762 0140: dt=110.976000, rms=0.652 (0.043%), neg=0, invalid=762 0141: dt=110.976000, rms=0.651 (0.042%), neg=0, invalid=762 0142: dt=110.976000, rms=0.651 (0.041%), neg=0, invalid=762 0143: dt=110.976000, rms=0.651 (0.040%), neg=0, invalid=762 0144: dt=110.976000, rms=0.651 (0.041%), neg=0, invalid=762 0145: dt=110.976000, rms=0.650 (0.038%), neg=0, invalid=762 0146: dt=110.976000, rms=0.650 (0.036%), neg=0, invalid=762 0147: dt=110.976000, rms=0.650 (0.034%), neg=0, invalid=762 0148: dt=110.976000, rms=0.650 (0.035%), neg=0, invalid=762 0149: dt=110.976000, rms=0.649 (0.035%), neg=0, invalid=762 0150: dt=110.976000, rms=0.649 (0.034%), neg=0, invalid=762 0151: dt=110.976000, rms=0.649 (0.033%), neg=0, invalid=762 0152: dt=110.976000, rms=0.649 (0.033%), neg=0, invalid=762 0153: dt=110.976000, rms=0.649 (0.032%), neg=0, invalid=762 0154: dt=110.976000, rms=0.648 (0.033%), neg=0, invalid=762 0155: dt=110.976000, rms=0.648 (0.033%), neg=0, invalid=762 0156: dt=110.976000, rms=0.648 (0.033%), neg=0, invalid=762 0157: dt=110.976000, rms=0.648 (0.030%), neg=0, invalid=762 0158: dt=110.976000, rms=0.648 (0.031%), neg=0, invalid=762 0159: dt=110.976000, rms=0.647 (0.030%), neg=0, invalid=762 0160: dt=110.976000, rms=0.647 (0.028%), neg=0, invalid=762 0161: dt=110.976000, rms=0.647 (0.028%), neg=0, invalid=762 0162: dt=110.976000, rms=0.647 (0.003%), neg=0, invalid=762 0163: dt=110.976000, rms=0.647 (0.006%), neg=0, invalid=762 0164: dt=110.976000, rms=0.647 (0.008%), neg=0, invalid=762 0165: dt=110.976000, rms=0.647 (0.010%), neg=0, invalid=762 0166: dt=110.976000, rms=0.647 (0.011%), neg=0, invalid=762 0167: dt=110.976000, rms=0.647 (0.013%), neg=0, invalid=762 0168: dt=110.976000, rms=0.647 (0.014%), neg=0, invalid=762 0169: dt=110.976000, rms=0.646 (0.014%), neg=0, invalid=762 0170: dt=110.976000, rms=0.646 (0.015%), neg=0, invalid=762 0171: dt=110.976000, rms=0.646 (0.016%), neg=0, invalid=762 0172: dt=110.976000, rms=0.646 (0.016%), neg=0, invalid=762 0173: dt=1183.744000, rms=0.646 (0.012%), neg=0, invalid=762 0174: dt=147.968000, rms=0.646 (0.005%), neg=0, invalid=762 0175: dt=147.968000, rms=0.646 (0.017%), neg=0, invalid=762 0176: dt=147.968000, rms=0.646 (0.005%), neg=0, invalid=762 0177: dt=36.992000, rms=0.646 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.646, neg=0, invalid=762 0178: dt=129.472000, rms=0.645 (0.166%), neg=0, invalid=762 0179: dt=443.904000, rms=0.645 (0.112%), neg=0, invalid=762 0180: dt=92.480000, rms=0.644 (0.021%), neg=0, invalid=762 0181: dt=92.480000, rms=0.644 (0.017%), neg=0, invalid=762 0182: dt=92.480000, rms=0.644 (0.023%), neg=0, invalid=762 0183: dt=92.480000, rms=0.644 (0.027%), neg=0, invalid=762 0184: dt=92.480000, rms=0.644 (0.028%), neg=0, invalid=762 0185: dt=92.480000, rms=0.644 (0.029%), neg=0, invalid=762 0186: dt=92.480000, rms=0.643 (0.027%), neg=0, invalid=762 0187: dt=92.480000, rms=0.643 (0.024%), neg=0, invalid=762 0188: dt=92.480000, rms=0.643 (0.022%), neg=0, invalid=762 0189: dt=2071.552000, rms=0.642 (0.107%), neg=0, invalid=762 0190: dt=129.472000, rms=0.642 (0.052%), neg=0, invalid=762 0191: dt=0.000000, rms=0.642 (0.001%), neg=0, invalid=762 0192: dt=0.850000, rms=0.642 (-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=0.644, neg=0, invalid=762 0193: dt=98.666667, rms=0.641 (0.513%), neg=0, invalid=762 0194: dt=103.680000, rms=0.635 (0.881%), neg=0, invalid=762 0195: dt=145.152000, rms=0.632 (0.486%), neg=0, invalid=762 0196: dt=25.920000, rms=0.630 (0.216%), neg=0, invalid=762 0197: dt=6.480000, rms=0.630 (0.054%), neg=0, invalid=762 0198: dt=0.141750, rms=0.630 (0.002%), neg=0, invalid=762 0199: dt=0.070875, rms=0.630 (0.001%), neg=0, invalid=762 0200: dt=0.035437, rms=0.630 (0.001%), neg=0, invalid=762 0201: dt=0.017719, rms=0.630 (0.000%), neg=0, invalid=762 0202: dt=0.008859, rms=0.630 (0.000%), neg=0, invalid=762 0203: dt=0.007594, rms=0.630 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=762 0204: dt=135.245283, rms=0.625 (0.819%), neg=0, invalid=762 0205: dt=82.944000, rms=0.622 (0.489%), neg=0, invalid=762 0206: dt=86.276243, rms=0.621 (0.213%), neg=0, invalid=762 0207: dt=145.152000, rms=0.618 (0.406%), neg=0, invalid=762 0208: dt=36.288000, rms=0.617 (0.175%), neg=0, invalid=762 0209: dt=145.152000, rms=0.616 (0.242%), neg=0, invalid=762 0210: dt=88.000000, rms=0.614 (0.263%), neg=0, invalid=762 0211: dt=73.552239, rms=0.613 (0.143%), neg=0, invalid=762 0212: dt=145.152000, rms=0.612 (0.275%), neg=0, invalid=762 0213: dt=36.288000, rms=0.611 (0.103%), neg=0, invalid=762 0214: dt=145.152000, rms=0.610 (0.198%), neg=0, invalid=762 0215: dt=103.680000, rms=0.609 (0.195%), neg=0, invalid=762 0216: dt=62.728477, rms=0.608 (0.109%), neg=0, invalid=762 0217: dt=145.152000, rms=0.607 (0.212%), neg=0, invalid=762 0218: dt=82.944000, rms=0.606 (0.094%), neg=0, invalid=762 0219: dt=103.680000, rms=0.605 (0.148%), neg=0, invalid=762 0220: dt=65.488372, rms=0.605 (0.098%), neg=0, invalid=762 0221: dt=145.152000, rms=0.604 (0.160%), neg=0, invalid=762 0222: dt=36.288000, rms=0.603 (0.072%), neg=0, invalid=762 0223: dt=103.680000, rms=0.603 (0.117%), neg=0, invalid=762 0224: dt=145.152000, rms=0.602 (0.139%), neg=0, invalid=762 0225: dt=9.072000, rms=0.602 (0.016%), neg=0, invalid=762 0226: dt=9.072000, rms=0.602 (0.018%), neg=0, invalid=762 0227: dt=2.268000, rms=0.602 (0.005%), neg=0, invalid=762 0228: dt=2.268000, rms=0.601 (0.005%), neg=0, invalid=762 0229: dt=0.008859, rms=0.601 (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=0.607, neg=0, invalid=762 0230: dt=0.000000, rms=0.606 (0.085%), neg=0, invalid=762 0231: dt=0.000000, rms=0.606 (0.000%), neg=0, invalid=762 0232: dt=0.000244, rms=0.606 (0.000%), neg=0, invalid=762 0233: dt=0.000001, rms=0.606 (0.000%), neg=0, invalid=762 0234: dt=0.000000, rms=0.606 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.607, neg=0, invalid=762 0235: dt=0.000000, rms=0.606 (0.085%), neg=0, invalid=762 0236: dt=0.000000, rms=0.606 (0.000%), neg=0, invalid=762 0237: dt=0.000002, rms=0.606 (0.000%), neg=0, invalid=762 0238: dt=0.000001, rms=0.606 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.622, neg=0, invalid=762 0239: dt=4.032000, rms=0.608 (2.205%), neg=0, invalid=762 0240: dt=4.032000, rms=0.598 (1.658%), neg=0, invalid=762 0241: dt=4.032000, rms=0.591 (1.253%), neg=0, invalid=762 0242: dt=4.032000, rms=0.585 (0.969%), neg=0, invalid=762 0243: dt=4.032000, rms=0.580 (0.774%), neg=0, invalid=762 0244: dt=4.032000, rms=0.577 (0.583%), neg=0, invalid=762 0245: dt=4.032000, rms=0.574 (0.525%), neg=0, invalid=762 0246: dt=4.032000, rms=0.572 (0.357%), neg=0, invalid=762 0247: dt=4.032000, rms=0.570 (0.374%), neg=0, invalid=762 0248: dt=4.032000, rms=0.569 (0.233%), neg=0, invalid=762 0249: dt=4.032000, rms=0.567 (0.272%), neg=0, invalid=762 0250: dt=4.032000, rms=0.566 (0.169%), neg=0, invalid=762 0251: dt=4.032000, rms=0.565 (0.193%), neg=0, invalid=762 0252: dt=4.032000, rms=0.564 (0.133%), neg=0, invalid=762 0253: dt=4.032000, rms=0.563 (0.127%), neg=0, invalid=762 0254: dt=4.032000, rms=0.563 (0.112%), neg=0, invalid=762 0255: dt=4.032000, rms=0.562 (0.079%), neg=0, invalid=762 0256: dt=4.032000, rms=0.562 (0.101%), neg=0, invalid=762 0257: dt=4.032000, rms=0.561 (0.068%), neg=0, invalid=762 0258: dt=1.008000, rms=0.561 (0.024%), neg=0, invalid=762 0259: dt=0.252000, rms=0.561 (0.007%), neg=0, invalid=762 0260: dt=0.063000, rms=0.561 (0.002%), neg=0, invalid=762 0261: dt=0.003938, rms=0.561 (0.000%), neg=0, invalid=762 0262: dt=0.002813, rms=0.561 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.562, neg=0, invalid=762 0263: dt=6.000000, rms=0.561 (0.149%), neg=0, invalid=762 0264: dt=3.428571, rms=0.561 (0.022%), neg=0, invalid=762 0265: dt=3.428571, rms=0.561 (0.028%), neg=0, invalid=762 0266: dt=3.428571, rms=0.561 (0.025%), neg=0, invalid=762 0267: dt=3.428571, rms=0.560 (0.011%), neg=0, invalid=762 0268: dt=4.032000, rms=0.560 (0.047%), neg=0, invalid=762 0269: dt=5.600000, rms=0.560 (0.025%), neg=0, invalid=762 0270: dt=5.600000, rms=0.560 (0.070%), neg=0, invalid=762 0271: dt=5.600000, rms=0.559 (0.087%), neg=0, invalid=762 0272: dt=5.600000, rms=0.558 (0.133%), neg=0, invalid=762 0273: dt=5.600000, rms=0.558 (0.132%), neg=0, invalid=762 0274: dt=5.600000, rms=0.557 (0.123%), neg=0, invalid=762 0275: dt=5.600000, rms=0.556 (0.131%), neg=0, invalid=762 0276: dt=5.600000, rms=0.556 (0.137%), neg=0, invalid=762 0277: dt=5.600000, rms=0.555 (0.130%), neg=0, invalid=762 0278: dt=5.600000, rms=0.554 (0.103%), neg=0, invalid=762 0279: dt=5.600000, rms=0.553 (0.136%), neg=0, invalid=762 0280: dt=5.600000, rms=0.553 (0.134%), neg=0, invalid=762 0281: dt=5.600000, rms=0.552 (0.096%), neg=0, invalid=762 0282: dt=5.600000, rms=0.552 (0.062%), neg=0, invalid=762 0283: dt=5.600000, rms=0.551 (0.090%), neg=0, invalid=762 0284: dt=5.600000, rms=0.551 (0.136%), neg=0, invalid=762 0285: dt=5.600000, rms=0.550 (0.069%), neg=0, invalid=762 0286: dt=5.600000, rms=0.550 (0.015%), neg=0, invalid=762 0287: dt=5.600000, rms=0.550 (0.096%), neg=0, invalid=762 0288: dt=5.600000, rms=0.549 (0.133%), neg=0, invalid=762 0289: dt=5.600000, rms=0.549 (0.001%), neg=0, invalid=762 0290: dt=5.600000, rms=0.549 (0.035%), neg=0, invalid=762 0291: dt=5.600000, rms=0.548 (0.112%), neg=0, invalid=762 0292: dt=5.600000, rms=0.548 (0.016%), neg=0, invalid=762 0293: dt=5.600000, rms=0.548 (0.014%), neg=0, invalid=762 0294: dt=4.032000, rms=0.547 (0.077%), neg=0, invalid=762 0295: dt=0.000000, rms=0.547 (0.000%), neg=0, invalid=762 0296: dt=0.150000, rms=0.547 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.563, neg=0, invalid=762 0297: dt=0.000000, rms=0.562 (0.088%), neg=0, invalid=762 0298: dt=0.000000, rms=0.562 (0.000%), neg=0, invalid=762 0299: dt=0.100000, rms=0.562 (-0.154%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.563, neg=0, invalid=762 0300: dt=0.000000, rms=0.562 (0.088%), neg=0, invalid=762 0301: dt=0.000000, rms=0.562 (0.000%), neg=0, invalid=762 0302: dt=0.100000, rms=0.562 (-0.144%), 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=0.538, neg=0, invalid=762 0303: dt=0.448000, rms=0.522 (2.898%), neg=0, invalid=762 0304: dt=0.448000, rms=0.519 (0.692%), neg=0, invalid=762 0305: dt=0.448000, rms=0.517 (0.379%), neg=0, invalid=762 0306: dt=0.448000, rms=0.516 (0.210%), neg=0, invalid=762 0307: dt=0.448000, rms=0.515 (0.184%), neg=0, invalid=762 0308: dt=0.384000, rms=0.514 (0.102%), neg=0, invalid=762 0309: dt=0.384000, rms=0.514 (0.107%), neg=0, invalid=762 0310: dt=0.112000, rms=0.513 (0.040%), neg=0, invalid=762 0311: dt=0.112000, rms=0.513 (0.031%), neg=0, invalid=762 0312: dt=0.112000, rms=0.513 (0.056%), neg=0, invalid=762 0313: dt=0.112000, rms=0.513 (0.068%), neg=0, invalid=762 0314: dt=0.112000, rms=0.512 (0.077%), neg=0, invalid=762 0315: dt=0.112000, rms=0.512 (0.077%), neg=0, invalid=762 0316: dt=0.112000, rms=0.511 (0.078%), neg=0, invalid=762 0317: dt=0.112000, rms=0.511 (0.076%), neg=0, invalid=762 0318: dt=0.112000, rms=0.511 (0.071%), neg=0, invalid=762 0319: dt=0.112000, rms=0.510 (0.062%), neg=0, invalid=762 0320: dt=0.112000, rms=0.510 (0.053%), neg=0, invalid=762 0321: dt=0.112000, rms=0.510 (0.044%), neg=0, invalid=762 0322: dt=0.112000, rms=0.510 (0.035%), neg=0, invalid=762 0323: dt=0.112000, rms=0.509 (0.026%), neg=0, invalid=762 0324: dt=0.112000, rms=0.509 (0.023%), neg=0, invalid=762 0325: dt=0.112000, rms=0.509 (0.012%), neg=0, invalid=762 0326: dt=0.000000, rms=0.509 (0.004%), neg=0, invalid=762 0327: dt=0.050000, rms=0.509 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.510, neg=0, invalid=762 0328: dt=0.320000, rms=0.506 (0.809%), neg=0, invalid=762 0329: dt=0.320000, rms=0.505 (0.224%), neg=0, invalid=762 0330: dt=0.320000, rms=0.504 (0.070%), neg=0, invalid=762 0331: dt=0.192000, rms=0.504 (0.017%), neg=0, invalid=762 0332: dt=0.192000, rms=0.504 (0.016%), neg=0, invalid=762 0333: dt=0.192000, rms=0.504 (0.008%), neg=0, invalid=762 0334: dt=0.192000, rms=0.504 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.502, neg=0, invalid=762 0335: dt=23.120000, rms=0.501 (0.124%), neg=0, invalid=762 0336: dt=0.007902, rms=0.501 (0.002%), neg=0, invalid=762 0337: dt=0.007902, rms=0.501 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.502, neg=0, invalid=762 0338: dt=129.472000, rms=0.501 (0.176%), neg=0, invalid=762 0339: dt=129.472000, rms=0.501 (0.038%), neg=0, invalid=762 0340: dt=129.472000, rms=0.501 (-0.031%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.501, neg=0, invalid=762 0341: dt=9.072000, rms=0.501 (0.128%), neg=0, invalid=762 0342: dt=9.072000, rms=0.501 (0.015%), neg=0, invalid=762 0343: dt=9.072000, rms=0.501 (0.007%), neg=0, invalid=762 0344: dt=9.072000, rms=0.501 (-0.009%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.501, neg=0, invalid=762 0345: dt=98.102190, rms=0.499 (0.386%), neg=0, invalid=762 0346: dt=36.288000, rms=0.499 (0.138%), neg=0, invalid=762 0347: dt=36.288000, rms=0.498 (0.053%), neg=0, invalid=762 0348: dt=36.288000, rms=0.498 (0.086%), neg=0, invalid=762 0349: dt=36.288000, rms=0.497 (0.121%), neg=0, invalid=762 0350: dt=36.288000, rms=0.497 (0.116%), neg=0, invalid=762 0351: dt=36.288000, rms=0.496 (0.105%), neg=0, invalid=762 0352: dt=124.416000, rms=0.496 (0.033%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.497, neg=0, invalid=762 0353: dt=31.046070, rms=0.494 (0.658%), neg=0, invalid=762 0354: dt=6.400000, rms=0.494 (0.012%), neg=0, invalid=762 0355: dt=6.400000, rms=0.493 (0.112%), neg=0, invalid=762 0356: dt=6.400000, rms=0.492 (0.154%), neg=0, invalid=762 0357: dt=6.400000, rms=0.491 (0.170%), neg=0, invalid=762 0358: dt=6.400000, rms=0.491 (0.152%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0359: dt=6.400000, rms=0.490 (0.097%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 10 iterations, nbhd size=1, neg = 0 0360: dt=6.400000, rms=0.490 (0.038%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0361: dt=44.800000, rms=0.489 (0.205%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0362: dt=25.600000, rms=0.488 (0.155%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0363: dt=25.600000, rms=0.488 (-0.150%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 0364: dt=24.083333, rms=0.486 (0.462%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0365: dt=27.726210, rms=0.483 (0.816%), neg=0, invalid=762 0366: dt=2.800000, rms=0.482 (0.040%), neg=0, invalid=762 0367: dt=2.800000, rms=0.482 (0.036%), neg=0, invalid=762 0368: dt=2.800000, rms=0.482 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.487, neg=0, invalid=762 0369: dt=4.842105, rms=0.485 (0.264%), neg=0, invalid=762 iter 0, gcam->neg = 351 after 18 iterations, nbhd size=1, neg = 0 0370: dt=8.810573, rms=0.482 (0.638%), neg=0, invalid=762 0371: dt=0.720000, rms=0.482 (0.009%), neg=0, invalid=762 0372: dt=0.720000, rms=0.482 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0373: dt=2.731707, rms=0.482 (0.179%), neg=0, invalid=762 iter 0, gcam->neg = 116 after 13 iterations, nbhd size=1, neg = 0 0374: dt=17.261084, rms=0.478 (0.720%), neg=0, invalid=762 0375: dt=2.880000, rms=0.478 (0.043%), neg=0, invalid=762 0376: dt=2.880000, rms=0.478 (0.109%), neg=0, invalid=762 0377: dt=2.880000, rms=0.477 (0.161%), neg=0, invalid=762 0378: dt=2.880000, rms=0.476 (0.183%), neg=0, invalid=762 0379: dt=2.880000, rms=0.475 (0.179%), neg=0, invalid=762 0380: dt=2.880000, rms=0.475 (0.153%), neg=0, invalid=762 0381: dt=2.880000, rms=0.474 (0.128%), neg=0, invalid=762 0382: dt=2.880000, rms=0.473 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0383: dt=2.880000, rms=0.473 (0.125%), neg=0, invalid=762 0384: dt=2.880000, rms=0.472 (0.116%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0385: dt=11.520000, rms=0.472 (0.052%), neg=0, invalid=762 iter 0, gcam->neg = 113 after 13 iterations, nbhd size=1, neg = 0 0386: dt=11.520000, rms=0.472 (-0.016%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.477, neg=0, invalid=762 0387: dt=0.000050, rms=0.477 (0.130%), neg=0, invalid=762 0388: dt=0.000000, rms=0.477 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.477, neg=0, invalid=762 0389: dt=0.000000, rms=0.477 (0.130%), neg=0, invalid=762 0390: dt=0.000000, rms=0.477 (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=0.469, neg=0, invalid=762 iter 0, gcam->neg = 1495 after 14 iterations, nbhd size=1, neg = 0 0391: dt=1.724373, rms=0.445 (5.215%), neg=0, invalid=762 0392: dt=0.000013, rms=0.445 (0.006%), neg=0, invalid=762 0393: dt=0.000013, rms=0.445 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.446, neg=0, invalid=762 0394: dt=0.064000, rms=0.445 (0.198%), neg=0, invalid=762 0395: dt=0.005000, rms=0.445 (0.002%), neg=0, invalid=762 0396: dt=0.005000, rms=0.445 (-0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.434, neg=0, invalid=762 0397: dt=18.496000, rms=0.434 (0.012%), neg=0, invalid=762 0398: dt=0.361250, rms=0.434 (0.000%), neg=0, invalid=762 0399: dt=0.361250, rms=0.434 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=762 0400: dt=92.480000, rms=0.434 (0.026%), neg=0, invalid=762 0401: dt=73.984000, rms=0.434 (0.002%), neg=0, invalid=762 0402: dt=73.984000, rms=0.434 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.434, neg=0, invalid=762 0403: dt=0.000000, rms=0.434 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=762 0404: dt=5.333333, rms=0.434 (0.000%), neg=0, invalid=762 0405: dt=6.480000, rms=0.434 (0.000%), neg=0, invalid=762 0406: dt=6.480000, rms=0.434 (0.001%), neg=0, invalid=762 0407: dt=6.480000, rms=0.434 (0.000%), neg=0, invalid=762 0408: dt=6.480000, rms=0.434 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.434, neg=0, invalid=762 0409: dt=11.200000, rms=0.434 (0.133%), neg=0, invalid=762 0410: dt=8.000000, rms=0.434 (0.030%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0411: dt=8.000000, rms=0.434 (0.001%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 8 iterations, nbhd size=1, neg = 0 0412: dt=8.000000, rms=0.434 (-0.076%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0413: dt=38.400000, rms=0.432 (0.351%), neg=0, invalid=762 iter 0, gcam->neg = 56 after 10 iterations, nbhd size=1, neg = 0 0414: dt=75.764706, rms=0.430 (0.537%), neg=0, invalid=762 0415: dt=9.600000, rms=0.429 (0.086%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0416: dt=9.600000, rms=0.429 (-0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.432, neg=0, invalid=762 iter 0, gcam->neg = 16 after 9 iterations, nbhd size=1, neg = 0 0417: dt=6.800000, rms=0.431 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 11 iterations, nbhd size=1, neg = 0 0418: dt=9.061224, rms=0.430 (0.136%), neg=0, invalid=762 0419: dt=0.252000, rms=0.430 (0.000%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0420: dt=0.252000, rms=0.430 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.430, neg=0, invalid=762 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0421: dt=7.444444, rms=0.430 (0.192%), neg=0, invalid=762 iter 0, gcam->neg = 144 after 13 iterations, nbhd size=1, neg = 0 0422: dt=14.734177, rms=0.428 (0.430%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0423: dt=2.000000, rms=0.428 (0.011%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0424: dt=2.000000, rms=0.428 (0.016%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 0425: dt=2.000000, rms=0.428 (0.015%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 0426: dt=2.000000, rms=0.428 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 50 after 9 iterations, nbhd size=1, neg = 0 0427: dt=15.272727, rms=0.427 (0.163%), neg=0, invalid=762 0428: dt=0.252000, rms=0.427 (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=0.432, neg=0, invalid=762 0429: dt=0.000000, rms=0.432 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.432, neg=0, invalid=762 0430: dt=0.000000, rms=0.432 (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=0.423, neg=0, invalid=762 iter 0, gcam->neg = 626 after 16 iterations, nbhd size=1, neg = 0 0431: dt=0.937273, rms=0.415 (1.956%), neg=0, invalid=762 0432: dt=0.012000, rms=0.415 (0.001%), neg=0, invalid=762 0433: dt=0.012000, rms=0.415 (0.000%), neg=0, invalid=762 0434: dt=0.012000, rms=0.415 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=762 0435: dt=0.256000, rms=0.414 (0.216%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0436: dt=0.384000, rms=0.413 (0.228%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 0 iterations, nbhd size=0, neg = 0 0437: dt=0.448000, rms=0.413 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0438: dt=0.448000, rms=0.413 (0.042%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 1 iterations, nbhd size=0, neg = 0 0439: dt=0.448000, rms=0.412 (0.083%), neg=0, invalid=762 iter 0, gcam->neg = 46 after 11 iterations, nbhd size=1, neg = 0 0440: dt=0.448000, rms=0.412 (-0.008%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 4 minutes and 11 seconds. mri_ca_register utimesec 8419.642019 mri_ca_register stimesec 8.907645 mri_ca_register ru_maxrss 1342232 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4178803 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 65040 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 3917 mri_ca_register ru_nivcsw 26296 FSRUNTIME@ mri_ca_register 2.0696 hours 2 threads #-------------------------------------- #@# SubCort Seg Sat Oct 7 19:32:14 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-900 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-6.0.0/0051324/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 2 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.97 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 = 0.09046 (14) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (4010 voxels, overlap=0.743) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (4010 voxels, peak = 14), gca=14.1 gca peak = 0.17677 (13) mri peak = 0.09826 (16) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (4715 voxels, overlap=0.810) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (4715 voxels, peak = 13), gca=13.5 gca peak = 0.28129 (95) mri peak = 0.10915 (101) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (621 voxels, overlap=1.014) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (621 voxels, peak = 100), gca=100.2 gca peak = 0.16930 (96) mri peak = 0.09150 (101) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (612 voxels, overlap=0.872) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (612 voxels, peak = 101), gca=101.3 gca peak = 0.24553 (55) mri peak = 0.07445 (65) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1218 voxels, overlap=0.939) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1218 voxels, peak = 62), gca=62.4 gca peak = 0.30264 (59) mri peak = 0.07400 (65) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (963 voxels, overlap=1.016) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (963 voxels, peak = 67), gca=67.0 gca peak = 0.07580 (103) mri peak = 0.07596 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (38034 voxels, overlap=0.693) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (38034 voxels, peak = 107), gca=106.6 gca peak = 0.07714 (104) mri peak = 0.07017 (109) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (38575 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (38575 voxels, peak = 109), gca=108.7 gca peak = 0.09712 (58) mri peak = 0.03180 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23335 voxels, overlap=0.913) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23335 voxels, peak = 59), gca=59.4 gca peak = 0.11620 (58) mri peak = 0.03293 (62) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (25291 voxels, overlap=0.869) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (25291 voxels, peak = 64), gca=63.5 gca peak = 0.30970 (66) mri peak = 0.08179 (75) Right_Caudate (50): linear fit = 1.14 x + 0.0 (1181 voxels, overlap=0.171) Right_Caudate (50): linear fit = 1.14 x + 0.0 (1181 voxels, peak = 76), gca=75.6 gca peak = 0.15280 (69) mri peak = 0.08788 (75) Left_Caudate (11): linear fit = 1.04 x + 0.0 (1172 voxels, overlap=0.925) Left_Caudate (11): linear fit = 1.04 x + 0.0 (1172 voxels, peak = 72), gca=72.1 gca peak = 0.13902 (56) mri peak = 0.04175 (58) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (5213 voxels, overlap=0.657) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (5213 voxels, peak = 59), gca=58.5 gca peak = 0.14777 (55) mri peak = 0.05372 (63) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (7018 voxels, overlap=0.587) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (7018 voxels, peak = 62), gca=62.4 gca peak = 0.16765 (84) mri peak = 0.05028 