Sat Oct 7 16:52:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0051362 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_a/0051362/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0051362 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-382 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: 264648728 256941216 7707512 1743000 0 252490564 -/+ buffers/cache: 4450652 260198076 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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: 2017/10/07-14:52:35-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-382 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-6.0.0/0051362 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_a/0051362/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/MaxMun_a/0051362/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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_a/0051362/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-6.0.0/0051362/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 16:52:38 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 16:52:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-382 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 16:52:47 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.27153 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27153/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27153/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.27153/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 16:52:49 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.27153/nu0.mnc ./tmp.mri_nu_correct.mni.27153/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27153/0/ -iterations 1000 -distance 50 [ntraut@tars-382:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/] [2017-10-07 16:52:49] 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.27153/0/ ./tmp.mri_nu_correct.mni.27153/nu0.mnc ./tmp.mri_nu_correct.mni.27153/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 35 CV of field change: 0.000960407 mri_convert ./tmp.mri_nu_correct.mni.27153/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.27153/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.27153/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 16:53:52 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 16:53:52 CEST 2017 Ended at Sat Oct 7 16:54:34 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 16:54:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7202, 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-6.0.0/0051362/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/transforms/talairach_avi.log TalAviQA: 0.97897 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 16:54:37 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-6.0.0/0051362/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-382 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 16:54:37 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.27866 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27866/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27866/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.27866/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 16:54:39 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.27866/nu0.mnc ./tmp.mri_nu_correct.mni.27866/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27866/0/ [ntraut@tars-382:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/] [2017-10-07 16:54:39] 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.27866/0/ ./tmp.mri_nu_correct.mni.27866/nu0.mnc ./tmp.mri_nu_correct.mni.27866/nu1.imp Processing:.................................................................Done 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./tmp.mri_nu_correct.mni.27866/1/ [ntraut@tars-382:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/] [2017-10-07 16:55:29] 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.27866/1/ ./tmp.mri_nu_correct.mni.27866/nu1.mnc ./tmp.mri_nu_correct.mni.27866/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 Number of iterations: 16 CV of field change: 0.000999003 mri_binarize --i ./tmp.mri_nu_correct.mni.27866/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27866/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-6.0.0/0051362/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.27866/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27866/ones.mgz sysname Linux hostname tars-382 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.27866/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.27866/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.27866/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27866/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.27866/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27866/input.mean.dat sysname Linux hostname tars-382 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27866/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.27866/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27866/ones.mgz --i ./tmp.mri_nu_correct.mni.27866/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27866/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.27866/ones.mgz --i ./tmp.mri_nu_correct.mni.27866/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27866/output.mean.dat sysname Linux hostname tars-382 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27866/ones.mgz Loading ./tmp.mri_nu_correct.mni.27866/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.27866/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.27866/nu2.mnc ./tmp.mri_nu_correct.mni.27866/nu2.mnc mul 1.01814933025425786766 Saving result to './tmp.mri_nu_correct.mni.27866/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.27866/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.27866/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.27866/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 9 seconds. mapping (13, 142) to ( 3, 110) Sat Oct 7 16:56:40 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 16:56:41 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 1.07462 0.01554 -0.05627 0.84462; 0.07216 1.01207 0.32031 -7.10692; -0.00487 -0.35952 1.10685 -30.69774; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 19 Starting OpenSpline(): npoints = 19 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 107 gm peak at 66 (66), valley at 30 (30) csf peak at 33, setting threshold to 55 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 64 (64), valley at 30 (30) csf peak at 32, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 13 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 16:58:55 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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, 18, 17) --> (208, 168, 191) using (99, 68, 104) as brain centroid... mean wm in atlas = 108, using box (79,50,83) --> (119, 86,125) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 7.6 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -4.727 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.481188 @ (-9.091, 27.273, -9.091) max log p = -4.463854 @ (13.636, 4.545, 4.545) max log p = -4.383637 @ (-2.273, -6.818, -6.818) max log p = -4.374402 @ (-1.136, -3.409, 3.409) max log p = -4.367147 @ (0.568, 3.977, -1.705) max log p = -4.367147 @ (0.000, 0.000, 0.000) Found translation: (1.7, 25.6, -9.7): log p = -4.367 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.058, old_max_log_p =-4.367 (thresh=-4.4) 1.07500 0.00000 0.00000 -15.03327; 0.00000 1.14759 0.45276 -38.73721; 0.00000 -0.43171 0.98772 42.16184; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.041, old_max_log_p =-4.058 (thresh=-4.1) 1.14574 -0.16103 -0.06353 1.14499; 0.12979 1.05244 0.41522 -40.62932; 0.00000 -0.43171 0.98772 42.16184; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.031, old_max_log_p =-4.041 (thresh=-4.0) 1.06628 -0.01489 -0.02412 -9.39476; -0.02362 1.19475 0.31027 -24.06453; 0.01821 -0.31245 1.11098 11.98691; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.031, old_max_log_p =-4.031 (thresh=-4.0) 1.06628 -0.01489 -0.02412 -9.39476; -0.02362 1.19475 0.31027 -24.06453; 0.01821 -0.31245 1.11098 11.98691; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.938, old_max_log_p =-4.031 (thresh=-4.0) 1.12572 -0.04849 0.04787 -20.03093; -0.02676 1.12839 0.36782 -21.21245; -0.04728 -0.36655 1.02715 38.29771; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.928, old_max_log_p =-3.938 (thresh=-3.9) 1.10488 -0.08378 0.03514 -11.99217; 0.01028 1.14732 0.37611 -29.01690; -0.04640 -0.35968 1.00789 39.65944; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.913, old_max_log_p =-3.928 (thresh=-3.9) 1.10578 -0.07445 0.00141 -9.22585; 0.01329 1.16839 0.30939 -25.86450; -0.00927 -0.28109 1.01160 25.80788; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.908, old_max_log_p =-3.913 (thresh=-3.9) 1.08505 -0.07305 0.00138 -6.71145; 0.01298 1.15856 0.34232 -26.68442; -0.00952 -0.31318 0.98217 32.84350; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.908, old_max_log_p =-3.908 (thresh=-3.9) 1.08505 -0.07305 0.00138 -6.71145; 0.01298 1.15856 0.34232 -26.68442; -0.00952 -0.31318 0.98217 32.84350; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.887, old_max_log_p =-3.908 (thresh=-3.9) 1.08597 -0.08705 -0.02005 -3.27618; 0.03049 1.16840 0.30982 -27.65715; 0.00899 -0.27695 0.99630 24.35400; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 10 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.877, old_max_log_p =-3.887 (thresh=-3.9) 1.08724 -0.08715 -0.02007 -3.42635; 0.03067 1.17020 0.31908 -28.95969; 0.00877 -0.28750 0.99723 25.44662; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 11 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.877, old_max_log_p =-3.877 (thresh=-3.9) 1.08724 -0.08715 -0.02007 -3.42635; 0.03067 1.17020 0.31908 -28.95969; 0.00877 -0.28750 0.99723 25.44662; 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 1.08724 -0.08715 -0.02007 -3.42635; 0.03067 1.17020 0.31908 -28.95969; 0.00877 -0.28750 0.99723 25.44662; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.08724 -0.08715 -0.02007 -3.42635; 0.03067 1.17020 0.31908 -28.95969; 0.00877 -0.28750 0.99723 25.44662; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 014: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.08724 -0.08715 -0.02007 -3.42635; 0.03067 1.17020 0.31908 -28.95969; 0.00877 -0.28750 0.99723 25.44662; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.877 (old=-4.727) transform before final EM align: 1.08724 -0.08715 -0.02007 -3.42635; 0.03067 1.17020 0.31908 -28.95969; 0.00877 -0.28750 0.99723 25.44662; 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 1.08724 -0.08715 -0.02007 -3.42635; 0.03067 1.17020 0.31908 -28.95969; 0.00877 -0.28750 0.99723 25.44662; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.08724 -0.08715 -0.02007 -3.42635; 0.03067 1.17020 0.31908 -28.95969; 0.00877 -0.28750 0.99723 25.44662; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 016: -log(p) = 4.3 tol 0.000000 final transform: 1.08724 -0.08715 -0.02007 -3.42635; 0.03067 1.17020 0.31908 -28.95969; 0.00877 -0.28750 0.99723 25.44662; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1966.520043 mri_em_register stimesec 2.616602 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 157604 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 285 mri_em_register ru_nivcsw 11258 registration took 16 minutes and 51 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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=126 y=82 z=109 r=68 first estimation of the main basin volume: 1343203 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=148, y=80, z=80, Imax=255 CSF=17, 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=8640522601 voxels, voxel volume =1.000 = 8640522601 mmm3 = 8640522.240 cm3 done. PostAnalyze...Basin Prior 209 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=127,y=93, z=105, r=9665 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=28 , nb = 45406 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = -1037683078 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=24 , nb = -1045574127 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=29 , nb = 1075535482 LEFT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=27 , nb = 1078867158 OTHER CSF_MIN=0, CSF_intensity=12, CSF_MAX=42 , nb = 1075114488 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 28, 29, 32, 63 after analyzing : 28, 31, 32, 39 RIGHT_CER before analyzing : 24, 41, 55, 71 after analyzing : 24, 50, 55, 55 LEFT_CER before analyzing : 24, 27, 32, 63 after analyzing : 24, 30, 32, 38 RIGHT_BRAIN before analyzing : 29, 30, 32, 63 after analyzing : 29, 31, 32, 39 LEFT_BRAIN before analyzing : 27, 29, 32, 60 after analyzing : 27, 31, 32, 38 OTHER before analyzing : 42, 74, 84, 93 after analyzing : 42, 80, 84, 83 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 67.135, std = 7.972 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.13, sigma = 4.60 after rotation: sse = 3.13, sigma = 4.60 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.20, its var is 3.89 before Erosion-Dilatation 0.40% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...48 iterations mri_strip_skull: done peeling brain Brain Size = 1482468 voxels, voxel volume = 1.000 mm3 = 1482468 mmm3 = 1482.468 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 25.756084 mri_watershed stimesec 0.574912 mri_watershed ru_maxrss 821576 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212733 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2568 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1148 mri_watershed ru_nivcsw 1191 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Oct 7 17:16:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach.log reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (61, 33, 34) --> (192, 167, 190) using (105, 78, 112) as brain centroid... mean wm in atlas = 107, using box (89,62,93) --> (121, 94,131) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 7.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.535 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.021096 @ (-9.091, 27.273, -9.091) max log p = -3.959297 @ (4.545, -4.545, 4.545) max log p = -3.893008 @ (6.818, 2.273, -2.273) max log p = -3.870114 @ (-3.409, -1.136, 5.682) max log p = -3.867781 @ (-0.568, 0.568, 1.705) max log p = -3.861741 @ (-0.284, -1.420, -0.852) Found translation: (-2.0, 23.0, -0.3): log p = -3.862 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.634, old_max_log_p =-3.862 (thresh=-3.9) 1.07500 0.00000 0.00000 -11.64308; 0.00000 1.19413 0.31997 -29.50821; 0.00000 -0.25882 0.96593 28.23727; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.634, old_max_log_p =-3.634 (thresh=-3.6) 1.07500 0.00000 0.00000 -11.64308; 0.00000 1.19413 0.31997 -29.50821; 0.00000 -0.25882 0.96593 28.23727; 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=-3.487, old_max_log_p =-3.634 (thresh=-3.6) 1.05409 0.00000 0.00000 -8.95114; 0.00000 1.12932 0.37285 -25.11861; 0.00000 -0.34312 0.97986 36.51017; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.487, old_max_log_p =-3.487 (thresh=-3.5) 1.05409 0.00000 0.00000 -8.95114; 0.00000 1.12932 0.37285 -25.11861; 0.00000 -0.34312 0.97986 36.51017; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.463, old_max_log_p =-3.487 (thresh=-3.5) 1.05405 -0.00919 -0.00325 -7.75645; 0.00857 1.12249 0.37949 -26.73352; 0.00014 -0.35196 0.97562 37.75048; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.456, old_max_log_p =-3.463 (thresh=-3.5) 1.05525 -0.01208 0.00471 -8.93147; 0.00855 1.11986 0.37860 -26.39127; -0.00847 -0.35063 0.97219 39.08956; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.456, old_max_log_p =-3.456 (thresh=-3.5) 1.05525 -0.01208 0.00471 -8.93147; 0.00855 1.11986 0.37860 -26.39127; -0.00847 -0.35063 0.97219 39.08956; 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 1.05525 -0.01208 0.00471 -8.93147; 0.00855 1.11986 0.37860 -26.39127; -0.00847 -0.35063 0.97219 39.08956; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.05525 -0.01208 0.00471 -8.93147; 0.00855 1.11986 0.37860 -26.39127; -0.00847 -0.35063 0.97219 39.08956; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05525 -0.01208 0.00471 -8.93147; 0.00855 1.11986 0.37860 -26.39127; -0.00847 -0.35063 0.97219 39.08956; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.456 (old=-4.535) transform before final EM align: 1.05525 -0.01208 0.00471 -8.93147; 0.00855 1.11986 0.37860 -26.39127; -0.00847 -0.35063 0.97219 39.08956; 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 1.05525 -0.01208 0.00471 -8.93147; 0.00855 1.11986 0.37860 -26.39127; -0.00847 -0.35063 0.97219 39.08956; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.05525 -0.01208 0.00471 -8.93147; 0.00855 1.11986 0.37860 -26.39127; -0.00847 -0.35063 0.97219 39.08956; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.05525 -0.01208 0.00471 -8.93147; 0.00855 1.11986 0.37860 -26.39127; -0.00847 -0.35063 0.97219 39.08956; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1026.881890 mri_em_register stimesec 1.394787 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 158955 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 139 mri_em_register ru_nivcsw 4252 registration took 8 minutes and 53 seconds. #-------------------------------------- #@# CA Normalize Sat Oct 7 17:25:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (61, 33, 34) --> (192, 167, 190) using (105, 78, 112) as brain centroid... mean wm in atlas = 107, using box (89,62,93) --> (121, 94,131) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 7.6 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246344 sample points... INFO: compute sample coordinates transform 1.05525 -0.01208 0.00471 -8.93147; 0.00855 1.11986 0.37860 -26.39127; -0.00847 -0.35063 0.97219 39.08956; 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 (129, 37, 32) --> (191, 143, 189) Left_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0 2 of 19 (10.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 37, 31) --> (130, 136, 189) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 14 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 119, 62) --> (176, 155, 114) finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 119, 59) --> (129, 154, 114) Right_Cerebellum_White_Matter: limiting intensities to 104.0 --> 132.0 4 of 10 (40.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 104, 95) --> (146, 163, 124) Brain_Stem: limiting intensities to 113.0 --> 132.0 3 of 7 (42.9%) samples deleted using 50 total control points for intensity normalization... bias field = 0.914 +- 0.090 0 of 41 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 37, 32) --> (191, 143, 189) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 121 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 37, 31) --> (130, 136, 189) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 98 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 119, 62) --> (176, 155, 114) finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 119, 59) --> (129, 154, 114) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 132.0 3 of 10 (30.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 104, 95) --> (146, 163, 124) Brain_Stem: limiting intensities to 90.0 --> 132.0 14 of 32 (43.8%) samples deleted using 261 total control points for intensity normalization... bias field = 1.023 +- 0.074 0 of 244 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 37, 32) --> (191, 143, 189) Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 132.0 55 of 202 (27.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 37, 31) --> (130, 136, 189) Right_Cerebral_White_Matter: limiting intensities to 102.0 --> 132.0 80 of 227 (35.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 119, 62) --> (176, 155, 114) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0 3 of 6 (50.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 119, 59) --> (