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (3375 voxels, overlap=0.905) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (3375 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.07351 (84) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (2280 voxels, overlap=0.910) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (2280 voxels, peak = 86), gca=86.1 gca peak = 0.29869 (57) mri peak = 0.07955 (65) Left_Amygdala (18): linear fit = 1.13 x + 0.0 (449 voxels, overlap=1.025) Left_Amygdala (18): linear fit = 1.13 x + 0.0 (449 voxels, peak = 65), gca=64.7 gca peak = 0.33601 (57) mri peak = 0.08146 (67) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (580 voxels, overlap=0.565) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (580 voxels, peak = 65), gca=64.7 gca peak = 0.11131 (90) mri peak = 0.05949 (88) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (3910 voxels, overlap=0.835) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (3910 voxels, peak = 95), gca=94.9 gca peak = 0.11793 (83) mri peak = 0.07152 (87) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3873 voxels, overlap=0.680) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3873 voxels, peak = 88), gca=88.4 gca peak = 0.08324 (81) mri peak = 0.05566 (86) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1654 voxels, overlap=0.877) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1654 voxels, peak = 85), gca=84.6 gca peak = 0.10360 (77) mri peak = 0.05988 (84) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1665 voxels, overlap=0.884) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1665 voxels, peak = 83), gca=82.8 gca peak = 0.08424 (78) mri peak = 0.08742 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (8904 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.10 x + 0.0 (8904 voxels, peak = 85), gca=85.4 gca peak = 0.12631 (89) mri peak = 0.06725 (97) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1316 voxels, overlap=0.567) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1316 voxels, peak = 100), gca=100.1 gca peak = 0.14500 (87) mri peak = 0.07034 (96) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1237 voxels, overlap=0.778) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1237 voxels, peak = 95), gca=95.3 gca peak = 0.14975 (24) mri peak = 0.12346 (21) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (243 voxels, overlap=0.477) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (243 voxels, peak = 18), gca=17.9 gca peak = 0.19357 (14) mri peak = 0.14050 (16) Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (120 voxels, overlap=0.842) Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (120 voxels, peak = 15), gca=15.3 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) 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 1.11 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.90 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.19905 (14) mri peak = 0.09046 (14) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (4010 voxels, overlap=0.990) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (4010 voxels, peak = 14), gca=14.5 gca peak = 0.19108 (13) mri peak = 0.09826 (16) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (4715 voxels, overlap=0.745) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (4715 voxels, peak = 13), gca=13.5 gca peak = 0.27298 (101) mri peak = 0.10915 (101) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (621 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (621 voxels, peak = 100), gca=100.5 gca peak = 0.16685 (101) mri peak = 0.09150 (101) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (612 voxels, overlap=1.007) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (612 voxels, peak = 102), gca=101.5 gca peak = 0.26834 (63) mri peak = 0.07445 (65) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1218 voxels, overlap=1.011) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1218 voxels, peak = 63), gca=63.0 gca peak = 0.28034 (64) mri peak = 0.07400 (65) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (963 voxels, overlap=1.012) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (963 voxels, peak = 64), gca=64.0 gca peak = 0.07501 (106) mri peak = 0.07596 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38034 voxels, overlap=0.825) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38034 voxels, peak = 105), gca=105.5 gca peak = 0.07788 (109) mri peak = 0.07017 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38575 voxels, overlap=0.801) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38575 voxels, peak = 109), gca=109.0 gca peak = 0.09505 (59) mri peak = 0.03180 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23335 voxels, overlap=0.952) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23335 voxels, peak = 60), gca=60.5 gca peak = 0.10617 (64) mri peak = 0.03293 (62) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (25291 voxels, overlap=0.975) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (25291 voxels, peak = 68), gca=67.5 gca peak = 0.24441 (76) mri peak = 0.08179 (75) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1181 voxels, overlap=1.005) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1181 voxels, peak = 74), gca=74.1 gca peak = 0.15227 (72) mri peak = 0.08788 (75) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1172 voxels, overlap=1.002) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1172 voxels, peak = 71), gca=70.9 gca peak = 0.13202 (57) mri peak = 0.04175 (58) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (5213 voxels, overlap=0.833) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (5213 voxels, peak = 58), gca=58.4 gca peak = 0.13429 (62) mri peak = 0.05372 (63) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7018 voxels, overlap=0.973) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7018 voxels, peak = 61), gca=61.1 gca peak = 0.15744 (86) mri peak = 0.05028 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3375 voxels, overlap=0.961) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3375 voxels, peak = 86), gca=85.6 gca peak = 0.15728 (86) mri peak = 0.07351 (84) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (2280 voxels, overlap=0.966) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (2280 voxels, peak = 86), gca=85.6 gca peak = 0.24352 (66) mri peak = 0.07955 (65) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (449 voxels, overlap=1.020) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (449 voxels, peak = 67), gca=67.0 gca peak = 0.31297 (65) mri peak = 0.08146 (67) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (580 voxels, overlap=1.012) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (580 voxels, peak = 66), gca=66.0 gca peak = 0.10558 (95) mri peak = 0.05949 (88) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3910 voxels, overlap=0.972) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3910 voxels, peak = 93), gca=92.6 gca peak = 0.10630 (86) mri peak = 0.07152 (87) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3873 voxels, overlap=0.926) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3873 voxels, peak = 86), gca=86.0 gca peak = 0.07460 (79) mri peak = 0.05566 (86) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1654 voxels, overlap=0.983) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1654 voxels, peak = 78), gca=77.8 gca peak = 0.10530 (81) mri peak = 0.05988 (84) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1665 voxels, overlap=0.992) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1665 voxels, peak = 80), gca=79.8 gca peak = 0.07773 (86) mri peak = 0.08742 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8904 voxels, overlap=0.726) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8904 voxels, peak = 86), gca=85.6 gca peak = 0.09997 (100) mri peak = 0.06725 (97) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1316 voxels, overlap=0.880) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1316 voxels, peak = 100), gca=100.5 gca peak = 0.13986 (95) mri peak = 0.07034 (96) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1237 voxels, overlap=0.933) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1237 voxels, peak = 95), gca=95.5 gca peak = 0.21286 (19) mri peak = 0.12346 (21) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (243 voxels, overlap=1.009) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (243 voxels, peak = 19), gca=19.0 gca peak = 0.19627 (16) mri peak = 0.14050 (16) Fourth_Ventricle (15): linear fit = 0.92 x + 0.0 (120 voxels, overlap=0.793) Fourth_Ventricle (15): linear fit = 0.92 x + 0.0 (120 voxels, peak = 15), gca=14.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.15131 (30) gca peak Left_Thalamus = 0.64095 (104) gca peak CSF = 0.22410 (32) gca peak Left_Accumbens_area = 0.73030 (65) 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 = 0.21972 (26) gca peak Right_Accumbens_area = 0.29776 (74) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.54107 (29) gca peak WM_hypointensities = 0.07747 (79) gca peak non_WM_hypointensities = 0.09744 (45) gca peak Optic_Chiasm = 0.61094 (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 1.00 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 71034 voxels changed in iteration 0 of unlikely voxel relabeling 200 voxels changed in iteration 1 of unlikely voxel relabeling 12 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 46393 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 429 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 76736 changed. image ll: -2.135, PF=0.500 pass 2: 20917 changed. image ll: -2.134, PF=0.500 pass 3: 6361 changed. pass 4: 2183 changed. 47416 voxels changed in iteration 0 of unlikely voxel relabeling 254 voxels changed in iteration 1 of unlikely voxel relabeling 10 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 8656 voxels changed in iteration 0 of unlikely voxel relabeling 131 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7353 voxels changed in iteration 0 of unlikely voxel relabeling 77 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6047 voxels changed in iteration 0 of unlikely voxel relabeling 33 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3651.648864 mri_ca_label stimesec 1.626752 mri_ca_label ru_maxrss 2104848 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 714478 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 65032 mri_ca_label ru_oublock 496 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 241 mri_ca_label ru_nivcsw 8275 auto-labeling took 60 minutes and 7 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/transforms/cc_up.lta 0051324 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-6.0.0/0051324/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/norm.mgz 26625 voxels in left wm, 24657 in right wm, xrange [126, 132] searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 global minimum found at slice 129.0, rotations (-0.26, -0.50) final transformation (x=129.0, yr=-0.257, zr=-0.498): 0.99995 0.00868 -0.00448 -1.69739; -0.00868 0.99996 0.00004 -0.87857; 0.00448 0.00000 0.99999 32.42331; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 130 95 eigenvectors: 0.00064 0.00145 1.00000; -0.31115 -0.95036 0.00158; 0.95036 -0.31115 -0.00016; error in mid anterior detected - correcting... writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/aseg.auto.mgz... corpus callosum segmentation took 0.5 minutes #-------------------------------------- #@# Merge ASeg Sat Oct 7 20:32:53 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Oct 7 20:32:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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... 1651 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 108 gm peak at 65 (65), valley at 33 (33) csf peak at 17, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 65 (65), valley at 33 (33) csf peak at 15, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 58 seconds. #-------------------------------------------- #@# Mask BFS Sat Oct 7 20:35:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1557809 voxels in mask (pct= 9.29) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Oct 7 20:35:53 CEST 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 105.1 +- 5.1 [79.0 --> 125.0] GM (71.0) : 68.2 +- 10.4 [30.0 --> 95.0] setting bottom of white matter range to 78.6 setting top of gray matter range to 89.0 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... 5369 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3174 filled 1247 bright non-wm voxels segmented. 3837 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 0.49 minutes reading wm segmentation from wm.seg.mgz... 133 voxels added to wm to prevent paths from MTL structures to cortex 3502 additional wm voxels added 0 additional wm voxels added SEG EDIT: 68735 voxels turned on, 20596 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+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 19 found - 19 modified | TOTAL: 41 pass 2 (xy-): 0 found - 19 modified | TOTAL: 41 pass 1 (yz+): 14 found - 14 modified | TOTAL: 55 pass 2 (yz+): 0 found - 14 modified | TOTAL: 55 pass 1 (yz-): 20 found - 20 modified | TOTAL: 75 pass 2 (yz-): 0 found - 20 modified | TOTAL: 75 pass 1 (xz+): 21 found - 21 modified | TOTAL: 96 pass 2 (xz+): 0 found - 21 modified | TOTAL: 96 pass 1 (xz-): 19 found - 19 modified | TOTAL: 115 pass 2 (xz-): 0 found - 19 modified | TOTAL: 115 Iteration Number : 1 pass 1 (+++): 38 found - 38 modified | TOTAL: 38 pass 2 (+++): 0 found - 38 modified | TOTAL: 38 pass 1 (+++): 39 found - 39 modified | TOTAL: 77 pass 2 (+++): 0 found - 39 modified | TOTAL: 77 pass 1 (+++): 23 found - 23 modified | TOTAL: 100 pass 2 (+++): 0 found - 23 modified | TOTAL: 100 pass 1 (+++): 31 found - 31 modified | TOTAL: 131 pass 2 (+++): 0 found - 31 modified | TOTAL: 131 Iteration Number : 1 pass 1 (++): 122 found - 122 modified | TOTAL: 122 pass 2 (++): 0 found - 122 modified | TOTAL: 122 pass 1 (+-): 114 found - 114 modified | TOTAL: 236 pass 2 (+-): 0 found - 114 modified | TOTAL: 236 pass 1 (--): 105 found - 105 modified | TOTAL: 341 pass 2 (--): 0 found - 105 modified | TOTAL: 341 pass 1 (-+): 103 found - 103 modified | TOTAL: 444 pass 2 (-+): 0 found - 103 modified | TOTAL: 444 Iteration Number : 2 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 12 found - 12 modified | TOTAL: 21 pass 2 (xy-): 0 found - 12 modified | TOTAL: 21 pass 1 (yz+): 16 found - 16 modified | TOTAL: 37 pass 2 (yz+): 0 found - 16 modified | TOTAL: 37 pass 1 (yz-): 20 found - 20 modified | TOTAL: 57 pass 2 (yz-): 0 found - 20 modified | TOTAL: 57 pass 1 (xz+): 10 found - 10 modified | TOTAL: 67 pass 2 (xz+): 0 found - 10 modified | TOTAL: 67 pass 1 (xz-): 6 found - 6 modified | TOTAL: 73 pass 2 (xz-): 0 found - 6 modified | TOTAL: 73 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 5 found - 5 modified | TOTAL: 11 pass 2 (+-): 0 found - 5 modified | TOTAL: 11 pass 1 (--): 7 found - 7 modified | TOTAL: 18 pass 2 (--): 0 found - 7 modified | TOTAL: 18 pass 1 (-+): 5 found - 5 modified | TOTAL: 23 pass 2 (-+): 0 found - 5 modified | TOTAL: 23 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 3 found - 3 modified | TOTAL: 3 pass 2 (yz-): 0 found - 3 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 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 = 793 (out of 576958: 0.137445) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Oct 7 20:38:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92711; -0.00027 -0.34918 0.97783 57.13052; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.02179 -0.03348 -0.01112 0.96157; 0.03353 1.02236 0.34844 -71.92711; -0.00027 -0.34918 0.97783 57.13052; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1327 (min = 350, max = 1400), aspect = 0.42 (min = 0.10, max = 0.75) no need to search using seed (126, 120, 154), TAL = (2.0, 26.0, 8.0) talairach voxel to voxel transform 0.97763 0.03193 -0.00026 1.37141; -0.02866 0.87107 -0.31072 80.43234; -0.00996 0.31107 0.91171 -29.70296; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 120, 154) --> (2.0, 26.0, 8.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (2.00, 26.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 26.00, 8.00) SRC: (110.75, 134.01, 146.95) search lh wm seed point around talairach space (-16.00, 26.00, 8.00), SRC: (145.94, 132.98, 146.59) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sat Oct 7 20:38:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 4 found - 4 modified | TOTAL: 6 pass 2 (xy-): 0 found - 4 modified | TOTAL: 6 pass 1 (yz+): 1 found - 1 modified | TOTAL: 7 pass 2 (yz+): 0 found - 1 modified | TOTAL: 7 pass 1 (yz-): 4 found - 4 modified | TOTAL: 11 pass 2 (yz-): 0 found - 4 modified | TOTAL: 11 pass 1 (xz+): 1 found - 1 modified | TOTAL: 12 pass 2 (xz+): 0 found - 1 modified | TOTAL: 12 pass 1 (xz-): 3 found - 3 modified | TOTAL: 15 pass 2 (xz-): 0 found - 3 modified | TOTAL: 15 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 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 0 found - 0 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 21 (out of 280659: 0.007482) 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: 212 vertices, 255 faces slice 40: 4540 vertices, 4816 faces slice 50: 14760 vertices, 15242 faces slice 60: 28200 vertices, 28678 faces slice 70: 41509 vertices, 41981 faces slice 80: 54439 vertices, 54871 faces slice 90: 66510 vertices, 66974 faces slice 100: 79603 vertices, 80106 faces slice 110: 92307 vertices, 92856 faces slice 120: 104655 vertices, 105148 faces slice 130: 116115 vertices, 116599 faces slice 140: 126219 vertices, 126614 faces slice 150: 134747 vertices, 135146 faces slice 160: 141655 vertices, 142029 faces slice 170: 147781 vertices, 148074 faces slice 180: 152073 vertices, 152351 faces slice 190: 154208 vertices, 154352 faces slice 200: 154208 vertices, 154352 faces slice 210: 154208 vertices, 154352 faces slice 220: 154208 vertices, 154352 faces slice 230: 154208 vertices, 154352 faces slice 240: 154208 vertices, 154352 faces slice 250: 154208 vertices, 154352 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... 154208 voxel in cpt #1: X=-144 [v=154208,e=463056,f=308704] located at (-27.504442, -28.624397, -16.073608) For the whole surface: X=-144 [v=154208,e=463056,f=308704] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat Oct 7 20:38:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 2 found - 2 modified | TOTAL: 4 pass 2 (yz-): 0 found - 2 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 0 found - 0 modified | TOTAL: 6 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 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 = 6 (out of 282182: 0.002126) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 2667 vertices, 2866 faces slice 50: 10261 vertices, 10615 faces slice 60: 22329 vertices, 22850 faces slice 70: 35390 vertices, 35829 faces slice 80: 48733 vertices, 49196 faces slice 90: 61241 vertices, 61691 faces slice 100: 74007 vertices, 74453 faces slice 110: 86033 vertices, 86495 faces slice 120: 98116 vertices, 98591 faces slice 130: 109130 vertices, 109622 faces slice 140: 119864 vertices, 120274 faces slice 150: 128759 vertices, 129134 faces slice 160: 136262 vertices, 136591 faces slice 170: 142326 vertices, 142588 faces slice 180: 146609 vertices, 146824 faces slice 190: 149018 vertices, 149118 faces slice 200: 149018 vertices, 149118 faces slice 210: 149018 vertices, 149118 faces slice 220: 149018 vertices, 149118 faces slice 230: 149018 vertices, 149118 faces slice 240: 149018 vertices, 149118 faces slice 250: 149018 vertices, 149118 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... 149018 voxel in cpt #1: X=-100 [v=149018,e=447354,f=298236] located at (26.743710, -25.983231, -16.277033) For the whole surface: X=-100 [v=149018,e=447354,f=298236] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Oct 7 20:38:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sat Oct 7 20:38:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 10144 of (10144 10147) to complete... Waiting for PID 10147 of (10144 10147) 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 (10144 10147) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sat Oct 7 20:39:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sat Oct 7 20:39:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 10193 of (10193 10196) to complete... Waiting for PID 10196 of (10193 10196) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.8 mm, total surface area = 79873 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.163 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.097 (target=0.015) step 015: RMS=0.083 (target=0.015) step 020: RMS=0.073 (target=0.015) step 025: RMS=0.065 (target=0.015) step 030: RMS=0.061 (target=0.015) step 035: RMS=0.057 (target=0.015) step 040: RMS=0.055 (target=0.015) step 045: RMS=0.053 (target=0.015) step 050: RMS=0.053 (target=0.015) step 055: RMS=0.053 (target=0.015) step 060: RMS=0.053 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 47.701748 mris_inflate stimesec 0.108983 mris_inflate ru_maxrss 225816 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 32374 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10872 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2337 mris_inflate ru_nivcsw 3356 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 47.7 mm, total surface area = 77779 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.159 (target=0.015) step 005: RMS=0.121 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.044 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.040 (target=0.015) step 060: RMS=0.039 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 45.993008 mris_inflate stimesec 0.095985 mris_inflate ru_maxrss 217940 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31426 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10504 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2072 mris_inflate ru_nivcsw 3381 PIDs (10193 10196) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sat Oct 7 20:39:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sat Oct 7 20:39:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 10255 of (10255 10259) to complete... Waiting for PID 10259 of (10255 10259) 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 0.92 +- 0.58 (0.00-->8.61) (max @ vno 65483 --> 65493) face area 0.03 +- 0.03 (-0.21-->0.62) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.314... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.175, avgs=0 005/300: dt: 0.9000, rms radial error=174.916, avgs=0 010/300: dt: 0.9000, rms radial error=174.361, avgs=0 015/300: dt: 0.9000, rms radial error=173.631, avgs=0 020/300: dt: 0.9000, rms radial error=172.799, avgs=0 025/300: dt: 0.9000, rms radial error=171.909, avgs=0 030/300: dt: 0.9000, rms radial error=170.987, avgs=0 035/300: dt: 0.9000, rms radial error=170.051, avgs=0 040/300: dt: 0.9000, rms radial error=169.107, avgs=0 045/300: dt: 0.9000, rms radial error=168.161, avgs=0 050/300: dt: 0.9000, rms radial error=167.215, avgs=0 055/300: dt: 0.9000, rms radial error=166.272, avgs=0 060/300: dt: 0.9000, rms radial error=165.331, avgs=0 065/300: dt: 0.9000, rms radial error=164.395, avgs=0 070/300: dt: 0.9000, rms radial error=163.464, avgs=0 075/300: dt: 0.9000, rms radial error=162.539, avgs=0 080/300: dt: 0.9000, rms radial error=161.619, avgs=0 085/300: dt: 0.9000, rms radial error=160.704, avgs=0 090/300: dt: 0.9000, rms radial error=159.794, avgs=0 095/300: dt: 0.9000, rms radial error=158.890, avgs=0 100/300: dt: 0.9000, rms radial error=157.990, avgs=0 105/300: dt: 0.9000, rms radial error=157.095, avgs=0 110/300: dt: 0.9000, rms radial error=156.204, avgs=0 115/300: dt: 0.9000, rms radial error=155.319, avgs=0 120/300: dt: 0.9000, rms radial error=154.438, avgs=0 125/300: dt: 0.9000, rms radial error=153.566, avgs=0 130/300: dt: 0.9000, rms radial error=152.702, avgs=0 135/300: dt: 0.9000, rms radial error=151.843, avgs=0 140/300: dt: 0.9000, rms radial error=150.990, avgs=0 145/300: dt: 0.9000, rms radial error=150.141, avgs=0 150/300: dt: 0.9000, rms radial error=149.299, avgs=0 155/300: dt: 0.9000, rms radial error=148.460, avgs=0 160/300: dt: 0.9000, rms radial error=147.626, avgs=0 165/300: dt: 0.9000, rms radial error=146.796, avgs=0 170/300: dt: 0.9000, rms radial error=145.971, avgs=0 175/300: dt: 0.9000, rms radial error=145.151, avgs=0 180/300: dt: 0.9000, rms radial error=144.335, avgs=0 185/300: dt: 0.9000, rms radial error=143.524, avgs=0 190/300: dt: 0.9000, rms radial error=142.717, avgs=0 195/300: dt: 0.9000, rms radial error=141.915, avgs=0 200/300: dt: 0.9000, rms radial error=141.117, avgs=0 205/300: dt: 0.9000, rms radial error=140.324, avgs=0 210/300: dt: 0.9000, rms radial error=139.535, avgs=0 215/300: dt: 0.9000, rms radial error=138.750, avgs=0 220/300: dt: 0.9000, rms radial error=137.970, avgs=0 225/300: dt: 0.9000, rms radial error=137.194, avgs=0 230/300: dt: 0.9000, rms radial error=136.422, avgs=0 235/300: dt: 0.9000, rms radial error=135.655, avgs=0 240/300: dt: 0.9000, rms radial error=134.892, avgs=0 245/300: dt: 0.9000, rms radial error=134.132, avgs=0 250/300: dt: 0.9000, rms radial error=133.378, avgs=0 255/300: dt: 0.9000, rms radial error=132.627, avgs=0 260/300: dt: 0.9000, rms radial error=131.880, avgs=0 265/300: dt: 0.9000, rms radial error=131.138, avgs=0 270/300: dt: 0.9000, rms radial error=130.400, avgs=0 275/300: dt: 0.9000, rms radial error=129.665, avgs=0 280/300: dt: 0.9000, rms radial error=128.935, avgs=0 285/300: dt: 0.9000, rms radial error=128.209, avgs=0 290/300: dt: 0.9000, rms radial error=127.487, avgs=0 295/300: dt: 0.9000, rms radial error=126.769, avgs=0 300/300: dt: 0.9000, rms radial error=126.056, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18124.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 2 (K=40.0), pass 1, starting sse = 3149.30 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 368.90 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00191 epoch 4 (K=640.0), pass 1, starting sse = 37.29 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00354 final distance error %29.43 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 269.001105 mris_sphere stimesec 0.184971 mris_sphere ru_maxrss 226016 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 32932 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10896 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8360 mris_sphere ru_nivcsw 19073 FSRUNTIME@ mris_sphere 0.0748 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 0.95 +- 0.56 (0.00-->6.71) (max @ vno 116374 --> 116383) face area 0.03 +- 0.03 (-0.28-->0.95) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.322... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.161, avgs=0 005/300: dt: 0.9000, rms radial error=174.903, avgs=0 010/300: dt: 0.9000, rms radial error=174.351, avgs=0 015/300: dt: 0.9000, rms radial error=173.628, avgs=0 020/300: dt: 0.9000, rms radial error=172.805, avgs=0 025/300: dt: 0.9000, rms radial error=171.924, avgs=0 030/300: dt: 0.9000, rms radial error=171.011, avgs=0 035/300: dt: 0.9000, rms radial error=170.082, avgs=0 040/300: dt: 0.9000, rms radial error=169.143, avgs=0 045/300: dt: 0.9000, rms radial error=168.202, avgs=0 050/300: dt: 0.9000, rms radial error=167.260, avgs=0 055/300: dt: 0.9000, rms radial error=166.321, avgs=0 060/300: dt: 0.9000, rms radial error=165.383, avgs=0 065/300: dt: 0.9000, rms radial error=164.450, avgs=0 070/300: dt: 0.9000, rms radial error=163.521, avgs=0 075/300: dt: 0.9000, rms radial error=162.596, avgs=0 080/300: dt: 0.9000, rms radial error=161.678, avgs=0 085/300: dt: 0.9000, rms radial error=160.767, avgs=0 090/300: dt: 0.9000, rms radial error=159.861, avgs=0 095/300: dt: 0.9000, rms radial error=158.961, avgs=0 100/300: dt: 0.9000, rms radial error=158.067, avgs=0 105/300: dt: 0.9000, rms radial error=157.178, avgs=0 110/300: dt: 0.9000, rms radial error=156.294, avgs=0 115/300: dt: 0.9000, rms radial error=155.414, avgs=0 120/300: dt: 0.9000, rms radial error=154.539, avgs=0 125/300: dt: 0.9000, rms radial error=153.670, avgs=0 130/300: dt: 0.9000, rms radial error=152.806, avgs=0 135/300: dt: 0.9000, rms radial error=151.947, avgs=0 140/300: dt: 0.9000, rms radial error=151.093, avgs=0 145/300: dt: 0.9000, rms radial error=150.244, avgs=0 150/300: dt: 0.9000, rms radial error=149.399, avgs=0 155/300: dt: 0.9000, rms radial error=148.559, avgs=0 160/300: dt: 0.9000, rms radial error=147.724, avgs=0 165/300: dt: 0.9000, rms radial error=146.893, avgs=0 170/300: dt: 0.9000, rms radial error=146.068, avgs=0 175/300: dt: 0.9000, rms radial error=145.247, avgs=0 180/300: dt: 0.9000, rms radial error=144.431, avgs=0 185/300: dt: 0.9000, rms radial error=143.619, avgs=0 190/300: dt: 0.9000, rms radial error=142.812, avgs=0 195/300: dt: 0.9000, rms radial error=142.010, avgs=0 200/300: dt: 0.9000, rms radial error=141.211, avgs=0 205/300: dt: 0.9000, rms radial error=140.417, avgs=0 210/300: dt: 0.9000, rms radial error=139.627, avgs=0 215/300: dt: 0.9000, rms radial error=138.842, avgs=0 220/300: dt: 0.9000, rms radial error=138.060, avgs=0 225/300: dt: 0.9000, rms radial error=137.284, avgs=0 230/300: dt: 0.9000, rms radial error=136.511, avgs=0 235/300: dt: 0.9000, rms radial error=135.743, avgs=0 240/300: dt: 0.9000, rms radial error=134.979, avgs=0 245/300: dt: 0.9000, rms radial error=134.220, avgs=0 250/300: dt: 0.9000, rms radial error=133.465, avgs=0 255/300: dt: 0.9000, rms radial error=132.714, avgs=0 260/300: dt: 0.9000, rms radial error=131.968, avgs=0 265/300: dt: 0.9000, rms radial error=131.226, avgs=0 270/300: dt: 0.9000, rms radial error=130.487, avgs=0 275/300: dt: 0.9000, rms radial error=129.753, avgs=0 280/300: dt: 0.9000, rms radial error=129.023, avgs=0 285/300: dt: 0.9000, rms radial error=128.297, avgs=0 290/300: dt: 0.9000, rms radial error=127.575, avgs=0 295/300: dt: 0.9000, rms radial error=126.857, avgs=0 300/300: dt: 0.9000, rms radial error=126.143, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17300.57 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 2871.85 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00031 epoch 3 (K=160.0), pass 1, starting sse = 293.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/11 = 0.00777 epoch 4 (K=640.0), pass 1, starting sse = 20.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/16 = 0.01147 final distance error %26.06 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 287.851239 mris_sphere stimesec 0.145977 mris_sphere ru_maxrss 218132 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 31982 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 10488 mris_sphere ru_oublock 10528 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 9176 mris_sphere ru_nivcsw 19511 FSRUNTIME@ mris_sphere 0.0780 hours 1 threads PIDs (10255 10259) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sat Oct 7 20:44:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat Oct 7 20:44:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat Oct 7 20:44:30 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051324 lh #@# Fix Topology rh Sat Oct 7 20:44:30 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051324 rh Waiting for PID 10482 of (10482 10485) to complete... Waiting for PID 10485 of (10482 10485) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051324 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=-144 (nv=154208, nf=308704, ne=463056, g=73) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 14157 ambiguous faces found in tessellation segmenting defects... 57 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 34 into 33 -merging segment 56 into 55 55 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4492 (-4.7246) -vertex loglikelihood: -6.3537 (-3.1769) -normal dot loglikelihood: -3.6408 (-3.6408) -quad curv loglikelihood: -6.2155 (-3.1078) Total Loglikelihood : -25.6593 CORRECTING DEFECT 0 (vertices=86, convex hull=106, v0=526) After retessellation of defect 0 (v0=526), euler #=-52 (146201,436427,290174) : difference with theory (-52) = 0 CORRECTING DEFECT 1 (vertices=35, convex hull=78, v0=1159) After retessellation of defect 1 (v0=1159), euler #=-51 (146215,436501,290235) : difference with theory (-51) = 0 CORRECTING DEFECT 2 (vertices=217, convex hull=189, v0=1162) After retessellation of defect 2 (v0=1162), euler #=-51 (146296,436863,290516) : difference with theory (-50) = 1 CORRECTING DEFECT 3 (vertices=63, convex hull=130, v0=6039) After retessellation of defect 3 (v0=6039), euler #=-50 (146312,436967,290605) : difference with theory (-49) = 1 CORRECTING DEFECT 4 (vertices=41, convex hull=73, v0=8647) After retessellation of defect 4 (v0=8647), euler #=-49 (146337,437071,290685) : difference with theory (-48) = 1 CORRECTING DEFECT 5 (vertices=77, convex hull=109, v0=8745) After retessellation of defect 5 (v0=8745), euler #=-48 (146381,437252,290823) : difference with theory (-47) = 1 CORRECTING DEFECT 6 (vertices=21, convex hull=68, v0=12100) After retessellation of defect 6 (v0=12100), euler #=-47 (146389,437300,290864) : difference with theory (-46) = 1 CORRECTING DEFECT 7 (vertices=41, convex hull=70, v0=19716) After retessellation of defect 7 (v0=19716), euler #=-46 (146410,437390,290934) : difference with theory (-45) = 1 CORRECTING DEFECT 8 (vertices=27, convex hull=52, v0=24803) After retessellation of defect 8 (v0=24803), euler #=-45 (146419,437436,290972) : difference with theory (-44) = 1 CORRECTING DEFECT 9 (vertices=39, convex hull=59, v0=26458) After retessellation of defect 9 (v0=26458), euler #=-44 (146428,437487,291015) : difference with theory (-43) = 1 CORRECTING DEFECT 10 (vertices=8, convex hull=27, v0=28192) After retessellation of defect 10 (v0=28192), euler #=-43 (146430,437506,291033) : difference with theory (-42) = 1 CORRECTING DEFECT 11 (vertices=62, convex hull=89, v0=32774) After retessellation of defect 11 (v0=32774), euler #=-42 (146469,437664,291153) : difference with theory (-41) = 1 CORRECTING DEFECT 12 (vertices=30, convex hull=46, v0=33220) After retessellation of defect 12 (v0=33220), euler #=-41 (146477,437704,291186) : difference with theory (-40) = 1 CORRECTING DEFECT 13 (vertices=18, convex hull=26, v0=45114) After retessellation of defect 13 (v0=45114), euler #=-40 (146479,437717,291198) : difference with theory (-39) = 1 CORRECTING DEFECT 14 (vertices=72, convex hull=80, v0=48915) After retessellation of defect 14 (v0=48915), euler #=-39 (146506,437831,291286) : difference with theory (-38) = 1 CORRECTING DEFECT 15 (vertices=53, convex hull=84, v0=50064) After retessellation of defect 15 (v0=50064), euler #=-38 (146517,437901,291346) : difference with theory (-37) = 1 CORRECTING DEFECT 16 (vertices=32, convex hull=32, v0=50507) After retessellation of defect 16 (v0=50507), euler #=-37 (146519,437918,291362) : difference with theory (-36) = 1 CORRECTING DEFECT 17 (vertices=39, convex hull=76, v0=51224) After retessellation of defect 17 (v0=51224), euler #=-36 (146534,437997,291427) : difference with theory (-35) = 1 CORRECTING DEFECT 18 (vertices=10, convex hull=18, v0=53151) After retessellation of defect 18 (v0=53151), euler #=-35 (146535,438004,291434) : difference with theory (-34) = 1 CORRECTING DEFECT 19 (vertices=66, convex hull=105, v0=58434) After retessellation of defect 19 (v0=58434), euler #=-34 (146576,438173,291563) : difference with theory (-33) = 1 CORRECTING DEFECT 20 (vertices=4396, convex hull=831, v0=60196) XL defect detected... After retessellation of defect 20 (v0=60196), euler #=-34 (146922,439657,292701) : difference with theory (-32) = 2 CORRECTING DEFECT 21 (vertices=109, convex hull=110, v0=61371) After retessellation of defect 21 (v0=61371), euler #=-33 (146950,439794,292811) : difference with theory (-31) = 2 CORRECTING DEFECT 22 (vertices=34, convex hull=62, v0=63972) After retessellation of defect 22 (v0=63972), euler #=-32 (146967,439869,292870) : difference with theory (-30) = 2 CORRECTING DEFECT 23 (vertices=80, convex hull=105, v0=66310) After retessellation of defect 23 (v0=66310), euler #=-31 (147002,440017,292984) : difference with theory (-29) = 2 CORRECTING DEFECT 24 (vertices=53, convex hull=44, v0=67335) After retessellation of defect 24 (v0=67335), euler #=-30 (147012,440063,293021) : difference with theory (-28) = 2 CORRECTING DEFECT 25 (vertices=21, convex hull=49, v0=68526) After retessellation of defect 25 (v0=68526), euler #=-29 (147023,440115,293063) : difference with theory (-27) = 2 CORRECTING DEFECT 26 (vertices=24, convex hull=70, v0=77488) After retessellation of defect 26 (v0=77488), euler #=-28 (147036,440182,293118) : difference with theory (-26) = 2 CORRECTING DEFECT 27 (vertices=34, convex hull=42, v0=78109) After retessellation of defect 27 (v0=78109), euler #=-27 (147040,440213,293146) : difference with theory (-25) = 2 CORRECTING DEFECT 28 (vertices=120, convex hull=46, v0=89365) After retessellation of defect 28 (v0=89365), euler #=-26 (147054,440272,293192) : difference with theory (-24) = 2 CORRECTING DEFECT 29 (vertices=38, convex hull=54, v0=97170) After retessellation of defect 29 (v0=97170), euler #=-25 (147072,440348,293251) : difference with theory (-23) = 2 CORRECTING DEFECT 30 (vertices=49, convex hull=73, v0=101234) After retessellation of defect 30 (v0=101234), euler #=-24 (147095,440448,293329) : difference with theory (-22) = 2 CORRECTING DEFECT 31 (vertices=14, convex hull=22, v0=107836) After retessellation of defect 31 (v0=107836), euler #=-23 (147098,440463,293342) : difference with theory (-21) = 2 CORRECTING DEFECT 32 (vertices=53, convex hull=118, v0=108037) After retessellation of defect 32 (v0=108037), euler #=-22 (147127,440596,293447) : difference with theory (-20) = 2 CORRECTING DEFECT 33 (vertices=413, convex hull=172, v0=110323) After retessellation of defect 33 (v0=110323), euler #=-20 (147136,440706,293550) : difference with theory (-19) = 1 CORRECTING DEFECT 34 (vertices=26, convex hull=41, v0=112333) After retessellation of defect 34 (v0=112333), euler #=-19 (147149,440760,293592) : difference with theory (-18) = 1 CORRECTING DEFECT 35 (vertices=41, convex hull=59, v0=114858) After retessellation of defect 35 (v0=114858), euler #=-18 (147166,440832,293648) : difference with theory (-17) = 1 CORRECTING DEFECT 36 (vertices=33, convex hull=69, v0=116297) After retessellation of defect 36 (v0=116297), euler #=-17 (147190,440930,293723) : difference with theory (-16) = 1 CORRECTING DEFECT 37 (vertices=11, convex hull=23, v0=119370) After retessellation of defect 37 (v0=119370), euler #=-16 (147191,440940,293733) : difference with theory (-15) = 1 CORRECTING DEFECT 38 (vertices=119, convex hull=57, v0=120218) After retessellation of defect 38 (v0=120218), euler #=-15 (147197,440982,293770) : difference with theory (-14) = 1 CORRECTING DEFECT 39 (vertices=40, convex hull=64, v0=122632) After retessellation of defect 39 (v0=122632), euler #=-14 (147208,441040,293818) : difference with theory (-13) = 1 CORRECTING DEFECT 40 (vertices=67, convex hull=99, v0=125202) After retessellation of defect 40 (v0=125202), euler #=-13 (147232,441160,293915) : difference with theory (-12) = 1 CORRECTING DEFECT 41 (vertices=237, convex hull=150, v0=128614) After retessellation of defect 41 (v0=128614), euler #=-12 (147304,441449,294133) : difference with theory (-11) = 1 CORRECTING DEFECT 42 (vertices=47, convex hull=74, v0=129541) After retessellation of defect 42 (v0=129541), euler #=-11 (147320,441533,294202) : difference with theory (-10) = 1 CORRECTING DEFECT 43 (vertices=144, convex hull=99, v0=130249) After retessellation of defect 43 (v0=130249), euler #=-10 (147357,441688,294321) : difference with theory (-9) = 1 CORRECTING DEFECT 44 (vertices=77, convex hull=84, v0=130347) After retessellation of defect 44 (v0=130347), euler #=-9 (147370,441763,294384) : difference with theory (-8) = 1 CORRECTING DEFECT 45 (vertices=23, convex hull=20, v0=131042) After retessellation of defect 45 (v0=131042), euler #=-8 (147370,441770,294392) : difference with theory (-7) = 1 CORRECTING DEFECT 46 (vertices=232, convex hull=81, v0=133698) After retessellation of defect 46 (v0=133698), euler #=-7 (147426,441971,294538) : difference with theory (-6) = 1 CORRECTING DEFECT 47 (vertices=35, convex hull=78, v0=135243) After retessellation of defect 47 (v0=135243), euler #=-6 (147447,442068,294615) : difference with theory (-5) = 1 CORRECTING DEFECT 48 (vertices=50, convex hull=105, v0=138174) After retessellation of defect 48 (v0=138174), euler #=-5 (147481,442210,294724) : difference with theory (-4) = 1 CORRECTING DEFECT 49 (vertices=34, convex hull=75, v0=139048) After retessellation of defect 49 (v0=139048), euler #=-4 (147492,442272,294776) : difference with theory (-3) = 1 CORRECTING DEFECT 50 (vertices=63, convex hull=82, v0=147728) After retessellation of defect 50 (v0=147728), euler #=-3 (147513,442373,294857) : difference with theory (-2) = 1 CORRECTING DEFECT 51 (vertices=74, convex hull=89, v0=150523) After retessellation of defect 51 (v0=150523), euler #=-2 (147545,442504,294957) : difference with theory (-1) = 1 CORRECTING DEFECT 52 (vertices=36, convex hull=74, v0=152512) After retessellation of defect 52 (v0=152512), euler #=-1 (147557,442566,295008) : difference with theory (0) = 1 CORRECTING DEFECT 53 (vertices=117, convex hull=115, v0=153208) After retessellation of defect 53 (v0=153208), euler #=0 (147602,442750,295148) : difference with theory (1) = 1 CORRECTING DEFECT 54 (vertices=60, convex hull=122, v0=153298) After retessellation of defect 54 (v0=153298), euler #=2 (147611,442827,295218) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.26 (0.06-->25.24) (max @ vno 85076 --> 89893) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.26 (0.06-->25.24) (max @ vno 85076 --> 89893) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 157 mutations (31.5%), 341 crossovers (68.5%), 950 vertices were eliminated building final representation... 6597 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=147611, nf=295218, ne=442827, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 60.0 minutes 0 defective edges removing intersecting faces 000: 606 intersecting 001: 23 intersecting 002: 5 intersecting mris_fix_topology utimesec 3598.889885 mris_fix_topology stimesec 0.236963 mris_fix_topology ru_maxrss 537184 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 64148 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 10856 mris_fix_topology ru_oublock 14328 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 551 mris_fix_topology ru_nivcsw 4687 FSRUNTIME@ mris_fix_topology lh 0.9994 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051324 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=-100 (nv=149018, nf=298236, ne=447354, g=51) 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... 4769 ambiguous faces found in tessellation segmenting defects... 56 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 56 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2603 (-4.6302) -vertex loglikelihood: -6.2528 (-3.1264) -normal dot loglikelihood: -3.6160 (-3.6160) -quad curv loglikelihood: -6.6193 (-3.3097) Total Loglikelihood : -25.7485 CORRECTING DEFECT 0 (vertices=41, convex hull=82, v0=2115) After retessellation of defect 0 (v0=2115), euler #=-52 (145929,436074,290093) : difference with theory (-53) = -1 CORRECTING DEFECT 1 (vertices=52, convex hull=102, v0=3156) After retessellation of defect 1 (v0=3156), euler #=-51 (145967,436234,290216) : difference with theory (-52) = -1 CORRECTING DEFECT 2 (vertices=23, convex hull=61, v0=6495) After retessellation of defect 2 (v0=6495), euler #=-50 (145980,436294,290264) : difference with theory (-51) = -1 CORRECTING DEFECT 3 (vertices=137, convex hull=155, v0=7217) After retessellation of defect 3 (v0=7217), euler #=-49 (146037,436534,290448) : difference with theory (-50) = -1 CORRECTING DEFECT 4 (vertices=39, convex hull=42, v0=11949) After retessellation of defect 4 (v0=11949), euler #=-48 (146043,436569,290478) : difference with theory (-49) = -1 CORRECTING DEFECT 5 (vertices=225, convex hull=83, v0=12952) After retessellation of defect 5 (v0=12952), euler #=-47 (146059,436648,290542) : difference with theory (-48) = -1 CORRECTING DEFECT 6 (vertices=52, convex hull=85, v0=15064) After retessellation of defect 6 (v0=15064), euler #=-46 (146083,436759,290630) : difference with theory (-47) = -1 CORRECTING DEFECT 7 (vertices=57, convex hull=84, v0=20307) After retessellation of defect 7 (v0=20307), euler #=-45 (146104,436860,290711) : difference with theory (-46) = -1 CORRECTING DEFECT 8 (vertices=23, convex hull=56, v0=33362) After retessellation of defect 8 (v0=33362), euler #=-44 (146114,436911,290753) : difference with theory (-45) = -1 CORRECTING DEFECT 9 (vertices=168, convex hull=202, v0=40764) After retessellation of defect 9 (v0=40764), euler #=-43 (146173,437180,290964) : difference with theory (-44) = -1 CORRECTING DEFECT 10 (vertices=31, convex hull=59, v0=41257) After retessellation of defect 10 (v0=41257), euler #=-42 (146183,437232,291007) : difference with theory (-43) = -1 CORRECTING DEFECT 11 (vertices=9, convex hull=31, v0=43095) After retessellation of defect 11 (v0=43095), euler #=-41 (146184,437246,291021) : difference with theory (-42) = -1 CORRECTING DEFECT 12 (vertices=34, convex hull=52, v0=47374) After retessellation of defect 12 (v0=47374), euler #=-40 (146202,437322,291080) : difference with theory (-41) = -1 CORRECTING DEFECT 13 (vertices=87, convex hull=106, v0=51353) After retessellation of defect 13 (v0=51353), euler #=-39 (146239,437481,291203) : difference with theory (-40) = -1 CORRECTING DEFECT 14 (vertices=33, convex hull=59, v0=52856) After retessellation of defect 14 (v0=52856), euler #=-38 (146249,437537,291250) : difference with theory (-39) = -1 CORRECTING DEFECT 15 (vertices=41, convex hull=65, v0=54408) After retessellation of defect 15 (v0=54408), euler #=-37 (146265,437612,291310) : difference with theory (-38) = -1 CORRECTING DEFECT 16 (vertices=34, convex hull=49, v0=55727) After retessellation of defect 16 (v0=55727), euler #=-36 (146279,437672,291357) : difference with theory (-37) = -1 CORRECTING DEFECT 17 (vertices=10, convex hull=14, v0=57799) After retessellation of defect 17 (v0=57799), euler #=-35 (146280,437677,291362) : difference with theory (-36) = -1 CORRECTING DEFECT 18 (vertices=55, convex hull=94, v0=63686) After retessellation of defect 18 (v0=63686), euler #=-34 (146313,437814,291467) : difference with theory (-35) = -1 CORRECTING DEFECT 19 (vertices=38, convex hull=91, v0=67140) After retessellation of defect 19 (v0=67140), euler #=-33 (146326,437890,291531) : difference with theory (-34) = -1 CORRECTING DEFECT 20 (vertices=45, convex hull=64, v0=73645) After retessellation of defect 20 (v0=73645), euler #=-32 (146346,437978,291600) : difference with theory (-33) = -1 CORRECTING DEFECT 21 (vertices=151, convex hull=120, v0=77109) After retessellation of defect 21 (v0=77109), euler #=-31 (146358,438070,291681) : difference with theory (-32) = -1 CORRECTING DEFECT 22 (vertices=36, convex hull=51, v0=78422) After retessellation of defect 22 (v0=78422), euler #=-30 (146374,438138,291734) : difference with theory (-31) = -1 CORRECTING DEFECT 23 (vertices=171, convex hull=184, v0=79513) After retessellation of defect 23 (v0=79513), euler #=-29 (146467,438504,292008) : difference with theory (-30) = -1 CORRECTING DEFECT 24 (vertices=55, convex hull=98, v0=84815) After retessellation of defect 24 (v0=84815), euler #=-28 (146498,438636,292110) : difference with theory (-29) = -1 CORRECTING DEFECT 25 (vertices=7, convex hull=14, v0=96525) After retessellation of defect 25 (v0=96525), euler #=-27 (146500,438644,292117) : difference with theory (-28) = -1 CORRECTING DEFECT 26 (vertices=65, convex hull=86, v0=97826) After retessellation of defect 26 (v0=97826), euler #=-26 (146525,438757,292206) : difference with theory (-27) = -1 CORRECTING DEFECT 27 (vertices=29, convex hull=70, v0=98070) After retessellation of defect 27 (v0=98070), euler #=-25 (146544,438843,292274) : difference with theory (-26) = -1 CORRECTING DEFECT 28 (vertices=49, convex hull=114, v0=104711) After retessellation of defect 28 (v0=104711), euler #=-24 (146580,439002,292398) : difference with theory (-25) = -1 CORRECTING DEFECT 29 (vertices=154, convex hull=114, v0=106488) After retessellation of defect 29 (v0=106488), euler #=-23 (146645,439253,292585) : difference with theory (-24) = -1 CORRECTING DEFECT 30 (vertices=26, convex hull=58, v0=110623) After retessellation of defect 30 (v0=110623), euler #=-22 (146661,439324,292641) : difference with theory (-23) = -1 CORRECTING DEFECT 31 (vertices=104, convex hull=137, v0=113229) After retessellation of defect 31 (v0=113229), euler #=-21 (146708,439526,292797) : difference with theory (-22) = -1 CORRECTING DEFECT 32 (vertices=8, convex hull=28, v0=115404) After retessellation of defect 32 (v0=115404), euler #=-20 (146708,439533,292805) : difference with theory (-21) = -1 CORRECTING DEFECT 33 (vertices=21, convex hull=15, v0=115450) After retessellation of defect 33 (v0=115450), euler #=-19 (146711,439544,292814) : difference with theory (-20) = -1 CORRECTING DEFECT 34 (vertices=67, convex hull=61, v0=115653) After retessellation of defect 34 (v0=115653), euler #=-18 (146729,439625,292878) : difference with theory (-19) = -1 CORRECTING DEFECT 35 (vertices=13, convex hull=33, v0=117547) After retessellation of defect 35 (v0=117547), euler #=-17 (146733,439650,292900) : difference with theory (-18) = -1 CORRECTING DEFECT 36 (vertices=20, convex hull=28, v0=118860) After retessellation of defect 36 (v0=118860), euler #=-16 (146734,439664,292914) : difference with theory (-17) = -1 CORRECTING DEFECT 37 (vertices=31, convex hull=55, v0=118926) After retessellation of defect 37 (v0=118926), euler #=-15 (146750,439738,292973) : difference with theory (-16) = -1 CORRECTING DEFECT 38 (vertices=10, convex hull=30, v0=119566) After retessellation of defect 38 (v0=119566), euler #=-14 (146751,439751,292986) : difference with theory (-15) = -1 CORRECTING DEFECT 39 (vertices=53, convex hull=93, v0=119627) After retessellation of defect 39 (v0=119627), euler #=-13 (146779,439871,293079) : difference with theory (-14) = -1 CORRECTING DEFECT 40 (vertices=25, convex hull=66, v0=121748) After retessellation of defect 40 (v0=121748), euler #=-12 (146793,439937,293132) : difference with theory (-13) = -1 CORRECTING DEFECT 41 (vertices=27, convex hull=30, v0=122838) After retessellation of defect 41 (v0=122838), euler #=-11 (146797,439961,293153) : difference with theory (-12) = -1 CORRECTING DEFECT 42 (vertices=28, convex hull=26, v0=125289) After retessellation of defect 42 (v0=125289), euler #=-10 (146802,439983,293171) : difference with theory (-11) = -1 CORRECTING DEFECT 43 (vertices=96, convex hull=84, v0=127763) After retessellation of defect 43 (v0=127763), euler #=-9 (146821,440073,293243) : difference with theory (-10) = -1 CORRECTING DEFECT 44 (vertices=82, convex hull=92, v0=127926) After retessellation of defect 44 (v0=127926), euler #=-8 (146847,440195,293340) : difference with theory (-9) = -1 CORRECTING DEFECT 45 (vertices=98, convex hull=94, v0=128689) After retessellation of defect 45 (v0=128689), euler #=-8 (146873,440327,293446) : difference with theory (-8) = 0 CORRECTING DEFECT 46 (vertices=20, convex hull=19, v0=131093) After retessellation of defect 46 (v0=131093), euler #=-7 (146874,440335,293454) : difference with theory (-7) = 0 CORRECTING DEFECT 47 (vertices=102, convex hull=101, v0=131783) After retessellation of defect 47 (v0=131783), euler #=-6 (146897,440455,293552) : difference with theory (-6) = 0 CORRECTING DEFECT 48 (vertices=33, convex hull=42, v0=131902) After retessellation of defect 48 (v0=131902), euler #=-5 (146904,440497,293588) : difference with theory (-5) = 0 CORRECTING DEFECT 49 (vertices=11, convex hull=24, v0=132764) After retessellation of defect 49 (v0=132764), euler #=-4 (146906,440512,293602) : difference with theory (-4) = 0 CORRECTING DEFECT 50 (vertices=108, convex hull=111, v0=135532) After retessellation of defect 50 (v0=135532), euler #=-3 (146947,440693,293743) : difference with theory (-3) = 0 CORRECTING DEFECT 51 (vertices=27, convex hull=51, v0=139358) After retessellation of defect 51 (v0=139358), euler #=-2 (146962,440758,293794) : difference with theory (-2) = 0 CORRECTING DEFECT 52 (vertices=39, convex hull=76, v0=142535) After retessellation of defect 52 (v0=142535), euler #=-1 (146987,440865,293877) : difference with theory (-1) = 0 CORRECTING DEFECT 53 (vertices=19, convex hull=76, v0=145132) After retessellation of defect 53 (v0=145132), euler #=0 (146998,440926,293928) : difference with theory (0) = 0 CORRECTING DEFECT 54 (vertices=52, convex hull=77, v0=145898) After retessellation of defect 54 (v0=145898), euler #=1 (147019,441022,294004) : difference with theory (1) = 0 CORRECTING DEFECT 55 (vertices=40, convex hull=67, v0=148248) After retessellation of defect 55 (v0=148248), euler #=2 (147034,441096,294064) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.05-->8.64) (max @ vno 128465 --> 134743) 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 (0.05-->8.64) (max @ vno 128465 --> 134743) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 156 mutations (32.7%), 321 crossovers (67.3%), 147 vertices were eliminated building final representation... 1984 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=147034, nf=294064, ne=441096, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 29.7 minutes 0 defective edges removing intersecting faces 000: 233 intersecting 001: 8 intersecting 002: 5 intersecting expanding nbhd size to 2 003: 8 intersecting mris_fix_topology utimesec 1779.022547 mris_fix_topology stimesec 0.275958 mris_fix_topology ru_maxrss 463172 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 54692 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 10488 mris_fix_topology ru_oublock 14144 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 421 mris_fix_topology ru_nivcsw 5340 FSRUNTIME@ mris_fix_topology rh 0.4942 hours 1 threads PIDs (10482 10485) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 147611 - 442827 + 295218 = 2 --> 0 holes F =2V-4: 295218 = 295222-4 (0) 2E=3F: 885654 = 885654 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 147034 - 441096 + 294064 = 2 --> 0 holes F =2V-4: 294064 = 294068-4 (0) 2E=3F: 882192 = 882192 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 165 intersecting 001: 18 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 25 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Oct 7 21:44:38 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051324 lh #-------------------------------------------- #@# Make White Surf rh Sat Oct 7 21:44:38 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051324 rh Waiting for PID 14460 of (14460 14463) to complete... Waiting for PID 14463 of (14460 14463) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051324 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-6.0.0/0051324/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... 22813 bright wm thresholded. 1864 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.orig... computing class statistics... border white: 280448 voxels (1.67%) border gray 318193 voxels (1.90%) WM (95.0): 95.7 +- 8.4 [70.0 --> 110.0] GM (71.0) : 69.5 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.0 (was 70) setting MAX_BORDER_WHITE to 107.4 (was 105) setting MIN_BORDER_WHITE to 66.0 (was 85) setting MAX_CSF to 43.9 (was 40) setting MAX_GRAY to 90.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.9 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.01-->8.75) (max @ vno 72451 --> 146753) face area 0.28 +- 0.13 (0.00-->5.22) mean absolute distance = 0.77 +- 0.94 3607 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=99+-7.0, GM=66+-8.7 mean inside = 91.1, mean outside = 72.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=77.6, 74 (74) missing vertices, mean dist 0.3 [0.7 (%33.7)->0.8 (%66.3))] %49 local maxima, %46 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 +- 0.26 (0.11-->8.41) (max @ vno 72451 --> 146753) face area 0.28 +- 0.13 (0.00-->4.03) mean absolute distance = 0.41 +- 0.72 5138 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3693419.5, rms=10.469 001: dt: 0.5000, sse=2138268.2, rms=7.446 (28.876%) 002: dt: 0.5000, sse=1440795.9, rms=5.554 (25.406%) 003: dt: 0.5000, sse=1116766.0, rms=4.405 (20.687%) 004: dt: 0.5000, sse=970289.6, rms=3.770 (14.420%) 005: dt: 0.5000, sse=912555.4, rms=3.486 (7.533%) 006: dt: 0.5000, sse=887152.8, rms=3.349 (3.939%) rms = 3.30, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=878634.3, rms=3.301 (1.411%) 008: dt: 0.2500, sse=718718.6, rms=2.166 (34.391%) 009: dt: 0.2500, sse=685997.4, rms=1.864 (13.935%) 010: dt: 0.2500, sse=679482.4, rms=1.794 (3.788%) rms = 1.76, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=675635.5, rms=1.755 (2.143%) rms = 1.71, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=671438.6, rms=1.708 (2.701%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... mean border=80.5, 116 (34) missing vertices, mean dist -0.2 [0.5 (%68.0)->0.3 (%32.0))] %60 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.26 (0.08-->8.21) (max @ vno 72451 --> 146753) face area 0.35 +- 0.17 (0.00-->4.97) mean absolute distance = 0.33 +- 0.49 4582 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1308464.2, rms=4.481 013: dt: 0.5000, sse=990543.6, rms=2.964 (33.856%) rms = 2.96, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=899453.4, rms=2.358 (20.453%) 015: dt: 0.2500, sse=841479.5, rms=1.868 (20.762%) 016: dt: 0.2500, sse=828080.0, rms=1.651 (11.620%) 017: dt: 0.2500, sse=815103.6, rms=1.568 (5.054%) 018: dt: 0.2500, sse=808513.6, rms=1.517 (3.208%) rms = 1.49, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=807461.8, rms=1.491 (1.712%) rms = 1.45, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=805071.7, rms=1.449 (2.827%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=82.9, 124 (30) missing vertices, mean dist -0.2 [0.4 (%65.9)->0.2 (%34.1))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.26 (0.08-->8.09) (max @ vno 72451 --> 146753) face area 0.34 +- 0.16 (0.00-->4.86) mean absolute distance = 0.29 +- 0.40 3713 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1066625.2, rms=3.477 021: dt: 0.5000, sse=905441.8, rms=2.506 (27.911%) rms = 2.74, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=824726.2, rms=1.805 (27.983%) 023: dt: 0.2500, sse=787705.4, rms=1.433 (20.609%) 024: dt: 0.2500, sse=782481.7, rms=1.341 (6.437%) rms = 1.32, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=775190.7, rms=1.324 (1.220%) rms = 1.28, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=771434.6, rms=1.281 (3.297%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=84.0, 147 (23) missing vertices, mean dist -0.1 [0.3 (%56.3)->0.2 (%43.7))] %80 local maxima, %14 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-6.0.0/0051324/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=816362.1, rms=1.921 027: dt: 0.5000, sse=803685.2, rms=1.804 (6.066%) rms = 2.38, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=752765.4, rms=1.207 (33.075%) 029: dt: 0.2500, sse=748012.3, rms=1.079 (10.623%) 030: dt: 0.2500, sse=737974.7, rms=0.998 (7.502%) rms = 1.03, time step reduction 2 of 3 to 0.125... rms = 0.98, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=736660.7, rms=0.984 (1.390%) positioning took 0.7 minutes generating cortex label... 10 non-cortical segments detected only using segment with 7989 vertices erasing segment 1 (vno[0] = 104455) erasing segment 2 (vno[0] = 110539) erasing segment 3 (vno[0] = 112526) erasing segment 4 (vno[0] = 112573) erasing segment 5 (vno[0] = 113611) erasing segment 6 (vno[0] = 115767) erasing segment 7 (vno[0] = 115816) erasing segment 8 (vno[0] = 119175) erasing segment 9 (vno[0] = 127103) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.area vertex spacing 0.89 +- 0.26 (0.01-->8.09) (max @ vno 72451 --> 146753) face area 0.33 +- 0.16 (0.00-->5.24) refinement took 5.7 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051324 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-6.0.0/0051324/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... 22813 bright wm thresholded. 1864 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.orig... computing class statistics... border white: 280448 voxels (1.67%) border gray 318193 voxels (1.90%) WM (95.0): 95.7 +- 8.4 [70.0 --> 110.0] GM (71.0) : 69.5 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.0 (was 70) setting MAX_BORDER_WHITE to 107.4 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 44.9 (was 40) setting MAX_GRAY to 90.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.9 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.04-->3.54) (max @ vno 41468 --> 42633) face area 0.28 +- 0.13 (0.00-->2.85) mean absolute distance = 0.80 +- 0.95 3893 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=99+-6.1, GM=67+-8.7 mean inside = 91.4, mean outside = 74.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=78.3, 76 (76) missing vertices, mean dist 0.3 [0.7 (%33.5)->0.8 (%66.5))] %51 local maxima, %44 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.07-->3.74) (max @ vno 41468 --> 42633) face area 0.28 +- 0.13 (0.00-->2.58) mean absolute distance = 0.43 +- 0.71 4558 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3582054.2, rms=10.258 001: dt: 0.5000, sse=2057120.4, rms=7.268 (29.151%) 002: dt: 0.5000, sse=1373987.5, rms=5.353 (26.352%) 003: dt: 0.5000, sse=1065612.1, rms=4.210 (21.349%) 004: dt: 0.5000, sse=926173.8, rms=3.574 (15.105%) 005: dt: 0.5000, sse=873151.0, rms=3.287 (8.042%) 006: dt: 0.5000, sse=847574.4, rms=3.147 (4.251%) rms = 3.10, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=843471.2, rms=3.099 (1.528%) 008: dt: 0.2500, sse=699420.8, rms=2.028 (34.566%) 009: dt: 0.2500, sse=671933.8, rms=1.761 (13.163%) 010: dt: 0.2500, sse=667386.4, rms=1.698 (3.538%) rms = 1.67, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=664361.2, rms=1.666 (1.938%) rms = 1.62, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=660105.1, rms=1.624 (2.517%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.3, 62 (15) missing vertices, mean dist -0.3 [0.5 (%68.0)->0.3 (%32.0))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.05-->3.68) (max @ vno 41468 --> 42633) face area 0.35 +- 0.16 (0.00-->3.43) mean absolute distance = 0.34 +- 0.49 4501 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1338250.9, rms=4.606 013: dt: 0.5000, sse=1001027.6, rms=3.015 (34.539%) 014: dt: 0.5000, sse=963120.9, rms=2.840 (5.807%) rms = 2.80, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=952867.4, rms=2.799 (1.439%) 016: dt: 0.2500, sse=826343.8, rms=1.755 (37.287%) 017: dt: 0.2500, sse=803032.3, rms=1.487 (15.312%) rms = 1.44, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=799172.8, rms=1.438 (3.247%) 019: dt: 0.1250, sse=795757.6, rms=1.374 (4.488%) rms = 1.37, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=793486.0, rms=1.369 (0.366%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=83.9, 68 (14) missing vertices, mean dist -0.2 [0.4 (%67.4)->0.2 (%32.6))] %76 local maxima, %19 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 (0.05-->3.61) (max @ vno 41468 --> 42633) face area 0.34 +- 0.16 (0.00-->3.43) mean absolute distance = 0.29 +- 0.39 3686 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1079040.6, rms=3.583 021: dt: 0.5000, sse=887797.9, rms=2.389 (33.326%) rms = 2.55, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=807775.8, rms=1.738 (27.246%) 023: dt: 0.2500, sse=776065.2, rms=1.365 (21.460%) 024: dt: 0.2500, sse=770686.1, rms=1.273 (6.730%) rms = 1.26, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=770128.3, rms=1.261 (0.947%) rms = 1.22, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=763109.2, rms=1.225 (2.878%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=85.0, 72 (12) missing vertices, mean dist -0.1 [0.3 (%57.1)->0.2 (%42.9))] %83 local maxima, %12 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-6.0.0/0051324/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=811371.1, rms=1.914 027: dt: 0.5000, sse=790542.3, rms=1.655 (13.490%) rms = 2.22, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=743547.6, rms=1.130 (31.713%) 029: dt: 0.2500, sse=739053.9, rms=1.019 (9.819%) 030: dt: 0.2500, sse=732321.3, rms=0.955 (6.343%) rms = 0.98, time step reduction 2 of 3 to 0.125... rms = 0.95, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=731008.6, rms=0.946 (0.916%) positioning took 0.7 minutes generating cortex label... 10 non-cortical segments detected only using segment with 8011 vertices erasing segment 0 (vno[0] = 46249) erasing segment 2 (vno[0] = 107978) erasing segment 3 (vno[0] = 110104) erasing segment 4 (vno[0] = 112222) erasing segment 5 (vno[0] = 112231) erasing segment 6 (vno[0] = 112364) erasing segment 7 (vno[0] = 115245) erasing segment 8 (vno[0] = 115282) erasing segment 9 (vno[0] = 116306) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.area vertex spacing 0.89 +- 0.25 (0.04-->3.93) (max @ vno 100441 --> 100456) face area 0.34 +- 0.16 (0.00-->3.37) refinement took 5.7 minutes PIDs (14460 14463) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sat Oct 7 21:50:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sat Oct 7 21:50:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 14738 of (14738 14741) to complete... Waiting for PID 14741 of (14738 14741) 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 (14738 14741) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sat Oct 7 21:50:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sat Oct 7 21:50:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 14787 of (14787 14790) to complete... Waiting for PID 14790 of (14787 14790) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 48.8 mm, total surface area = 88471 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=0.127 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 1.0 minutes mris_inflate utimesec 60.485804 mris_inflate stimesec 0.160975 mris_inflate ru_maxrss 216368 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31161 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11560 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2226 mris_inflate ru_nivcsw 4431 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 47.7 mm, total surface area = 88330 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.181 (target=0.015) step 005: RMS=0.126 (target=0.015) step 010: RMS=0.094 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 1.0 minutes mris_inflate utimesec 59.552946 mris_inflate stimesec 0.148977 mris_inflate ru_maxrss 215172 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31372 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11512 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1997 mris_inflate ru_nivcsw 4398 PIDs (14787 14790) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sat Oct 7 21:51:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 Sat Oct 7 21:51:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 14891 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... Waiting for PID 14894 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... Waiting for PID 14897 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... Waiting for PID 14900 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... Waiting for PID 14903 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... Waiting for PID 14906 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... Waiting for PID 14909 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... Waiting for PID 14912 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... Waiting for PID 14915 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... Waiting for PID 14918 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... Waiting for PID 14921 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... Waiting for PID 14924 of (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 3.695*4pi (46.434) --> -3 handles ICI = 229.9, FI = 1890.0, variation=31634.216 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 176 vertices thresholded to be in k1 ~ [-0.29 0.34], k2 ~ [-0.10 0.07] total integrated curvature = 0.407*4pi (5.112) --> 1 handles ICI = 1.5, FI = 9.6, variation=165.060 141 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 140 vertices thresholded to be in [-0.13 0.17] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.021 done. mris_curvature -w rh.white.preaparc total integrated curvature = 10.810*4pi (135.845) --> -10 handles ICI = 229.3, FI = 1864.4, variation=31133.241 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 196 vertices thresholded to be in k1 ~ [-0.73 0.47], k2 ~ [-0.36 0.08] total integrated curvature = 0.463*4pi (5.821) --> 1 handles ICI = 1.5, FI = 9.7, variation=166.611 173 vertices thresholded to be in [-0.05 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 114 vertices thresholded to be in [-0.27 0.13] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023 done. PIDs (14891 14894 14897 14900 14903 14906 14909 14912 14915 14918 14921 14924) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sat Oct 7 21:53:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051324 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 [ 0051324/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 [ 311 ] Gb_filter = 0 WARN: S lookup min: -0.978619 WARN: S explicit min: 0.000000 vertex = 792 #----------------------------------------- #@# Curvature Stats rh Sat Oct 7 21:53:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051324 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 [ 0051324/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 [ 283 ] Gb_filter = 0 WARN: S lookup min: -0.102663 WARN: S explicit min: 0.000000 vertex = 26 #-------------------------------------------- #@# Sphere lh Sat Oct 7 21:53:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sat Oct 7 21:53:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 15077 of (15077 15080) to complete... Waiting for PID 15080 of (15077 15080) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0.296... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.14 pass 1: epoch 2 of 3 starting distance error %20.12 unfolding complete - removing small folds... starting distance error %20.04 removing remaining folds... final distance error %20.06 MRISunfold() return, current seed 1234 -01: dt=0.0000, 192 negative triangles 191: dt=0.9900, 192 negative triangles 192: dt=0.9900, 90 negative triangles 193: dt=0.9900, 73 negative triangles 194: dt=0.9900, 61 negative triangles 195: dt=0.9900, 54 negative triangles 196: dt=0.9900, 49 negative triangles 197: dt=0.9900, 41 negative triangles 198: dt=0.9900, 43 negative triangles 199: dt=0.9900, 33 negative triangles 200: dt=0.9900, 37 negative triangles 201: dt=0.9900, 29 negative triangles 202: dt=0.9900, 30 negative triangles 203: dt=0.9900, 23 negative triangles 204: dt=0.9900, 21 negative triangles 205: dt=0.9900, 22 negative triangles 206: dt=0.9900, 16 negative triangles 207: dt=0.9900, 18 negative triangles 208: dt=0.9900, 13 negative triangles 209: dt=0.9900, 16 negative triangles 210: dt=0.9900, 20 negative triangles 211: dt=0.9900, 11 negative triangles 212: dt=0.9900, 11 negative triangles 213: dt=0.9900, 10 negative triangles 214: dt=0.9900, 6 negative triangles 215: dt=0.9900, 2 negative triangles 216: dt=0.9900, 6 negative triangles 217: dt=0.9900, 3 negative triangles 218: dt=0.9900, 1 negative triangles 219: dt=0.9900, 3 negative triangles 220: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.15 hours mris_sphere utimesec 4153.816523 mris_sphere stimesec 2.461625 mris_sphere ru_maxrss 303812 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 53174 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10432 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 148383 mris_sphere ru_nivcsw 336352 FSRUNTIME@ mris_sphere 1.1540 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0.300... 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 %19.84 pass 1: epoch 2 of 3 starting distance error %19.80 unfolding complete - removing small folds... starting distance error %19.72 removing remaining folds... final distance error %19.74 MRISunfold() return, current seed 1234 -01: dt=0.0000, 149 negative triangles 213: dt=0.9900, 149 negative triangles 214: dt=0.9900, 64 negative triangles 215: dt=0.9900, 47 negative triangles 216: dt=0.9900, 42 negative triangles 217: dt=0.9900, 27 negative triangles 218: dt=0.9900, 31 negative triangles 219: dt=0.9900, 29 negative triangles 220: dt=0.9900, 26 negative triangles 221: dt=0.9900, 24 negative triangles 222: dt=0.9900, 29 negative triangles 223: dt=0.9900, 31 negative triangles 224: dt=0.9900, 26 negative triangles 225: dt=0.9900, 30 negative triangles 226: dt=0.9900, 29 negative triangles 227: dt=0.9900, 27 negative triangles 228: dt=0.9900, 31 negative triangles 229: dt=0.9900, 25 negative triangles 230: dt=0.9900, 26 negative triangles 231: dt=0.9405, 26 negative triangles 232: dt=0.9405, 23 negative triangles 233: dt=0.9405, 23 negative triangles 234: dt=0.9405, 25 negative triangles 235: dt=0.9405, 24 negative triangles 236: dt=0.9405, 23 negative triangles 237: dt=0.9405, 22 negative triangles 238: dt=0.9405, 22 negative triangles 239: dt=0.9405, 19 negative triangles 240: dt=0.9405, 24 negative triangles 241: dt=0.9405, 17 negative triangles 242: dt=0.9405, 16 negative triangles 243: dt=0.9405, 18 negative triangles 244: dt=0.9405, 18 negative triangles 245: dt=0.9405, 15 negative triangles 246: dt=0.9405, 15 negative triangles 247: dt=0.9405, 16 negative triangles 248: dt=0.9405, 15 negative triangles 249: dt=0.9405, 14 negative triangles 250: dt=0.9405, 13 negative triangles 251: dt=0.9405, 12 negative triangles 252: dt=0.9405, 11 negative triangles 253: dt=0.9405, 11 negative triangles 254: dt=0.9405, 14 negative triangles 255: dt=0.9405, 13 negative triangles 256: dt=0.9405, 14 negative triangles 257: dt=0.9405, 14 negative triangles 258: dt=0.9405, 13 negative triangles 259: dt=0.9405, 15 negative triangles 260: dt=0.9405, 17 negative triangles 261: dt=0.9405, 10 negative triangles 262: dt=0.9405, 11 negative triangles 263: dt=0.9405, 11 negative triangles 264: dt=0.9405, 7 negative triangles 265: dt=0.9405, 11 negative triangles 266: dt=0.9405, 8 negative triangles 267: dt=0.9405, 10 negative triangles 268: dt=0.9405, 6 negative triangles 269: dt=0.9405, 8 negative triangles 270: dt=0.9405, 8 negative triangles 271: dt=0.9405, 9 negative triangles 272: dt=0.9405, 5 negative triangles 273: dt=0.9405, 6 negative triangles 274: dt=0.9405, 6 negative triangles 275: dt=0.9405, 5 negative triangles 276: dt=0.9405, 8 negative triangles 277: dt=0.9405, 3 negative triangles 278: dt=0.9405, 5 negative triangles 279: dt=0.9405, 3 negative triangles 280: dt=0.9405, 3 negative triangles 281: dt=0.9405, 4 negative triangles 282: dt=0.9405, 4 negative triangles 283: dt=0.9405, 4 negative triangles 284: dt=0.9405, 3 negative triangles 285: dt=0.9405, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.26 hours mris_sphere utimesec 4842.580815 mris_sphere stimesec 2.401634 mris_sphere ru_maxrss 302256 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 53271 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10400 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 150589 mris_sphere ru_nivcsw 340356 FSRUNTIME@ mris_sphere 1.2602 hours 1 threads PIDs (15077 15080) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sat Oct 7 23:08:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 Sat Oct 7 23:08:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 18909 of (18909 18912) to complete... Waiting for PID 18912 of (18909 18912) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 = 5.509 curvature mean = 0.043, std = 0.821 curvature mean = 0.019, std = 0.856 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, -16.00) sse = 354634.8, tmin=1.1725 d=32.00 min @ (0.00, -8.00, 8.00) sse = 256545.1, tmin=2.3463 d=16.00 min @ (4.00, 4.00, -4.00) sse = 205444.7, tmin=3.5396 d=8.00 min @ (0.00, 0.00, 2.00) sse = 201204.4, tmin=4.7716 d=4.00 min @ (0.00, 0.00, -1.00) sse = 199611.5, tmin=6.0150 d=2.00 min @ (0.00, 0.00, 0.50) sse = 199462.1, tmin=7.2680 d=1.00 min @ (0.25, 0.25, -0.25) sse = 199282.3, tmin=8.5053 d=0.50 min @ (-0.12, -0.12, 0.00) sse = 199233.7, tmin=9.7397 tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 9.74 min curvature mean = 0.007, std = 0.832 curvature mean = 0.007, std = 0.945 curvature mean = 0.002, std = 0.842 curvature mean = 0.003, std = 0.978 curvature mean = -0.002, std = 0.842 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.029, std = 0.315 curvature mean = 0.040, std = 0.248 curvature mean = 0.058, std = 0.316 curvature mean = 0.034, std = 0.306 curvature mean = 0.035, std = 0.488 curvature mean = 0.033, std = 0.331 curvature mean = 0.021, std = 0.623 curvature mean = 0.033, std = 0.342 curvature mean = 0.007, std = 0.737 MRISregister() return, current seed 0 -01: dt=0.0000, 57 negative triangles 118: dt=0.9900, 57 negative triangles expanding nbhd size to 1 119: dt=0.9900, 94 negative triangles 120: dt=0.9405, 59 negative triangles 121: dt=0.9405, 61 negative triangles 122: dt=0.9405, 56 negative triangles 123: dt=0.9405, 57 negative triangles 124: dt=0.9405, 54 negative triangles 125: dt=0.9405, 47 negative triangles 126: dt=0.9405, 41 negative triangles 127: dt=0.9405, 38 negative triangles 128: dt=0.9405, 28 negative triangles 129: dt=0.9405, 31 negative triangles 130: dt=0.9405, 25 negative triangles 131: dt=0.9405, 20 negative triangles 132: dt=0.9405, 20 negative triangles 133: dt=0.9405, 13 negative triangles 134: dt=0.9405, 13 negative triangles 135: dt=0.9405, 15 negative triangles 136: dt=0.9405, 11 negative triangles 137: dt=0.9405, 8 negative triangles 138: dt=0.9405, 9 negative triangles 139: dt=0.9405, 9 negative triangles 140: dt=0.9405, 8 negative triangles 141: dt=0.9405, 7 negative triangles 142: dt=0.9405, 7 negative triangles 143: dt=0.9405, 4 negative triangles 144: dt=0.9405, 3 negative triangles 145: dt=0.9405, 3 negative triangles 146: dt=0.9405, 2 negative triangles 147: dt=0.9405, 3 negative triangles 148: dt=0.9405, 3 negative triangles 149: dt=0.9405, 4 negative triangles 150: dt=0.9405, 2 negative triangles 151: dt=0.9405, 3 negative triangles 152: dt=0.9405, 1 negative triangles 153: dt=0.9405, 2 negative triangles 154: dt=0.9405, 2 negative triangles 155: dt=0.9405, 5 negative triangles 156: dt=0.9405, 1 negative triangles 157: dt=0.9405, 1 negative triangles 158: dt=0.9405, 2 negative triangles 159: dt=0.9405, 2 negative triangles 160: dt=0.9405, 2 negative triangles 161: dt=0.9405, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.30 hours mris_register utimesec 4687.306421 mris_register stimesec 4.057383 mris_register ru_maxrss 271664 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 38741 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10488 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 296978 mris_register ru_nivcsw 215040 FSRUNTIME@ mris_register 1.3030 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 = 5.544 curvature mean = 0.019, std = 0.818 curvature mean = 0.021, std = 0.857 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 380038.0, tmin=1.1468 d=32.00 min @ (-8.00, -8.00, -8.00) sse = 218746.2, tmin=2.2943 d=16.00 min @ (0.00, 4.00, 0.00) sse = 209322.5, tmin=3.4650 d=8.00 min @ (0.00, -2.00, 2.00) sse = 186174.4, tmin=4.6466 d=1.00 min @ (-0.25, -0.25, 0.00) sse = 185935.2, tmin=8.2161 d=0.50 min @ (0.00, 0.12, -0.12) sse = 185857.5, tmin=9.4144 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 9.41 min curvature mean = 0.002, std = 0.830 curvature mean = 0.007, std = 0.947 curvature mean = -0.000, std = 0.840 curvature mean = 0.002, std = 0.979 curvature mean = -0.002, std = 0.841 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.028, std = 0.295 curvature mean = 0.036, std = 0.243 curvature mean = 0.064, std = 0.337 curvature mean = 0.033, std = 0.300 curvature mean = 0.037, std = 0.523 curvature mean = 0.033, std = 0.327 curvature mean = 0.021, std = 0.666 curvature mean = 0.033, std = 0.339 curvature mean = 0.007, std = 0.779 MRISregister() return, current seed 0 -01: dt=0.0000, 55 negative triangles 115: dt=0.9900, 55 negative triangles expanding nbhd size to 1 116: dt=0.9900, 63 negative triangles 117: dt=0.9900, 42 negative triangles 118: dt=0.9900, 38 negative triangles 119: dt=0.9900, 39 negative triangles 120: dt=0.9900, 34 negative triangles 121: dt=0.9900, 38 negative triangles 122: dt=0.9900, 38 negative triangles 123: dt=0.9900, 41 negative triangles 124: dt=0.9900, 33 negative triangles 125: dt=0.9900, 32 negative triangles 126: dt=0.9900, 27 negative triangles 127: dt=0.9900, 27 negative triangles 128: dt=0.9900, 27 negative triangles 129: dt=0.9900, 25 negative triangles 130: dt=0.9900, 21 negative triangles 131: dt=0.9900, 22 negative triangles 132: dt=0.9900, 18 negative triangles 133: dt=0.9900, 17 negative triangles 134: dt=0.9900, 17 negative triangles 135: dt=0.9900, 20 negative triangles 136: dt=0.9900, 15 negative triangles 137: dt=0.9900, 16 negative triangles 138: dt=0.9900, 14 negative triangles 139: dt=0.9900, 18 negative triangles 140: dt=0.9900, 17 negative triangles 141: dt=0.9900, 15 negative triangles 142: dt=0.9900, 15 negative triangles 143: dt=0.9900, 14 negative triangles 144: dt=0.9900, 11 negative triangles 145: dt=0.9900, 11 negative triangles 146: dt=0.9900, 10 negative triangles 147: dt=0.9900, 11 negative triangles 148: dt=0.9900, 14 negative triangles 149: dt=0.9900, 10 negative triangles 150: dt=0.9900, 11 negative triangles 151: dt=0.9900, 10 negative triangles 152: dt=0.9900, 9 negative triangles 153: dt=0.9900, 10 negative triangles 154: dt=0.9900, 9 negative triangles 155: dt=0.9900, 9 negative triangles 156: dt=0.9900, 9 negative triangles 157: dt=0.9900, 9 negative triangles 158: dt=0.9900, 12 negative triangles 159: dt=0.9900, 10 negative triangles 160: dt=0.9900, 8 negative triangles 161: dt=0.9900, 8 negative triangles 162: dt=0.9900, 8 negative triangles 163: dt=0.9900, 8 negative triangles 164: dt=0.9900, 8 negative triangles 165: dt=0.9900, 9 negative triangles 166: dt=0.9900, 6 negative triangles 167: dt=0.9900, 5 negative triangles 168: dt=0.9900, 4 negative triangles 169: dt=0.9900, 4 negative triangles 170: dt=0.9900, 5 negative triangles 171: dt=0.9900, 4 negative triangles 172: dt=0.9900, 4 negative triangles 173: dt=0.9900, 2 negative triangles 174: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.35 hours mris_register utimesec 4967.927760 mris_register stimesec 4.651292 mris_register ru_maxrss 270260 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 37935 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10432 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 317144 mris_register ru_nivcsw 210605 FSRUNTIME@ mris_register 1.3501 hours 1 threads PIDs (18909 18912) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 00:29:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 00:29:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 21872 of (21872 21875) to complete... Waiting for PID 21875 of (21872 21875) 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 (21872 21875) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 00:29:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 00:29:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 21922 of (21922 21925) to complete... Waiting for PID 21925 of (21922 21925) 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 (21922 21925) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 00:29:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051324 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 00:29:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051324 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 21991 of (21991 21994) to complete... Waiting for PID 21994 of (21991 21994) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051324 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... 1053 labels changed using aseg relabeling using gibbs priors... 000: 3226 changed, 147611 examined... 001: 689 changed, 13476 examined... 002: 163 changed, 3928 examined... 003: 57 changed, 1006 examined... 004: 25 changed, 360 examined... 005: 11 changed, 139 examined... 006: 5 changed, 69 examined... 007: 1 changed, 36 examined... 008: 1 changed, 8 examined... 009: 1 changed, 6 examined... 010: 0 changed, 7 examined... 225 labels changed using aseg 000: 115 total segments, 69 labels (265 vertices) changed 001: 47 total segments, 3 labels (5 vertices) changed 002: 44 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... 2200 vertices marked for relabeling... 2200 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 16 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051324 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... 1235 labels changed using aseg relabeling using gibbs priors... 000: 2896 changed, 147034 examined... 001: 656 changed, 12564 examined... 002: 157 changed, 3678 examined... 003: 53 changed, 936 examined... 004: 18 changed, 298 examined... 005: 3 changed, 118 examined... 006: 0 changed, 25 examined... 184 labels changed using aseg 000: 100 total segments, 60 labels (254 vertices) changed 001: 43 total segments, 3 labels (4 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2183 vertices marked for relabeling... 2183 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 16 seconds. PIDs (21991 21994) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 00:30:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051324 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 00:30:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051324 rh Waiting for PID 22056 of (22056 22059) to complete... Waiting for PID 22059 of (22056 22059) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051324 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-6.0.0/0051324/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... 22813 bright wm thresholded. 1864 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.orig... computing class statistics... border white: 280448 voxels (1.67%) border gray 318193 voxels (1.90%) WM (95.0): 95.7 +- 8.4 [70.0 --> 110.0] GM (71.0) : 69.5 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.0 (was 70) setting MAX_BORDER_WHITE to 107.4 (was 105) setting MIN_BORDER_WHITE to 66.0 (was 85) setting MAX_CSF to 43.9 (was 40) setting MAX_GRAY to 90.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.9 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=99+-7.0, GM=66+-8.7 mean inside = 91.1, mean outside = 72.9 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.26 (0.01-->8.09) (max @ vno 72451 --> 146753) face area 0.33 +- 0.16 (0.00-->5.20) mean absolute distance = 0.68 +- 0.91 3003 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 36 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 6 points - only 0.00% unknown deleting segment 4 with 47 points - only 0.00% unknown deleting segment 6 with 247 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 27 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 22 points - only 0.00% unknown deleting segment 12 with 62 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown mean border=77.6, 160 (160) missing vertices, mean dist 0.4 [1.1 (%14.6)->0.6 (%85.4))] %48 local maxima, %48 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 +- 0.27 (0.11-->7.99) (max @ vno 72451 --> 146753) face area 0.33 +- 0.17 (0.00-->4.84) mean absolute distance = 0.40 +- 0.71 4849 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2552500.2, rms=8.097 001: dt: 0.5000, sse=1423126.1, rms=5.043 (37.713%) 002: dt: 0.5000, sse=1087751.4, rms=3.714 (26.368%) 003: dt: 0.5000, sse=1023763.6, rms=3.405 (8.316%) 004: dt: 0.5000, sse=974888.5, rms=3.156 (7.293%) rms = 3.25, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=857680.6, rms=2.338 (25.938%) 006: dt: 0.2500, sse=812157.9, rms=1.929 (17.493%) 007: dt: 0.2500, sse=801479.1, rms=1.804 (6.462%) rms = 1.76, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=797401.5, rms=1.763 (2.295%) 009: dt: 0.1250, sse=791864.5, rms=1.709 (3.023%) rms = 1.70, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=791293.1, rms=1.700 (0.558%) positioning took 1.2 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 42 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 7 points - only 0.00% unknown deleting segment 4 with 33 points - only 0.00% unknown deleting segment 5 with 27 points - only 0.00% unknown deleting segment 6 with 97 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown mean border=80.4, 143 (50) missing vertices, mean dist -0.2 [0.5 (%66.5)->0.2 (%33.5))] %60 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.26 (0.10-->7.89) (max @ vno 72451 --> 146753) face area 0.35 +- 0.17 (0.00-->5.25) mean absolute distance = 0.33 +- 0.49 4621 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1272019.4, rms=4.293 011: dt: 0.5000, sse=980139.1, rms=2.845 (33.721%) rms = 2.83, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=971614.9, rms=2.829 (0.567%) 013: dt: 0.2500, sse=839207.6, rms=1.747 (38.260%) 014: dt: 0.2500, sse=818239.8, rms=1.505 (13.853%) 015: dt: 0.2500, sse=815696.4, rms=1.452 (3.508%) rms = 1.42, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=817551.4, rms=1.416 (2.503%) rms = 1.38, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=806322.4, rms=1.376 (2.775%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 53 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 36 points - only 0.00% unknown deleting segment 5 with 33 points - only 0.00% unknown deleting segment 6 with 20 points - only 0.00% unknown deleting segment 7 with 114 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 7 points - only 0.00% unknown deleting segment 10 with 10 points - only 0.00% unknown deleting segment 11 with 23 points - only 0.00% unknown mean border=82.9, 140 (42) missing vertices, mean dist -0.2 [0.4 (%66.0)->0.2 (%34.0))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.26 (0.06-->7.83) (max @ vno 72451 --> 146753) face area 0.34 +- 0.17 (0.00-->5.10) mean absolute distance = 0.29 +- 0.40 3821 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1067216.1, rms=3.455 018: dt: 0.5000, sse=910681.0, rms=2.485 (28.071%) rms = 2.72, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=824519.2, rms=1.783 (28.252%) 020: dt: 0.2500, sse=790962.4, rms=1.411 (20.854%) 021: dt: 0.2500, sse=782633.4, rms=1.319 (6.549%) rms = 1.30, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=782944.1, rms=1.305 (1.070%) rms = 1.26, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=777586.1, rms=1.263 (3.204%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 53 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 36 points - only 0.00% unknown deleting segment 5 with 247 points - only 0.00% unknown deleting segment 6 with 21 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 9 with 37 points - only 0.00% unknown mean border=83.9, 161 (39) missing vertices, mean dist -0.1 [0.3 (%56.3)->0.2 (%43.7))] %81 local maxima, %14 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-6.0.0/0051324/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=822385.5, rms=1.907 024: dt: 0.5000, sse=812750.1, rms=1.796 (5.818%) rms = 2.37, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=759953.7, rms=1.198 (33.272%) 026: dt: 0.2500, sse=754470.7, rms=1.065 (11.147%) 027: dt: 0.2500, sse=744140.0, rms=0.985 (7.495%) rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 0.97, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=742925.0, rms=0.971 (1.457%) positioning took 0.7 minutes generating cortex label... 11 non-cortical segments detected only using segment with 8059 vertices erasing segment 1 (vno[0] = 97116) erasing segment 2 (vno[0] = 104465) erasing segment 3 (vno[0] = 112488) erasing segment 4 (vno[0] = 112539) erasing segment 5 (vno[0] = 112573) erasing segment 6 (vno[0] = 113611) erasing segment 7 (vno[0] = 115767) erasing segment 8 (vno[0] = 115816) erasing segment 9 (vno[0] = 119175) erasing segment 10 (vno[0] = 127103) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.area vertex spacing 0.89 +- 0.27 (0.01-->7.79) (max @ vno 72451 --> 146753) face area 0.34 +- 0.17 (0.00-->5.49) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=52.9, 156 (156) missing vertices, mean dist 1.9 [0.0 (%0.0)->2.5 (%100.0))] %18 local maxima, %54 large gradients and %23 min vals, 270 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=28948726.0, rms=31.688 001: dt: 0.0500, sse=25803634.0, rms=29.872 (5.733%) 002: dt: 0.0500, sse=23534700.0, rms=28.489 (4.628%) 003: dt: 0.0500, sse=21785114.0, rms=27.375 (3.910%) 004: dt: 0.0500, sse=20359220.0, rms=26.433 (3.443%) 005: dt: 0.0500, sse=19151116.0, rms=25.607 (3.124%) 006: dt: 0.0500, sse=18096332.0, rms=24.863 (2.904%) 007: dt: 0.0500, sse=17155832.0, rms=24.181 (2.744%) 008: dt: 0.0500, sse=16304355.0, rms=23.546 (2.625%) 009: dt: 0.0500, sse=15525029.0, rms=22.950 (2.533%) 010: dt: 0.0500, sse=14805379.0, rms=22.385 (2.462%) positioning took 1.0 minutes mean border=52.7, 86 (58) missing vertices, mean dist 1.5 [0.1 (%0.0)->1.9 (%100.0))] %18 local maxima, %54 large gradients and %23 min vals, 249 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=15537543.0, rms=22.958 011: dt: 0.0500, sse=14864653.0, rms=22.431 (2.297%) 012: dt: 0.0500, sse=14237045.0, rms=21.928 (2.244%) 013: dt: 0.0500, sse=13648955.0, rms=21.445 (2.200%) 014: dt: 0.0500, sse=13096643.0, rms=20.982 (2.160%) 015: dt: 0.0500, sse=12577644.0, rms=20.537 (2.120%) 016: dt: 0.0500, sse=12089305.0, rms=20.110 (2.082%) 017: dt: 0.0500, sse=11629650.0, rms=19.698 (2.044%) 018: dt: 0.0500, sse=11197194.0, rms=19.304 (2.004%) 019: dt: 0.0500, sse=10789915.0, rms=18.924 (1.966%) 020: dt: 0.0500, sse=10406299.0, rms=18.560 (1.927%) positioning took 1.0 minutes mean border=52.5, 107 (42) missing vertices, mean dist 1.2 [0.1 (%1.0)->1.6 (%99.0))] %19 local maxima, %55 large gradients and %22 min vals, 227 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=10522233.0, rms=18.677 021: dt: 0.0500, sse=10147766.0, rms=18.316 (1.931%) 022: dt: 0.0500, sse=9794916.0, rms=17.969 (1.892%) 023: dt: 0.0500, sse=9459357.0, rms=17.634 (1.869%) 024: dt: 0.0500, sse=9144617.0, rms=17.312 (1.821%) 025: dt: 0.0500, sse=8849081.0, rms=17.005 (1.774%) 026: dt: 0.0500, sse=8571029.0, rms=16.711 (1.730%) 027: dt: 0.0500, sse=8306758.0, rms=16.427 (1.703%) 028: dt: 0.0500, sse=8052266.5, rms=16.148 (1.697%) 029: dt: 0.0500, sse=7807326.0, rms=15.875 (1.691%) 030: dt: 0.0500, sse=7572114.5, rms=15.608 (1.680%) positioning took 1.0 minutes mean border=52.4, 151 (37) missing vertices, mean dist 1.0 [0.1 (%11.8)->1.4 (%88.2))] %19 local maxima, %55 large gradients and %22 min vals, 216 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=7677891.0, rms=15.728 031: dt: 0.5000, sse=6001290.5, rms=13.697 (12.910%) 032: dt: 0.5000, sse=4813593.5, rms=12.045 (12.060%) 033: dt: 0.5000, sse=3868977.0, rms=10.555 (12.376%) 034: dt: 0.5000, sse=3163265.5, rms=9.274 (12.128%) 035: dt: 0.5000, sse=2633503.2, rms=8.190 (11.696%) 036: dt: 0.5000, sse=2266980.8, rms=7.336 (10.419%) 037: dt: 0.5000, sse=2008502.5, rms=6.677 (8.985%) 038: dt: 0.5000, sse=1857223.1, rms=6.249 (6.406%) 039: dt: 0.5000, sse=1746651.1, rms=5.927 (5.153%) 040: dt: 0.5000, sse=1687294.0, rms=5.737 (3.219%) 041: dt: 0.5000, sse=1633990.9, rms=5.572 (2.872%) 042: dt: 0.5000, sse=1604564.8, rms=5.470 (1.826%) 043: dt: 0.5000, sse=1571491.5, rms=5.365 (1.923%) 044: dt: 0.5000, sse=1556904.5, rms=5.309 (1.040%) 045: dt: 0.5000, sse=1537218.6, rms=5.247 (1.174%) rms = 5.22, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1532350.6, rms=5.223 (0.447%) 047: dt: 0.2500, sse=1365600.2, rms=4.564 (12.620%) 048: dt: 0.2500, sse=1324187.5, rms=4.395 (3.695%) rms = 4.38, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1320846.4, rms=4.378 (0.396%) 050: dt: 0.1250, sse=1297668.9, rms=4.276 (2.331%) rms = 4.26, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1294771.2, rms=4.264 (0.289%) positioning took 2.7 minutes mean border=50.6, 1537 (9) missing vertices, mean dist 0.2 [0.2 (%43.5)->0.5 (%56.5))] %35 local maxima, %41 large gradients and %19 min vals, 117 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=1681085.1, rms=5.061 052: dt: 0.5000, sse=1534764.2, rms=4.518 (10.729%) rms = 4.53, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1386426.2, rms=3.861 (14.546%) 054: dt: 0.2500, sse=1330695.4, rms=3.590 (7.029%) 055: dt: 0.2500, sse=1309729.2, rms=3.483 (2.976%) rms = 3.44, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1300265.2, rms=3.436 (1.331%) 057: dt: 0.1250, sse=1275124.8, rms=3.294 (4.131%) rms = 3.26, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1268914.6, rms=3.262 (0.995%) positioning took 1.1 minutes mean border=49.4, 1691 (4) missing vertices, mean dist 0.1 [0.1 (%45.5)->0.4 (%54.5))] %48 local maxima, %29 large gradients and %18 min vals, 162 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=1387228.4, rms=3.831 rms = 4.14, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1315394.5, rms=3.473 (9.349%) 060: dt: 0.2500, sse=1286286.0, rms=3.319 (4.425%) rms = 3.30, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1280037.1, rms=3.295 (0.717%) 062: dt: 0.1250, sse=1262348.2, rms=3.192 (3.134%) rms = 3.17, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1258357.0, rms=3.173 (0.611%) positioning took 0.8 minutes mean border=48.5, 3357 (3) missing vertices, mean dist 0.1 [0.2 (%46.7)->0.3 (%53.3))] %53 local maxima, %23 large gradients and %17 min vals, 161 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-6.0.0/0051324/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1302442.2, rms=3.393 rms = 3.78, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1267690.0, rms=3.197 (5.757%) 065: dt: 0.2500, sse=1248403.5, rms=3.097 (3.134%) rms = 3.06, time step reduction 2 of 3 to 0.125... 066: dt: 0.2500, sse=1240297.6, rms=3.059 (1.228%) 067: dt: 0.1250, sse=1221515.8, rms=2.944 (3.765%) rms = 2.91, time step reduction 3 of 3 to 0.062... 068: dt: 0.1250, sse=1215080.4, rms=2.909 (1.196%) positioning took 0.8 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.area.pial vertex spacing 1.00 +- 0.44 (0.07-->8.27) (max @ vno 72451 --> 146753) face area 0.40 +- 0.32 (0.00-->6.82) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 147611 vertices processed 25000 of 147611 vertices processed 50000 of 147611 vertices processed 75000 of 147611 vertices processed 100000 of 147611 vertices processed 125000 of 147611 vertices processed 0 of 147611 vertices processed 25000 of 147611 vertices processed 50000 of 147611 vertices processed 75000 of 147611 vertices processed 100000 of 147611 vertices processed 125000 of 147611 vertices processed thickness calculation complete, 140:809 truncations. 38506 vertices at 0 distance 110457 vertices at 1 distance 85616 vertices at 2 distance 32480 vertices at 3 distance 9761 vertices at 4 distance 2964 vertices at 5 distance 997 vertices at 6 distance 395 vertices at 7 distance 159 vertices at 8 distance 60 vertices at 9 distance 41 vertices at 10 distance 30 vertices at 11 distance 15 vertices at 12 distance 13 vertices at 13 distance 6 vertices at 14 distance 8 vertices at 15 distance 11 vertices at 16 distance 7 vertices at 17 distance 8 vertices at 18 distance 3 vertices at 19 distance 11 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.thickness positioning took 16.1 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051324 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-6.0.0/0051324/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... 22813 bright wm thresholded. 1864 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.orig... computing class statistics... border white: 280448 voxels (1.67%) border gray 318193 voxels (1.90%) WM (95.0): 95.7 +- 8.4 [70.0 --> 110.0] GM (71.0) : 69.5 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.0 (was 70) setting MAX_BORDER_WHITE to 107.4 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 44.9 (was 40) setting MAX_GRAY to 90.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.9 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=99+-6.1, GM=67+-8.7 mean inside = 91.4, mean outside = 74.0 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.04-->3.93) (max @ vno 100441 --> 100456) face area 0.33 +- 0.16 (0.00-->3.35) mean absolute distance = 0.72 +- 0.93 3005 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 1 with 27 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 272 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 32 points - only 0.00% unknown mean border=78.4, 121 (121) missing vertices, mean dist 0.4 [1.1 (%14.2)->0.7 (%85.8))] %50 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.09-->4.03) (max @ vno 101557 --> 101558) face area 0.33 +- 0.16 (0.00-->3.00) mean absolute distance = 0.42 +- 0.71 4398 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2638416.8, rms=8.308 001: dt: 0.5000, sse=1461468.9, rms=5.210 (37.294%) 002: dt: 0.5000, sse=1080683.8, rms=3.706 (28.852%) 003: dt: 0.5000, sse=986256.4, rms=3.238 (12.649%) 004: dt: 0.5000, sse=938791.4, rms=2.976 (8.068%) rms = 3.02, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=837385.9, rms=2.221 (25.373%) 006: dt: 0.2500, sse=796289.1, rms=1.824 (17.870%) 007: dt: 0.2500, sse=787887.4, rms=1.704 (6.593%) rms = 1.66, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=781623.0, rms=1.661 (2.498%) rms = 1.62, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=777799.2, rms=1.615 (2.768%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 21 points - only 0.00% unknown deleting segment 1 with 92 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 22 points - only 0.00% unknown deleting segment 5 with 30 points - only 0.00% unknown mean border=81.3, 69 (21) missing vertices, mean dist -0.3 [0.5 (%66.7)->0.2 (%33.3))] %63 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.26 (0.05-->4.68) (max @ vno 101557 --> 101558) face area 0.35 +- 0.17 (0.00-->3.49) mean absolute distance = 0.35 +- 0.49 4654 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1284216.4, rms=4.364 010: dt: 0.5000, sse=977510.6, rms=2.859 (34.482%) 011: dt: 0.5000, sse=944815.9, rms=2.692 (5.842%) rms = 2.72, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=856821.4, rms=1.984 (26.299%) 013: dt: 0.2500, sse=814293.6, rms=1.531 (22.835%) 014: dt: 0.2500, sse=805588.7, rms=1.413 (7.727%) rms = 1.37, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=801468.5, rms=1.367 (3.246%) rms = 1.32, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=798612.2, rms=1.323 (3.178%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 1 with 27 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 208 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 32 points - only 0.00% unknown mean border=83.8, 66 (16) missing vertices, mean dist -0.2 [0.4 (%67.4)->0.2 (%32.6))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.26 (0.07-->4.71) (max @ vno 101557 --> 101558) face area 0.34 +- 0.17 (0.00-->3.70) mean absolute distance = 0.29 +- 0.39 3826 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1086471.0, rms=3.587 017: dt: 0.5000, sse=889880.8, rms=2.381 (33.619%) rms = 2.53, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=812892.0, rms=1.733 (27.197%) 019: dt: 0.2500, sse=780425.0, rms=1.356 (21.775%) 020: dt: 0.2500, sse=778685.9, rms=1.261 (6.995%) rms = 1.25, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=772219.4, rms=1.247 (1.074%) rms = 1.21, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=768464.9, rms=1.209 (3.063%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 1 with 24 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 238 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 32 points - only 0.00% unknown mean border=84.9, 77 (11) missing vertices, mean dist -0.1 [0.3 (%57.3)->0.2 (%42.7))] %83 local maxima, %12 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-6.0.0/0051324/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=816337.9, rms=1.901 023: dt: 0.5000, sse=796910.4, rms=1.643 (13.592%) rms = 2.20, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=750738.9, rms=1.116 (32.094%) 025: dt: 0.2500, sse=743540.4, rms=1.005 (9.921%) 026: dt: 0.2500, sse=738475.2, rms=0.938 (6.636%) rms = 0.97, time step reduction 2 of 3 to 0.125... rms = 0.93, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=737076.1, rms=0.929 (0.934%) positioning took 0.7 minutes generating cortex label... 11 non-cortical segments detected only using segment with 7992 vertices erasing segment 0 (vno[0] = 46249) erasing segment 2 (vno[0] = 107978) erasing segment 3 (vno[0] = 108068) erasing segment 4 (vno[0] = 110104) erasing segment 5 (vno[0] = 112222) erasing segment 6 (vno[0] = 112231) erasing segment 7 (vno[0] = 112364) erasing segment 8 (vno[0] = 115245) erasing segment 9 (vno[0] = 115282) erasing segment 10 (vno[0] = 116306) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.area vertex spacing 0.89 +- 0.26 (0.04-->4.73) (max @ vno 101557 --> 101558) face area 0.34 +- 0.17 (0.00-->3.83) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 100 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 6 with 17 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=53.9, 147 (147) missing vertices, mean dist 1.9 [1.9 (%0.0)->2.6 (%100.0))] %18 local maxima, %52 large gradients and %25 min vals, 207 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=28637940.0, rms=31.593 001: dt: 0.0500, sse=25650282.0, rms=29.856 (5.498%) 002: dt: 0.0500, sse=23497976.0, rms=28.539 (4.411%) 003: dt: 0.0500, sse=21837056.0, rms=27.479 (3.713%) 004: dt: 0.0500, sse=20483896.0, rms=26.585 (3.255%) 005: dt: 0.0500, sse=19336370.0, rms=25.802 (2.945%) 006: dt: 0.0500, sse=18334426.0, rms=25.098 (2.727%) 007: dt: 0.0500, sse=17439728.0, rms=24.453 (2.572%) 008: dt: 0.0500, sse=16628032.0, rms=23.852 (2.457%) 009: dt: 0.0500, sse=15883978.0, rms=23.287 (2.366%) 010: dt: 0.0500, sse=15194701.0, rms=22.752 (2.299%) positioning took 1.0 minutes mean border=53.8, 91 (73) missing vertices, mean dist 1.5 [0.1 (%0.0)->2.1 (%100.0))] %19 local maxima, %52 large gradients and %24 min vals, 167 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=15974967.0, rms=23.358 011: dt: 0.0500, sse=15329518.0, rms=22.859 (2.137%) 012: dt: 0.0500, sse=14724765.0, rms=22.381 (2.091%) 013: dt: 0.0500, sse=14156735.0, rms=21.922 (2.048%) 014: dt: 0.0500, sse=13621805.0, rms=21.482 (2.010%) 015: dt: 0.0500, sse=13117411.0, rms=21.057 (1.974%) 016: dt: 0.0500, sse=12640947.0, rms=20.649 (1.941%) 017: dt: 0.0500, sse=12190649.0, rms=20.255 (1.907%) 018: dt: 0.0500, sse=11764831.0, rms=19.875 (1.875%) 019: dt: 0.0500, sse=11362423.0, rms=19.510 (1.840%) 020: dt: 0.0500, sse=10981515.0, rms=19.157 (1.808%) positioning took 1.0 minutes mean border=53.6, 87 (48) missing vertices, mean dist 1.3 [0.1 (%0.7)->1.7 (%99.3))] %19 local maxima, %52 large gradients and %24 min vals, 169 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=11088671.0, rms=19.262 021: dt: 0.0500, sse=10717077.0, rms=18.914 (1.809%) 022: dt: 0.0500, sse=10365581.0, rms=18.578 (1.775%) 023: dt: 0.0500, sse=10030284.0, rms=18.252 (1.755%) 024: dt: 0.0500, sse=9713869.0, rms=17.939 (1.716%) 025: dt: 0.0500, sse=9414959.0, rms=17.638 (1.678%) 026: dt: 0.0500, sse=9132225.0, rms=17.348 (1.642%) 027: dt: 0.0500, sse=8862265.0, rms=17.067 (1.621%) 028: dt: 0.0500, sse=8601715.0, rms=16.791 (1.617%) 029: dt: 0.0500, sse=8350480.0, rms=16.521 (1.611%) 030: dt: 0.0500, sse=8107653.5, rms=16.255 (1.609%) positioning took 1.0 minutes mean border=53.5, 116 (39) missing vertices, mean dist 1.0 [0.1 (%10.0)->1.5 (%90.0))] %19 local maxima, %53 large gradients and %23 min vals, 157 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=8223200.0, rms=16.382 031: dt: 0.5000, sse=6485563.0, rms=14.357 (12.360%) 032: dt: 0.5000, sse=5213587.5, rms=12.664 (11.793%) 033: dt: 0.5000, sse=4199066.5, rms=11.136 (12.068%) 034: dt: 0.5000, sse=3422180.0, rms=9.796 (12.032%) 035: dt: 0.5000, sse=2831317.0, rms=8.644 (11.761%) 036: dt: 0.5000, sse=2412470.5, rms=7.715 (10.746%) 037: dt: 0.5000, sse=2111428.5, rms=6.978 (9.555%) 038: dt: 0.5000, sse=1916874.6, rms=6.449 (7.583%) 039: dt: 0.5000, sse=1781308.4, rms=6.060 (6.023%) 040: dt: 0.5000, sse=1692581.0, rms=5.784 (4.562%) 041: dt: 0.5000, sse=1621655.4, rms=5.561 (3.852%) 042: dt: 0.5000, sse=1574315.5, rms=5.399 (2.909%) 043: dt: 0.5000, sse=1536143.6, rms=5.273 (2.344%) 044: dt: 0.5000, sse=1512039.1, rms=5.184 (1.679%) 045: dt: 0.5000, sse=1490343.4, rms=5.113 (1.379%) rms = 5.07, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1479116.1, rms=5.067 (0.896%) 047: dt: 0.2500, sse=1315965.2, rms=4.395 (13.256%) 048: dt: 0.2500, sse=1272331.8, rms=4.209 (4.227%) rms = 4.19, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1268414.5, rms=4.188 (0.505%) 050: dt: 0.1250, sse=1248211.2, rms=4.094 (2.237%) rms = 4.08, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1244590.6, rms=4.078 (0.400%) positioning took 2.7 minutes mean border=51.7, 1390 (20) missing vertices, mean dist 0.2 [0.2 (%42.5)->0.5 (%57.5))] %36 local maxima, %39 large gradients and %20 min vals, 125 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=1645797.6, rms=4.965 052: dt: 0.5000, sse=1487138.4, rms=4.356 (12.261%) rms = 4.39, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1348174.4, rms=3.711 (14.817%) 054: dt: 0.2500, sse=1290657.1, rms=3.414 (7.997%) 055: dt: 0.2500, sse=1270905.4, rms=3.306 (3.163%) rms = 3.26, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1262752.6, rms=3.264 (1.276%) 057: dt: 0.1250, sse=1243549.6, rms=3.147 (3.577%) rms = 3.13, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1239945.9, rms=3.128 (0.614%) positioning took 1.1 minutes mean border=50.5, 1543 (15) missing vertices, mean dist 0.1 [0.1 (%45.1)->0.4 (%54.9))] %48 local maxima, %27 large gradients and %19 min vals, 113 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=1340613.6, rms=3.655 rms = 3.97, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1274872.1, rms=3.309 (9.475%) 060: dt: 0.2500, sse=1250284.4, rms=3.172 (4.151%) rms = 3.15, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1245320.0, rms=3.153 (0.577%) 062: dt: 0.1250, sse=1230488.9, rms=3.062 (2.895%) rms = 3.04, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1226835.4, rms=3.043 (0.628%) positioning took 0.9 minutes mean border=49.8, 3065 (15) missing vertices, mean dist 0.1 [0.2 (%47.3)->0.3 (%52.7))] %52 local maxima, %22 large gradients and %19 min vals, 132 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-6.0.0/0051324/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1257854.5, rms=3.209 rms = 3.57, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1228517.6, rms=3.036 (5.403%) 065: dt: 0.2500, sse=1212560.9, rms=2.950 (2.808%) rms = 2.92, time step reduction 2 of 3 to 0.125... 066: dt: 0.2500, sse=1205760.8, rms=2.919 (1.069%) 067: dt: 0.1250, sse=1189340.5, rms=2.813 (3.640%) rms = 2.78, time step reduction 3 of 3 to 0.062... 068: dt: 0.1250, sse=1183697.2, rms=2.781 (1.126%) positioning took 0.9 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.area.pial vertex spacing 1.00 +- 0.44 (0.09-->8.56) (max @ vno 101636 --> 101610) face area 0.40 +- 0.31 (0.00-->6.93) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 147034 vertices processed 25000 of 147034 vertices processed 50000 of 147034 vertices processed 75000 of 147034 vertices processed 100000 of 147034 vertices processed 125000 of 147034 vertices processed 0 of 147034 vertices processed 25000 of 147034 vertices processed 50000 of 147034 vertices processed 75000 of 147034 vertices processed 100000 of 147034 vertices processed 125000 of 147034 vertices processed thickness calculation complete, 350:1109 truncations. 35800 vertices at 0 distance 107979 vertices at 1 distance 85908 vertices at 2 distance 34427 vertices at 3 distance 10805 vertices at 4 distance 3331 vertices at 5 distance 1120 vertices at 6 distance 413 vertices at 7 distance 182 vertices at 8 distance 71 vertices at 9 distance 63 vertices at 10 distance 31 vertices at 11 distance 29 vertices at 12 distance 7 vertices at 13 distance 5 vertices at 14 distance 3 vertices at 15 distance 1 vertices at 16 distance 4 vertices at 17 distance 7 vertices at 18 distance 2 vertices at 19 distance 2 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.thickness positioning took 16.1 minutes PIDs (22056 22059) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 00:46:16 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0051324 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/lh.cortex.label Total face volume 248467 Total vertex volume 245112 (mask=0) #@# 0051324 lh 245112 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 00:46:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0051324 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/rh.cortex.label Total face volume 254085 Total vertex volume 250426 (mask=0) #@# 0051324 rh 250426 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 00:46:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0051324 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 = 212 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/ribbon.mgz mris_volmask took 14.52 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 01:00:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0051324 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 0051324 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 01:00:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0051324 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 0051324 rh pial Waiting for PID 23589 of (23589 23592 23595 23598) to complete... Waiting for PID 23592 of (23589 23592 23595 23598) to complete... Waiting for PID 23595 of (23589 23592 23595 23598) to complete... Waiting for PID 23598 of (23589 23592 23595 23598) 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 0051324 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 248467 Total vertex volume 245112 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 1519 1041 2175 2.354 0.464 0.099 0.019 7 1.4 bankssts 853 587 1475 2.579 0.578 0.129 0.019 12 0.7 caudalanteriorcingulate 3199 2074 5034 2.363 0.512 0.118 0.033 30 4.3 caudalmiddlefrontal 2955 1833 3697 1.850 0.458 0.149 0.042 45 5.2 cuneus 572 425 1984 3.282 0.847 0.131 0.035 5 0.7 entorhinal 4430 3081 10315 2.640 0.651 0.150 0.047 73 9.5 fusiform 6711 4595 11716 2.262 0.515 0.130 0.033 85 8.9 inferiorparietal 4866 3467 11032 2.603 0.705 0.155 0.045 82 9.7 inferiortemporal 1901 1223 3084 2.231 0.875 0.140 0.042 36 2.8 isthmuscingulate 8264 5540 12100 2.004 0.554 0.138 0.036 114 12.0 lateraloccipital 4025 2704 7423 2.511 0.666 0.140 0.045 64 7.4 lateralorbitofrontal 4883 3169 7026 2.030 0.577 0.141 0.047 71 8.9 lingual 3211 2097 5428 2.359 0.684 0.124 0.041 46 5.7 medialorbitofrontal 4401 3115 10711 2.690 0.710 0.136 0.040 66 7.1 middletemporal 854 587 1860 2.597 0.783 0.119 0.032 8 1.0 parahippocampal 2560 1661 4087 2.332 0.582 0.124 0.045 25 4.8 paracentral 2641 1750 4995 2.578 0.537 0.124 0.035 27 3.7 parsopercularis 839 584 1858 2.422 0.515 0.153 0.046 13 1.6 parsorbitalis 2082 1433 3659 2.195 0.537 0.133 0.034 23 3.0 parstriangularis 2404 1666 2445 1.622 0.392 0.134 0.036 27 3.4 pericalcarine 7136 4491 9892 2.023 0.618 0.123 0.038 78 10.6 postcentral 2029 1352 3868 2.718 0.630 0.145 0.040 34 3.0 posteriorcingulate 8563 5398 13001 2.299 0.604 0.127 0.042 96 15.3 precentral 6567 4409 11309 2.357 0.613 0.129 0.035 72 8.9 precuneus 1327 887 2485 2.584 0.840 0.132 0.038 19 2.1 rostralanteriorcingulate 9792 6667 16308 2.199 0.523 0.145 0.041 139 16.6 rostralmiddlefrontal 11785 8097 24921 2.644 0.609 0.135 0.038 137 18.0 superiorfrontal 10176 6701 16227 2.165 0.486 0.125 0.029 118 11.5 superiorparietal 5929 3892 10967 2.461 0.635 0.108 0.029 56 7.1 superiortemporal 6898 4649 11919 2.329 0.555 0.135 0.036 88 10.3 supramarginal 316 232 857 2.414 0.543 0.177 0.076 7 1.1 frontalpole 713 553 2545 3.320 0.940 0.164 0.074 14 2.0 temporalpole 813 412 1169 2.481 0.482 0.100 0.036 8 1.1 transversetemporal 3968 2715 7515 2.760 0.826 0.131 0.049 51 7.4 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 0051324 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 248467 Total vertex volume 245112 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 1519 842 2175 2.354 0.464 0.092 0.025 16 1.6 bankssts 853 659 1475 2.579 0.578 0.131 0.027 12 0.9 caudalanteriorcingulate 3199 2211 5034 2.363 0.512 0.117 0.029 34 3.8 caudalmiddlefrontal 2955 2204 3697 1.850 0.458 0.141 0.038 37 4.9 cuneus 572 782 1984 3.282 0.847 0.198 0.050 9 1.2 entorhinal 4430 4490 10315 2.640 0.651 0.182 0.047 73 9.8 fusiform 6711 5579 11716 2.262 0.515 0.144 0.029 75 8.4 inferiorparietal 4866 4646 11032 2.603 0.705 0.178 0.049 82 10.4 inferiortemporal 1901 1498 3084 2.231 0.875 0.152 0.041 33 3.2 isthmuscingulate 8264 6543 12100 2.004 0.554 0.140 0.030 101 10.9 lateraloccipital 4025 3119 7423 2.511 0.666 0.155 0.041 74 7.4 lateralorbitofrontal 4883 3861 7026 2.030 0.577 0.147 0.038 70 8.4 lingual 3211 2488 5428 2.359 0.684 0.144 0.035 50 5.2 medialorbitofrontal 4401 4529 10711 2.690 0.710 0.164 0.037 48 6.9 middletemporal 854 821 1860 2.597 0.783 0.170 0.040 11 1.6 parahippocampal 2560 1869 4087 2.332 0.582 0.125 0.036 30 3.8 paracentral 2641 2068 4995 2.578 0.537 0.131 0.027 26 3.1 parsopercularis 839 891 1858 2.422 0.515 0.187 0.046 12 1.7 parsorbitalis 2082 1796 3659 2.195 0.537 0.158 0.033 26 3.0 parstriangularis 2404 1454 2445 1.622 0.392 0.122 0.030 31 3.2 pericalcarine 7136 5311 9892 2.023 0.618 0.121 0.026 59 8.2 postcentral 2029 1517 3868 2.718 0.630 0.149 0.053 69 3.2 posteriorcingulate 8563 5933 13001 2.299 0.604 0.118 0.039 171 16.6 precentral 6567 4973 11309 2.357 0.613 0.137 0.034 90 10.0 precuneus 1327 1119 2485 2.584 0.840 0.146 0.035 19 2.2 rostralanteriorcingulate 9792 8054 16308 2.199 0.523 0.157 0.038 130 17.5 rostralmiddlefrontal 11785 10293 24921 2.644 0.609 0.152 0.038 151 19.7 superiorfrontal 10176 7986 16227 2.165 0.486 0.133 0.027 117 11.4 superiorparietal 5929 4622 10967 2.461 0.635 0.120 0.025 56 6.4 superiortemporal 6898 5463 11919 2.329 0.555 0.138 0.033 81 9.9 supramarginal 316 478 857 2.414 0.543 0.263 0.056 4 0.9 frontalpole 713 998 2545 3.320 0.940 0.229 0.048 12 1.7 temporalpole 813 556 1169 2.481 0.482 0.093 0.018 4 0.6 transversetemporal 3968 2624 7515 2.760 0.826 0.124 0.034 55 5.6 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 0051324 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 254085 Total vertex volume 250426 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 1411 1010 2292 2.396 0.505 0.102 0.020 8 1.2 bankssts 1301 894 2436 2.303 0.809 0.152 0.035 27 1.9 caudalanteriorcingulate 3265 2162 5357 2.337 0.487 0.124 0.034 31 4.2 caudalmiddlefrontal 2803 1770 3670 1.849 0.490 0.131 0.034 37 3.9 cuneus 736 527 2889 3.981 0.629 0.134 0.042 8 1.3 entorhinal 3923 2718 9139 2.804 0.713 0.139 0.041 53 6.2 fusiform 7323 5101 13051 2.371 0.524 0.127 0.030 78 9.1 inferiorparietal 4647 3286 11062 2.753 0.702 0.147 0.044 73 8.7 inferiortemporal 1548 1004 2765 2.343 0.851 0.145 0.044 27 2.7 isthmuscingulate 7426 4841 11802 2.200 0.554 0.145 0.044 103 12.9 lateraloccipital 3759 2557 6914 2.454 0.634 0.152 0.055 74 9.1 lateralorbitofrontal 5253 3495 7728 2.051 0.582 0.149 0.048 79 10.7 lingual 2961 2008 5534 2.349 0.644 0.129 0.038 45 4.5 medialorbitofrontal 5165 3618 12210 2.799 0.645 0.135 0.036 70 8.0 middletemporal 872 592 2133 2.912 0.922 0.112 0.025 7 0.7 parahippocampal 3004 1945 4301 2.198 0.609 0.139 0.045 37 5.5 paracentral 2198 1466 3749 2.376 0.422 0.117 0.034 23 2.8 parsopercularis 1241 829 2794 2.607 0.671 0.165 0.050 27 2.6 parsorbitalis 2195 1539 3630 2.177 0.552 0.134 0.040 26 3.6 parstriangularis 2922 1884 3144 1.732 0.444 0.134 0.040 34 5.1 pericalcarine 7524 4709 10852 2.111 0.634 0.119 0.032 74 9.7 postcentral 2259 1495 4063 2.330 0.747 0.148 0.039 38 3.5 posteriorcingulate 8560 5400 13053 2.289 0.589 0.124 0.039 83 14.4 precentral 7024 4785 12439 2.470 0.623 0.133 0.035 83 9.6 precuneus 949 661 2090 2.811 0.602 0.153 0.045 22 1.9 rostralanteriorcingulate 8735 6087 16251 2.265 0.584 0.149 0.046 143 17.4 rostralmiddlefrontal 11347 7735 23754 2.638 0.618 0.137 0.040 134 18.6 superiorfrontal 9152 5931 14380 2.207 0.505 0.119 0.029 93 10.5 superiorparietal 6109 4077 12877 2.783 0.609 0.120 0.031 66 7.7 superiortemporal 6546 4295 11602 2.482 0.543 0.122 0.031 75 8.0 supramarginal 439 293 1084 2.675 0.593 0.178 0.056 11 1.0 frontalpole 560 426 1942 3.255 0.875 0.173 0.079 12 2.1 temporalpole 693 360 922 2.281 0.480 0.119 0.041 9 1.3 transversetemporal 4828 3202 8514 2.566 0.901 0.126 0.043 61 8.1 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 0051324 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 254085 Total vertex volume 250426 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 1411 858 2292 2.396 0.505 0.103 0.025 13 1.4 bankssts 1301 1151 2436 2.303 0.809 0.160 0.038 24 2.1 caudalanteriorcingulate 3265 2408 5357 2.337 0.487 0.127 0.030 42 4.3 caudalmiddlefrontal 2803 2234 3670 1.849 0.490 0.134 0.028 27 3.3 cuneus 736 865 2889 3.981 0.629 0.180 0.040 13 1.3 entorhinal 3923 3590 9139 2.804 0.713 0.154 0.040 50 7.0 fusiform 7323 5747 13051 2.371 0.524 0.131 0.026 75 8.5 inferiorparietal 4647 4436 11062 2.753 0.702 0.164 0.039 68 8.7 inferiortemporal 1548 1218 2765 2.343 0.851 0.153 0.039 30 2.7 isthmuscingulate 7426 5758 11802 2.200 0.554 0.141 0.036 113 11.4 lateraloccipital 3759 3045 6914 2.454 0.634 0.174 0.052 86 9.1 lateralorbitofrontal 5253 4025 7728 2.051 0.582 0.141 0.038 92 8.6 lingual 2961 2588 5534 2.349 0.644 0.156 0.037 47 5.0 medialorbitofrontal 5165 4923 12210 2.799 0.645 0.159 0.035 65 8.4 middletemporal 872 775 2133 2.912 0.922 0.152 0.041 16 1.4 parahippocampal 3004 1989 4301 2.198 0.609 0.122 0.041 53 6.3 paracentral 2198 1691 3749 2.376 0.422 0.131 0.034 28 3.6 parsopercularis 1241 1242 2794 2.607 0.671 0.174 0.038 15 2.0 parsorbitalis 2195 1759 3630 2.177 0.552 0.142 0.037 29 4.3 parstriangularis 2922 1820 3144 1.732 0.444 0.123 0.027 37 3.5 pericalcarine 7524 5604 10852 2.111 0.634 0.119 0.024 67 7.9 postcentral 2259 1796 4063 2.330 0.747 0.153 0.044 66 4.2 posteriorcingulate 8560 5950 13053 2.289 0.589 0.115 0.027 104 10.3 precentral 7024 5168 12439 2.470 0.623 0.133 0.032 92 9.8 precuneus 949 882 2090 2.811 0.602 0.163 0.037 15 1.5 rostralanteriorcingulate 8735 8014 16251 2.265 0.584 0.175 0.042 130 17.5 rostralmiddlefrontal 11347 9844 23754 2.638 0.618 0.158 0.041 192 20.4 superiorfrontal 9152 6920 14380 2.207 0.505 0.123 0.026 91 9.6 superiorparietal 6109 5025 12877 2.783 0.609 0.128 0.026 63 6.9 superiortemporal 6546 4860 11602 2.482 0.543 0.119 0.024 60 6.8 supramarginal 439 518 1084 2.675 0.593 0.219 0.047 6 1.0 frontalpole 560 740 1942 3.255 0.875 0.220 0.050 9 1.4 temporalpole 693 423 922 2.281 0.480 0.093 0.019 4 0.5 transversetemporal 4828 3024 8514 2.566 0.901 0.129 0.036 77 7.4 insula PIDs (23589 23592 23595 23598) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 01:02:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051324 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 01:02:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051324 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 23695 of (23695 23698) to complete... Waiting for PID 23698 of (23695 23698) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051324 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... 89 labels changed using aseg relabeling using gibbs priors... 000: 9522 changed, 147611 examined... 001: 2243 changed, 37104 examined... 002: 633 changed, 11802 examined... 003: 266 changed, 3565 examined... 004: 134 changed, 1541 examined... 005: 95 changed, 772 examined... 006: 31 changed, 503 examined... 007: 18 changed, 184 examined... 008: 8 changed, 103 examined... 009: 3 changed, 45 examined... 010: 0 changed, 19 examined... 48 labels changed using aseg 000: 256 total segments, 176 labels (2509 vertices) changed 001: 91 total segments, 11 labels (45 vertices) changed 002: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1275 vertices marked for relabeling... 1275 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 0051324 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: 9142 changed, 147034 examined... 001: 2050 changed, 36312 examined... 002: 575 changed, 10924 examined... 003: 239 changed, 3310 examined... 004: 112 changed, 1344 examined... 005: 70 changed, 621 examined... 006: 31 changed, 357 examined... 007: 20 changed, 173 examined... 008: 6 changed, 106 examined... 009: 2 changed, 29 examined... 010: 2 changed, 15 examined... 011: 1 changed, 12 examined... 012: 0 changed, 7 examined... 1 labels changed using aseg 000: 254 total segments, 168 labels (1656 vertices) changed 001: 92 total segments, 6 labels (28 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 28 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1574 vertices marked for relabeling... 1574 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 20 seconds. PIDs (23695 23698) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 01:02:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0051324 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 01:02:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0051324 rh white Waiting for PID 23745 of (23745 23748) to complete... Waiting for PID 23748 of (23745 23748) 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 0051324 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 248467 Total vertex volume 245112 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 1284 875 2245 2.236 0.506 0.168 0.053 24 2.9 G&S_frontomargin 1745 1163 2985 2.317 0.663 0.149 0.042 25 2.9 G&S_occipital_inf 1933 1222 3129 2.161 0.633 0.136 0.050 23 3.9 G&S_paracentral 1784 1081 3152 2.493 0.509 0.124 0.045 22 2.8 G&S_subcentral 785 574 1629 2.119 0.557 0.183 0.070 19 2.4 G&S_transv_frontopol 2329 1606 4147 2.484 0.613 0.126 0.029 25 2.9 G&S_cingul-Ant 1180 858 2048 2.437 0.394 0.113 0.021 9 1.0 G&S_cingul-Mid-Ant 1492 1032 2858 2.728 0.489 0.121 0.034 16 1.9 G&S_cingul-Mid-Post 898 564 1936 2.722 0.687 0.162 0.053 19 1.6 G_cingul-Post-dorsal 383 250 987 2.696 0.900 0.152 0.070 10 0.9 G_cingul-Post-ventral 2692 1672 3415 1.780 0.476 0.152 0.046 47 4.9 G_cuneus 1608 1013 3388 2.686 0.575 0.130 0.043 21 2.6 G_front_inf-Opercular 602 380 1457 2.694 0.440 0.145 0.047 9 1.3 G_front_inf-Orbital 1219 848 2682 2.405 0.506 0.151 0.041 18 2.0 G_front_inf-Triangul 5549 3580 10500 2.350 0.545 0.144 0.044 89 10.1 G_front_middle 8612 5812 20152 2.758 0.626 0.146 0.046 122 15.8 G_front_sup 718 481 1491 2.731 0.690 0.162 0.069 17 2.0 G_Ins_lg&S_cent_ins 977 625 2735 3.375 0.837 0.139 0.066 16 2.2 G_insular_short 2265 1491 4606 2.274 0.576 0.153 0.044 45 4.0 G_occipital_middle 1761 1098 2725 2.063 0.484 0.137 0.041 24 2.9 G_occipital_sup 1950 1276 4824 2.838 0.594 0.155 0.054 36 4.3 G_oc-temp_lat-fusifor 3572 2276 5481 2.041 0.607 0.152 0.055 64 7.3 G_oc-temp_med-Lingual 1105 780 3325 3.057 0.812 0.123 0.032 10 1.3 G_oc-temp_med-Parahip 2107 1448 4727 2.397 0.683 0.152 0.059 48 4.9 G_orbital 2794 1902 6237 2.478 0.475 0.147 0.041 51 4.6 G_pariet_inf-Angular 3719 2518 7453 2.393 0.580 0.146 0.044 64 6.6 G_pariet_inf-Supramar 4059 2707 7336 2.250 0.497 0.133 0.030 58 4.7 G_parietal_sup 2651 1551 3975 2.089 0.591 0.125 0.039 33 4.3 G_postcentral 3522 2002 5764 2.340 0.623 0.133 0.054 53 8.2 G_precentral 3254 2181 7229 2.559 0.648 0.152 0.045 53 5.5 G_precuneus 1165 757 2501 2.457 0.736 0.158 0.060 26 3.4 G_rectus 789 459 1223 2.370 0.948 0.109 0.052 12 1.3 G_subcallosal 654 325 951 2.336 0.469 0.095 0.028 6 0.7 G_temp_sup-G_T_transv 1983 1248 5020 2.767 0.711 0.141 0.045 32 3.6 G_temp_sup-Lateral 965 679 2569 3.231 0.846 0.086 0.022 4 0.7 G_temp_sup-Plan_polar 883 605 1571 2.328 0.451 0.083 0.016 4 0.6 G_temp_sup-Plan_tempo 2605 1894 7183 2.706 0.740 0.172 0.056 59 6.7 G_temporal_inf 2356 1646 6678 2.863 0.621 0.146 0.046 45 4.4 G_temporal_middle 354 245 385 1.789 0.395 0.099 0.021 2 0.3 Lat_Fis-ant-Horizont 340 220 573 2.566 0.560 0.121 0.030 3 0.5 Lat_Fis-ant-Vertical 1354 885 1721 2.284 0.596 0.106 0.028 8 1.7 Lat_Fis-post 2111 1447 2896 1.806 0.457 0.143 0.034 35 3.1 Pole_occipital 1676 1325 5698 2.866 0.820 0.194 0.073 42 5.6 Pole_temporal 3122 2144 3434 1.797 0.540 0.130 0.033 30 4.4 S_calcarine 3439 2395 3672 1.814 0.577 0.124 0.032 27 4.9 S_central 1270 861 1865 2.428 0.580 0.116 0.025 9 1.3 S_cingul-Marginalis 437 308 800 2.659 0.693 0.102 0.023 2 0.4 S_circular_insula_ant 1415 945 1990 2.526 0.617 0.092 0.023 7 1.4 S_circular_insula_inf 1973 1369 2698 2.365 0.501 0.112 0.026 12 2.2 S_circular_insula_sup 907 636 1805 2.394 0.659 0.122 0.032 11 1.4 S_collat_transv_ant 676 458 669 1.811 0.462 0.150 0.045 8 1.2 S_collat_transv_post 3152 2148 4429 2.123 0.490 0.125 0.031 28 4.0 S_front_inf 1335 934 1853 2.057 0.494 0.126 0.025 13 1.4 S_front_middle 2605 1821 3921 2.373 0.440 0.105 0.023 14 2.6 S_front_sup 462 304 556 2.160 0.510 0.118 0.023 3 0.5 S_interm_prim-Jensen 3268 2231 4154 2.044 0.348 0.114 0.023 25 3.1 S_intrapariet&P_trans 1253 852 1383 1.844 0.334 0.104 0.022 6 1.2 S_oc_middle&Lunatus 1531 1019 1858 1.920 0.458 0.109 0.020 11 1.3 S_oc_sup&transversal 920 667 1429 2.272 0.534 0.129 0.027 10 1.1 S_occipital_ant 949 665 1852 2.624 0.553 0.117 0.027 7 1.0 S_oc-temp_lat 1671 1177 2371 2.246 0.486 0.113 0.024 10 1.8 S_oc-temp_med&Lingual 282 208 433 2.066 0.482 0.148 0.037 3 0.4 S_orbital_lateral 903 617 1076 2.137 0.516 0.109 0.017 7 0.7 S_orbital_med-olfact 1335 891 2324 2.685 0.691 0.139 0.038 15 2.1 S_orbital-H_Shaped 2387 1563 3023 2.084 0.512 0.109 0.027 17 2.6 S_parieto_occipital 1430 871 1261 2.017 0.876 0.139 0.030 29 1.6 S_pericallosal 3707 2445 4590 2.037 0.424 0.124 0.030 34 4.6 S_postcentral 1456 1020 2081 2.309 0.481 0.106 0.023 8 1.4 S_precentral-inf-part 1437 1012 1947 2.261 0.460 0.126 0.033 11 2.0 S_precentral-sup-part 745 508 1070 2.456 0.558 0.105 0.021 4 0.5 S_suborbital 1324 931 1912 2.330 0.495 0.124 0.030 11 1.6 S_subparietal 1584 1109 2380 2.415 0.622 0.121 0.028 11 1.9 S_temporal_inf 5834 3970 8211 2.242 0.538 0.109 0.027 43 6.4 S_temporal_sup 444 287 481 2.141 0.438 0.111 0.025 3 0.5 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 0051324 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 254085 Total vertex volume 250426 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 902 626 1715 2.378 0.666 0.160 0.053 16 2.1 G&S_frontomargin 1149 797 2135 2.462 0.545 0.159 0.051 18 2.2 G&S_occipital_inf 2007 1235 2973 2.123 0.612 0.145 0.047 28 3.8 G&S_paracentral 1883 1205 3398 2.497 0.510 0.131 0.033 22 2.6 G&S_subcentral 1321 940 2808 2.316 0.546 0.170 0.057 30 3.5 G&S_transv_frontopol 2805 1970 5432 2.474 0.618 0.135 0.039 40 4.7 G&S_cingul-Ant 1496 1037 2931 2.605 0.608 0.144 0.037 24 2.3 G&S_cingul-Mid-Ant 1706 1186 3211 2.557 0.575 0.136 0.038 20 2.7 G&S_cingul-Mid-Post 638 414 1614 2.794 0.611 0.158 0.043 12 1.1 G_cingul-Post-dorsal 375 235 1003 2.839 0.736 0.149 0.066 8 0.8 G_cingul-Post-ventral 2594 1623 3308 1.771 0.477 0.134 0.036 36 3.8 G_cuneus 1414 924 2841 2.441 0.428 0.125 0.041 20 2.2 G_front_inf-Opercular 390 256 915 2.650 0.473 0.149 0.050 6 0.7 G_front_inf-Orbital 1117 765 2158 2.275 0.567 0.153 0.047 19 2.2 G_front_inf-Triangul 4398 2937 9934 2.483 0.559 0.161 0.059 91 10.6 G_front_middle 7597 5031 18225 2.770 0.667 0.149 0.049 115 15.3 G_front_sup 693 491 1573 2.883 0.746 0.148 0.048 11 1.3 G_Ins_lg&S_cent_ins 874 568 2272 2.993 0.868 0.151 0.063 18 2.2 G_insular_short 2107 1362 4594 2.584 0.522 0.144 0.038 33 3.0 G_occipital_middle 1948 1176 2829 2.101 0.452 0.127 0.036 24 2.7 G_occipital_sup 1694 1116 4256 2.857 0.627 0.155 0.057 31 3.6 G_oc-temp_lat-fusifor 3388 2177 5359 2.078 0.624 0.159 0.055 59 8.1 G_oc-temp_med-Lingual 1629 1114 5093 3.509 0.946 0.138 0.044 24 2.8 G_oc-temp_med-Parahip 2773 1875 6702 2.646 0.653 0.169 0.064 73 7.7 G_orbital 3105 2088 6811 2.543 0.510 0.144 0.039 52 4.7 G_pariet_inf-Angular 3147 2053 6311 2.616 0.536 0.131 0.036 41 4.2 G_pariet_inf-Supramar 2691 1765 5597 2.405 0.501 0.139 0.040 40 4.1 G_parietal_sup 2755 1554 4149 2.155 0.579 0.117 0.038 31 4.0 G_postcentral 3262 1856 5843 2.439 0.644 0.128 0.050 41 7.0 G_precentral 3354 2217 7098 2.565 0.640 0.147 0.043 56 5.3 G_precuneus 949 611 2040 2.308 0.562 0.142 0.049 20 1.7 G_rectus 866 492 1279 2.079 1.422 0.105 0.046 14 1.3 G_subcallosal 493 245 771 2.280 0.584 0.108 0.045 7 1.0 G_temp_sup-G_T_transv 1990 1321 5466 3.038 0.621 0.137 0.037 29 3.0 G_temp_sup-Lateral 959 647 2256 2.876 0.843 0.128 0.056 14 2.3 G_temp_sup-Plan_polar 1011 673 1920 2.632 0.658 0.124 0.034 15 1.3 G_temp_sup-Plan_tempo 2530 1778 7034 2.848 0.746 0.160 0.052 49 5.5 G_temporal_inf 2765 1909 7997 3.008 0.591 0.143 0.043 51 4.8 G_temporal_middle 350 254 422 1.876 0.307 0.101 0.017 2 0.2 Lat_Fis-ant-Horizont 192 145 288 2.458 0.585 0.137 0.043 2 0.2 Lat_Fis-ant-Vertical 1564 1025 1892 2.204 0.431 0.113 0.028 13 1.9 Lat_Fis-post 3938 2492 5674 2.014 0.544 0.154 0.054 62 8.3 Pole_occipital 1798 1302 6154 3.174 0.786 0.158 0.058 34 4.7 Pole_temporal 2861 1970 3374 1.902 0.591 0.136 0.035 30 4.3 S_calcarine 3270 2267 3472 1.769 0.540 0.122 0.031 24 4.3 S_central 1530 1048 2226 2.322 0.531 0.108 0.025 10 1.5 S_cingul-Marginalis 618 416 875 2.411 0.509 0.113 0.040 4 1.0 S_circular_insula_ant 1247 853 1762 2.533 0.493 0.093 0.019 5 1.1 S_circular_insula_inf 1617 1114 2275 2.476 0.500 0.108 0.026 8 1.8 S_circular_insula_sup 1001 736 1649 2.386 0.428 0.092 0.013 4 0.6 S_collat_transv_ant 342 236 413 2.180 0.479 0.127 0.032 2 0.5 S_collat_transv_post 2395 1668 3691 2.187 0.504 0.125 0.027 23 2.5 S_front_inf 2190 1542 2993 2.058 0.446 0.117 0.024 16 2.4 S_front_middle 2670 1881 3928 2.275 0.421 0.118 0.027 19 2.7 S_front_sup 329 233 501 2.543 0.618 0.135 0.028 3 0.4 S_interm_prim-Jensen 3890 2627 4874 2.035 0.461 0.106 0.021 26 3.5 S_intrapariet&P_trans 912 639 1007 1.921 0.386 0.116 0.024 6 0.9 S_oc_middle&Lunatus 1474 1008 1929 2.142 0.448 0.111 0.022 9 1.4 S_oc_sup&transversal 577 389 857 2.210 0.459 0.122 0.028 6 0.7 S_occipital_ant 953 682 1826 2.799 0.520 0.149 0.036 12 1.5 S_oc-temp_lat 1834 1317 2644 2.335 0.569 0.115 0.028 13 2.1 S_oc-temp_med&Lingual 474 333 511 1.765 0.394 0.124 0.023 4 0.5 S_orbital_lateral 870 611 1127 2.311 0.646 0.100 0.017 5 0.6 S_orbital_med-olfact 1220 835 2019 2.455 0.586 0.150 0.046 18 2.4 S_orbital-H_Shaped 2808 1880 3834 2.258 0.606 0.117 0.027 22 3.1 S_parieto_occipital 1834 1142 1465 1.734 0.665 0.143 0.032 33 2.2 S_pericallosal 3580 2366 5118 2.265 0.485 0.112 0.026 26 3.6 S_postcentral 2071 1414 2661 2.155 0.497 0.107 0.024 12 2.0 S_precentral-inf-part 1454 1004 1836 2.182 0.472 0.124 0.030 10 2.0 S_precentral-sup-part 398 292 542 2.204 0.560 0.132 0.024 4 0.4 S_suborbital 1251 886 1934 2.441 0.497 0.111 0.028 7 1.3 S_subparietal 1470 1032 2176 2.549 0.539 0.142 0.032 14 2.4 S_temporal_inf 6518 4514 10057 2.423 0.508 0.107 0.023 40 6.5 S_temporal_sup 403 275 568 2.492 0.386 0.122 0.020 3 0.4 S_temporal_transverse PIDs (23745 23748) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 01:03:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051324 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 01:03:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051324 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 23815 of (23815 23818) to complete... Waiting for PID 23818 of (23815 23818) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051324 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... 1228 labels changed using aseg relabeling using gibbs priors... 000: 2146 changed, 147611 examined... 001: 503 changed, 9705 examined... 002: 123 changed, 2827 examined... 003: 63 changed, 739 examined... 004: 24 changed, 354 examined... 005: 16 changed, 126 examined... 006: 16 changed, 92 examined... 007: 9 changed, 71 examined... 008: 6 changed, 58 examined... 009: 4 changed, 37 examined... 010: 4 changed, 24 examined... 011: 3 changed, 16 examined... 012: 4 changed, 16 examined... 013: 2 changed, 23 examined... 014: 0 changed, 10 examined... 229 labels changed using aseg 000: 57 total segments, 24 labels (453 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 794 vertices marked for relabeling... 794 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051324 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... 1172 labels changed using aseg relabeling using gibbs priors... 000: 2189 changed, 147034 examined... 001: 486 changed, 10062 examined... 002: 126 changed, 2726 examined... 003: 52 changed, 710 examined... 004: 26 changed, 288 examined... 005: 12 changed, 132 examined... 006: 6 changed, 69 examined... 007: 1 changed, 38 examined... 008: 1 changed, 7 examined... 009: 1 changed, 7 examined... 010: 0 changed, 7 examined... 191 labels changed using aseg 000: 55 total segments, 22 labels (256 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, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1300 vertices marked for relabeling... 1300 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. PIDs (23815 23818) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 01:03:41 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0051324 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 01:03:41 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0051324 rh white Waiting for PID 23865 of (23865 23868) to complete... Waiting for PID 23868 of (23865 23868) 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 0051324 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 248467 Total vertex volume 245112 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 1872 1290 3320 2.535 0.527 0.121 0.021 22 1.6 caudalanteriorcingulate 3397 2204 5328 2.363 0.510 0.118 0.033 32 4.5 caudalmiddlefrontal 3803 2397 4977 1.901 0.482 0.145 0.041 55 6.4 cuneus 593 435 1977 3.286 0.871 0.133 0.037 5 0.8 entorhinal 4061 2780 8718 2.596 0.639 0.142 0.042 58 7.3 fusiform 6860 4707 12010 2.250 0.509 0.129 0.032 86 9.1 inferiorparietal 4864 3490 11571 2.601 0.721 0.158 0.048 87 11.1 inferiortemporal 1876 1210 3057 2.242 0.877 0.140 0.041 34 2.9 isthmuscingulate 8222 5489 12207 2.021 0.563 0.137 0.035 113 11.4 lateraloccipital 4260 2891 8090 2.503 0.682 0.146 0.048 74 8.2 lateralorbitofrontal 5064 3281 7209 2.020 0.574 0.142 0.048 75 9.5 lingual 2786 1799 4906 2.354 0.710 0.124 0.044 42 5.3 medialorbitofrontal 5903 4161 13474 2.657 0.683 0.135 0.038 83 9.1 middletemporal 886 614 1962 2.605 0.782 0.117 0.031 8 1.0 parahippocampal 2974 1947 5090 2.424 0.607 0.123 0.042 28 5.2 paracentral 2417 1592 4572 2.600 0.530 0.126 0.036 27 3.4 parsopercularis 1014 686 2133 2.499 0.536 0.124 0.034 9 1.5 parsorbitalis 2738 1875 4646 2.180 0.538 0.135 0.036 31 4.0 parstriangularis 2410 1674 2467 1.629 0.400 0.133 0.036 27 3.4 pericalcarine 8118 5184 11349 2.038 0.613 0.126 0.037 89 12.2 postcentral 2186 1459 4031 2.683 0.634 0.144 0.040 36 3.2 posteriorcingulate 8558 5388 12997 2.300 0.602 0.126 0.043 96 15.3 precentral 6466 4330 11386 2.368 0.617 0.131 0.036 76 9.1 precuneus 2013 1342 3721 2.583 0.726 0.131 0.031 26 2.6 rostralanteriorcingulate 7199 4858 11948 2.206 0.505 0.143 0.040 99 11.9 rostralmiddlefrontal 12146 8382 25238 2.564 0.637 0.141 0.042 159 21.1 superiorfrontal 8424 5544 13340 2.172 0.465 0.123 0.027 94 9.1 superiorparietal 7649 5166 14983 2.528 0.707 0.114 0.033 78 10.2 superiortemporal 6273 4226 10832 2.330 0.560 0.137 0.037 84 9.5 supramarginal 815 410 1164 2.480 0.480 0.099 0.036 8 1.1 transversetemporal 3190 2156 6409 2.811 0.828 0.124 0.046 38 5.6 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 0051324 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 254085 Total vertex volume 250426 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 1417 971 2605 2.287 0.811 0.151 0.034 29 2.1 caudalanteriorcingulate 3473 2294 5576 2.325 0.494 0.125 0.035 33 4.6 caudalmiddlefrontal 3417 2201 4416 1.843 0.473 0.132 0.034 43 4.7 cuneus 622 444 2274 3.933 0.631 0.124 0.034 5 0.8 entorhinal 3544 2465 8003 2.778 0.686 0.140 0.042 48 5.8 fusiform 7292 5056 13004 2.381 0.528 0.126 0.029 78 8.7 inferiorparietal 4979 3521 11994 2.766 0.733 0.146 0.044 77 9.1 inferiortemporal 1532 1000 2728 2.344 0.840 0.145 0.044 26 2.6 isthmuscingulate 7455 4852 11773 2.194 0.551 0.145 0.044 104 12.6 lateraloccipital 4527 3069 8810 2.537 0.663 0.160 0.060 96 12.0 lateralorbitofrontal 5161 3451 7617 2.053 0.586 0.148 0.046 73 9.7 lingual 2549 1630 4429 2.160 0.922 0.123 0.039 42 3.6 medialorbitofrontal 6225 4371 14265 2.756 0.644 0.132 0.034 80 9.2 middletemporal 981 662 2349 2.881 0.972 0.122 0.040 13 1.8 parahippocampal 3144 2037 4581 2.227 0.625 0.139 0.046 38 5.8 paracentral 2456 1643 4254 2.373 0.437 0.121 0.034 28 3.1 parsopercularis 990 660 2033 2.474 0.601 0.155 0.057 20 2.5 parsorbitalis 2221 1558 3792 2.190 0.562 0.136 0.038 27 3.3 parstriangularis 2829 1816 3023 1.739 0.449 0.134 0.040 33 4.9 pericalcarine 8370 5279 12327 2.138 0.639 0.118 0.031 80 10.5 postcentral 2260 1494 4048 2.344 0.738 0.146 0.039 36 3.5 posteriorcingulate 8180 5185 12659 2.291 0.586 0.123 0.039 80 13.6 precentral 7268 4869 12863 2.458 0.621 0.132 0.036 88 10.1 precuneus 1240 863 2568 2.732 0.660 0.143 0.044 26 2.3 rostralanteriorcingulate 6141 4282 11041 2.219 0.589 0.145 0.043 94 11.6 rostralmiddlefrontal 14525 9926 29798 2.571 0.620 0.140 0.042 187 25.1 superiorfrontal 7630 4967 12073 2.212 0.491 0.119 0.029 78 8.9 superiorparietal 7756 5266 16753 2.779 0.661 0.123 0.035 89 11.3 superiortemporal 6103 3999 10875 2.497 0.544 0.124 0.032 71 7.8 supramarginal 677 350 907 2.246 0.484 0.115 0.041 9 1.3 transversetemporal 3714 2520 6987 2.699 0.686 0.126 0.039 41 5.7 insula PIDs (23865 23868) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 01:04:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts pctsurfcon --s 0051324 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 01:04:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts pctsurfcon --s 0051324 --rh-only Waiting for PID 23933 of (23933 23943) to complete... Waiting for PID 23943 of (23933 23943) to complete... pctsurfcon --s 0051324 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts/pctsurfcon.log Sun Oct 8 01:04:24 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-6.0.0/0051324/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-900 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-6.0.0/0051324/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23933/lh.wm.mgh --regheader 0051324 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 = 79944 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23933/lh.wm.mgh Dim: 147611 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23933/lh.gm.mgh --projfrac 0.3 --regheader 0051324 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 = 95750 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23933/lh.gm.mgh Dim: 147611 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23933/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23933/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.w-g.pct.mgh --annot 0051324 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/surf/lh.w-g.pct.mgh --annot 0051324 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-900 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/surf/lh.w-g.pct.mgh Vertex Area is 0.667612 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 0051324 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/scripts/pctsurfcon.log Sun Oct 8 01:04:24 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-6.0.0/0051324/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-900 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-6.0.0/0051324/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23943/rh.wm.mgh --regheader 0051324 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 = 79606 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23943/rh.wm.mgh Dim: 147034 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23943/rh.gm.mgh --projfrac 0.3 --regheader 0051324 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 = 95550 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23943/rh.gm.mgh Dim: 147034 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23943/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/tmp.pctsurfcon.23943/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.w-g.pct.mgh --annot 0051324 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/surf/rh.w-g.pct.mgh --annot 0051324 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-900 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/surf/rh.w-g.pct.mgh Vertex Area is 0.667861 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 (23933 23943) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 01:04:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 3016 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 3600 voxels changed to hypointensity... 6630 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 01:04:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324 mri_aparc2aseg --s 0051324 --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 01:04:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324 mri_aparc2aseg --s 0051324 --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 01:04:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324 mri_aparc2aseg --s 0051324 --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 24109 of (24109 24112 24115) to complete... Waiting for PID 24112 of (24109 24112 24115) to complete... Waiting for PID 24115 of (24109 24112 24115) to complete... mri_aparc2aseg --s 0051324 --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 0051324 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/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-6.0.0/0051324/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.97 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 60 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 58 rescaling Left_Thalamus from 94 --> 106 rescaling Left_Thalamus_Proper from 84 --> 93 rescaling Left_Caudate from 75 --> 71 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 102 rescaling Third_Ventricle from 25 --> 19 rescaling Fourth_Ventricle from 22 --> 15 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 64 rescaling Left_Amygdala from 56 --> 67 rescaling CSF from 32 --> 32 rescaling Left_Accumbens_area from 62 --> 64 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 68 rescaling Right_Lateral_Ventricle from 13 --> 13 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 61 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 74 rescaling Right_Putamen from 80 --> 80 rescaling Right_Pallidum from 97 --> 100 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 66 rescaling Right_Accumbens_area from 65 --> 72 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 29 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 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 = 492112 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 135 changed. pass 2: 9 changed. pass 3: 2 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/aparc+aseg.mgz mri_aparc2aseg --s 0051324 --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 0051324 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/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-6.0.0/0051324/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.97 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 60 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 58 rescaling Left_Thalamus from 94 --> 106 rescaling Left_Thalamus_Proper from 84 --> 93 rescaling Left_Caudate from 75 --> 71 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 102 rescaling Third_Ventricle from 25 --> 19 rescaling Fourth_Ventricle from 22 --> 15 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 64 rescaling Left_Amygdala from 56 --> 67 rescaling CSF from 32 --> 32 rescaling Left_Accumbens_area from 62 --> 64 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 68 rescaling Right_Lateral_Ventricle from 13 --> 13 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 61 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 74 rescaling Right_Putamen from 80 --> 80 rescaling Right_Pallidum from 97 --> 100 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 66 rescaling Right_Accumbens_area from 65 --> 72 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 29 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 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 = 491899 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 135 changed. pass 2: 9 changed. pass 3: 2 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0051324 --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 0051324 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/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-6.0.0/0051324/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.97 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 60 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 58 rescaling Left_Thalamus from 94 --> 106 rescaling Left_Thalamus_Proper from 84 --> 93 rescaling Left_Caudate from 75 --> 71 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 102 rescaling Third_Ventricle from 25 --> 19 rescaling Fourth_Ventricle from 22 --> 15 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 64 rescaling Left_Amygdala from 56 --> 67 rescaling CSF from 32 --> 32 rescaling Left_Accumbens_area from 62 --> 64 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 68 rescaling Right_Lateral_Ventricle from 13 --> 13 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 61 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 74 rescaling Right_Putamen from 80 --> 80 rescaling Right_Pallidum from 97 --> 100 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 66 rescaling Right_Accumbens_area from 65 --> 72 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 29 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 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 = 491899 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 135 changed. pass 2: 9 changed. pass 3: 2 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (24109 24112 24115) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 01:12:10 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 01:12:10 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-6.0.0/0051324/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-900 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-6.0.0/0051324/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-900 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 01:12:10 CEST 2017 Ended at Sun Oct 8 01:12:17 CEST 2017 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 01:12:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324 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 0051324 $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 0051324 sysname Linux hostname tars-900 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1425500 mm^3 (det: 1.366612 ) Computing euler number orig.nofix lheno = -144, rheno = -100 orig.nofix lhholes = 73, rhholes = 51 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 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 01:14:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324 mri_aparc2aseg --s 0051324 --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 0051324 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-6.0.0/0051324/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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-6.0.0/0051324/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8429 vertices from left hemi Ripped 8356 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-6.0.0/0051324/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 = 961590 Used brute-force search on 164 voxels Fixing Parahip LH WM Found 5 clusters 0 k 1.000000 1 k 1.000000 2 k 10.000000 3 k 5.000000 4 k 1316.000000 Fixing Parahip RH WM Found 2 clusters 0 k 1362.000000 1 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 0051324 --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 0051324 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-900 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1425500 mm^3 (det: 1.366612 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 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-6.0.0/0051324/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 01:23:29 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 0051324 --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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 25392 of (25392 25398 25404 25409 25416) to complete... Waiting for PID 25398 of (25392 25398 25404 25409 25416) to complete... Waiting for PID 25404 of (25392 25398 25404 25409 25416) to complete... Waiting for PID 25409 of (25392 25398 25404 25409 25416) to complete... Waiting for PID 25416 of (25392 25398 25404 25409 25416) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 507 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4636 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 1030 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8939 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 216 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4293 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 447 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6430 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 1100 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6884 mri_label2label: Done PIDs (25392 25398 25404 25409 25416) 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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 25528 of (25528 25534 25540 25545) to complete... Waiting for PID 25534 of (25528 25534 25540 25545) to complete... Waiting for PID 25540 of (25528 25534 25540 25545) to complete... Waiting for PID 25545 of (25528 25534 25540 25545) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 572 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4642 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 1967 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15556 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 430 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4611 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 976 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4398 mri_label2label: Done PIDs (25528 25534 25540 25545) 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 0051324 --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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 25588 of (25588 25594 25600 25605 25611) to complete... Waiting for PID 25594 of (25588 25594 25600 25605 25611) to complete... Waiting for PID 25600 of (25588 25594 25600 25605 25611) to complete... Waiting for PID 25605 of (25588 25594 25600 25605 25611) to complete... Waiting for PID 25611 of (25588 25594 25600 25605 25611) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 1993 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6634 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 3787 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11901 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 430 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2448 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1352 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1275 mri_label2label: Done PIDs (25588 25594 25600 25605 25611) 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 0051324 --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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 25660 of (25660 25666 25672 25677 25684) to complete... Waiting for PID 25666 of (25660 25666 25672 25677 25684) to complete... Waiting for PID 25672 of (25660 25666 25672 25677 25684) to complete... Waiting for PID 25677 of (25660 25666 25672 25677 25684) to complete... Waiting for PID 25684 of (25660 25666 25672 25677 25684) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 125 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1139 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 372 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2464 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1564 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2137 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 478 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2797 mri_label2label: Done PIDs (25660 25666 25672 25677 25684) 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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 25749 of (25749 25755 25761 25765) to complete... Waiting for PID 25755 of (25749 25755 25761 25765) to complete... Waiting for PID 25761 of (25749 25755 25761 25765) to complete... Waiting for PID 25765 of (25749 25755 25761 25765) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1711 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 1030 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8065 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 167 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2079 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 403 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1554 mri_label2label: Done PIDs (25749 25755 25761 25765) 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 0051324 --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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 25859 of (25859 25865 25871 25877 25883) to complete... Waiting for PID 25865 of (25859 25865 25871 25877 25883) to complete... Waiting for PID 25871 of (25859 25865 25871 25877 25883) to complete... Waiting for PID 25877 of (25859 25865 25871 25877 25883) to complete... Waiting for PID 25883 of (25859 25865 25871 25877 25883) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 1461 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4866 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 1743 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 5077 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 651 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 495 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147611 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 472 mri_label2label: Done PIDs (25859 25865 25871 25877 25883) completed and logs appended. mris_label2annot --s 0051324 --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-6.0.0/0051324/label cmdline mris_label2annot --s 0051324 --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-900 machine x86_64 user ntraut subject 0051324 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-6.0.0/0051324/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 101131 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/lh.BA_exvivo.annot mris_label2annot --s 0051324 --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-6.0.0/0051324/label cmdline mris_label2annot --s 0051324 --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-900 machine x86_64 user ntraut subject 0051324 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-6.0.0/0051324/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 119472 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0051324 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 248467 Total vertex volume 245112 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 1206 698 1994 2.237 0.551 0.146 0.049 20 2.6 BA1_exvivo 4924 3118 7038 2.134 0.502 0.121 0.030 49 6.0 BA2_exvivo 1144 800 1089 1.706 0.404 0.149 0.041 13 1.9 BA3a_exvivo 2511 1661 3258 1.753 0.564 0.121 0.032 24 3.3 BA3b_exvivo 2235 1343 3487 2.328 0.641 0.135 0.054 27 5.3 BA4a_exvivo 1553 1055 1944 2.062 0.660 0.127 0.042 15 3.1 BA4p_exvivo 10382 6797 20664 2.579 0.615 0.133 0.042 125 17.5 BA6_exvivo 2295 1489 4183 2.516 0.540 0.122 0.036 24 3.2 BA44_exvivo 3418 2353 6199 2.296 0.567 0.141 0.038 44 5.2 BA45_exvivo 4222 2874 5052 1.702 0.472 0.136 0.040 54 6.7 V1_exvivo 9413 6054 12639 1.927 0.514 0.144 0.042 139 15.7 V2_exvivo 2019 1397 3863 2.402 0.581 0.143 0.036 29 2.9 MT_exvivo 530 369 1848 3.349 0.754 0.121 0.030 5 0.7 perirhinal_exvivo 628 460 1603 2.764 0.780 0.154 0.053 11 1.5 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 0051324 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 248467 Total vertex volume 245112 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 811 434 1194 2.124 0.552 0.151 0.050 15 1.9 BA1_exvivo 1991 1238 2631 2.069 0.520 0.115 0.030 18 2.4 BA2_exvivo 933 654 849 1.674 0.402 0.156 0.044 12 1.7 BA3a_exvivo 1477 1030 1497 1.442 0.274 0.113 0.027 11 1.7 BA3b_exvivo 2175 1320 3248 2.295 0.654 0.130 0.051 25 4.8 BA4a_exvivo 1218 857 1515 2.018 0.666 0.130 0.039 11 2.1 BA4p_exvivo 6151 3940 12483 2.620 0.635 0.136 0.046 78 11.9 BA6_exvivo 1448 938 2744 2.508 0.534 0.133 0.042 19 2.4 BA44_exvivo 1426 976 2895 2.426 0.531 0.145 0.039 19 2.1 BA45_exvivo 4504 3037 5525 1.718 0.480 0.141 0.042 63 7.6 V1_exvivo 4822 3100 5992 1.827 0.488 0.146 0.041 71 8.0 V2_exvivo 570 393 999 2.296 0.529 0.138 0.033 7 0.8 MT_exvivo 281 192 1079 3.547 0.714 0.109 0.024 2 0.3 perirhinal_exvivo 332 239 617 2.591 0.649 0.113 0.031 2 0.4 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 01:26:50 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 0051324 --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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 26084 of (26084 26090 26096 26101 26108) to complete... Waiting for PID 26090 of (26084 26090 26096 26101 26108) to complete... Waiting for PID 26096 of (26084 26090 26096 26101 26108) to complete... Waiting for PID 26101 of (26084 26090 26096 26101 26108) to complete... Waiting for PID 26108 of (26084 26090 26096 26101 26108) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 545 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4507 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 866 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7553 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 228 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4208 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 425 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4947 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 890 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6637 mri_label2label: Done PIDs (26084 26090 26096 26101 26108) 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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 26214 of (26214 26220 26226 26232) to complete... Waiting for PID 26220 of (26214 26220 26226 26232) to complete... Waiting for PID 26226 of (26214 26220 26226 26232) to complete... Waiting for PID 26232 of (26214 26220 26226 26232) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 357 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4830 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 1772 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 14028 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 1144 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8056 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 983 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6338 mri_label2label: Done PIDs (26214 26220 26226 26232) 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 0051324 --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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 26276 of (26276 26282 26288 26294 26299) to complete... Waiting for PID 26282 of (26276 26282 26288 26294 26299) to complete... Waiting for PID 26288 of (26276 26282 26288 26294 26299) to complete... Waiting for PID 26294 of (26276 26282 26288 26294 26299) to complete... Waiting for PID 26299 of (26276 26282 26288 26294 26299) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 2363 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 7090 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 3520 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11536 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 302 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2234 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 194 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1232 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 914 mri_label2label: Done PIDs (26276 26282 26288 26294 26299) 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 0051324 --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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 26508 of (26508 26514 26520 26526 26531) to complete... Waiting for PID 26514 of (26508 26514 26520 26526 26531) to complete... Waiting for PID 26520 of (26508 26514 26520 26526 26531) to complete... Waiting for PID 26526 of (26508 26514 26520 26526 26531) to complete... Waiting for PID 26531 of (26508 26514 26520 26526 26531) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1038 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 321 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 3009 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1755 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 212 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2395 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 316 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1704 mri_label2label: Done PIDs (26508 26514 26520 26526 26531) 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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 26642 of (26642 26648 26654 26659) to complete... Waiting for PID 26648 of (26642 26648 26654 26659) to complete... Waiting for PID 26654 of (26642 26648 26654 26659) to complete... Waiting for PID 26659 of (26642 26648 26654 26659) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1585 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 883 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7842 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 190 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1202 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1344 mri_label2label: Done PIDs (26642 26648 26654 26659) 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 0051324 --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 0051324 --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 0051324 --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 0051324 --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 0051324 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 26715 of (26715 26721 26727 26733 26738) to complete... Waiting for PID 26721 of (26715 26721 26727 26733 26738) to complete... Waiting for PID 26727 of (26715 26721 26727 26733 26738) to complete... Waiting for PID 26733 of (26715 26721 26727 26733 26738) to complete... Waiting for PID 26738 of (26715 26721 26727 26733 26738) 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 1641 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4873 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 297 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 118 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 812 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 0051324 --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 = 0051324 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-6.0.0/0051324/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 147034 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 346 mri_label2label: Done PIDs (26715 26721 26727 26733 26738) completed and logs appended. mris_label2annot --s 0051324 --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-6.0.0/0051324/label cmdline mris_label2annot --s 0051324 --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-900 machine x86_64 user ntraut subject 0051324 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-6.0.0/0051324/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 100347 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/label/rh.BA_exvivo.annot mris_label2annot --s 0051324 --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-6.0.0/0051324/label cmdline mris_label2annot --s 0051324 --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-900 machine x86_64 user ntraut subject 0051324 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-6.0.0/0051324/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 120392 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/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 0051324 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 254085 Total vertex volume 250426 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 1107 623 1844 2.275 0.556 0.128 0.042 14 1.8 BA1_exvivo 4308 2700 6475 2.303 0.490 0.110 0.028 34 4.6 BA2_exvivo 1195 834 1095 1.708 0.378 0.146 0.038 13 1.8 BA3a_exvivo 2299 1518 2710 1.641 0.532 0.125 0.032 24 3.2 BA3b_exvivo 1971 1250 2797 2.114 0.595 0.144 0.048 24 4.2 BA4a_exvivo 1323 902 1793 2.159 0.545 0.126 0.039 10 2.3 BA4p_exvivo 9239 5890 18116 2.588 0.663 0.134 0.045 106 16.9 BA6_exvivo 4186 2780 7137 2.366 0.474 0.115 0.030 40 4.9 BA44_exvivo 4227 2945 7607 2.229 0.566 0.143 0.042 64 7.1 BA45_exvivo 4761 3084 5947 1.821 0.502 0.140 0.043 63 8.6 V1_exvivo 9070 5868 12725 2.013 0.534 0.147 0.045 126 16.2 V2_exvivo 1851 1237 2946 2.290 0.552 0.126 0.030 18 2.2 MT_exvivo 686 484 2677 3.932 0.667 0.127 0.038 7 1.0 perirhinal_exvivo 464 306 1841 3.995 0.559 0.149 0.047 7 1.0 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 0051324 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051324/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 254085 Total vertex volume 250426 (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) = 1425500 mm^3 (det: 1.366612 ) lhCtxGM: 242802.422 242303.000 diff= 499.4 pctdiff= 0.206 rhCtxGM: 248736.437 248315.000 diff= 421.4 pctdiff= 0.169 lhCtxWM: 234785.593 234919.000 diff= -133.4 pctdiff=-0.057 rhCtxWM: 235609.475 236727.000 diff=-1117.5 pctdiff=-0.474 SubCortGMVol 57917.000 SupraTentVol 1056377.927 (1052299.000) diff=4078.927 pctdiff=0.386 SupraTentVolNotVent 1024382.927 (1020304.000) diff=4078.927 pctdiff=0.398 BrainSegVol 1121716.000 (1119271.000) diff=2445.000 pctdiff=0.218 BrainSegVolNotVent 1085717.000 (1085178.927) diff=538.073 pctdiff=0.050 BrainSegVolNotVent 1085717.000 CerebellumVol 65205.000 VentChorVol 31995.000 3rd4th5thCSF 4004.000 CSFVol 1559.000, OptChiasmVol 208.000 MaskVol 1577046.000 829 408 1136 2.136 0.559 0.118 0.040 11 1.3 BA1_exvivo 2360 1424 3658 2.345 0.515 0.104 0.027 17 2.4 BA2_exvivo 1018 723 890 1.691 0.345 0.151 0.041 10 1.6 BA3a_exvivo 1773 1208 1828 1.461 0.332 0.118 0.029 16 2.2 BA3b_exvivo 1335 829 1670 1.957 0.589 0.154 0.052 20 3.1 BA4a_exvivo 1045 732 1447 2.195 0.569 0.123 0.038 7 1.8 BA4p_exvivo 5791 3604 11063 2.597 0.637 0.132 0.046 66 10.9 BA6_exvivo 1006 677 1739 2.338 0.403 0.118 0.033 11 1.3 BA44_exvivo 1024 718 1927 2.205 0.546 0.155 0.047 18 2.0 BA45_exvivo 4623 2971 5520 1.804 0.491 0.140 0.043 61 8.5 V1_exvivo 4904 3183 7120 1.984 0.558 0.153 0.048 73 9.5 V2_exvivo 227 144 519 2.669 0.548 0.115 0.030 2 0.2 MT_exvivo 397 281 1432 3.870 0.662 0.116 0.034 3 0.5 perirhinal_exvivo 310 225 1054 4.030 0.535 0.132 0.031 3 0.4 entorhinal_exvivo Started at Sat Oct 7 16:58:33 CEST 2017 Ended at Sun Oct 8 01:30:12 CEST 2017 #@#%# recon-all-run-time-hours 8.528 recon-all -s 0051324 finished without error at Sun Oct 8 01:30:12 CEST 2017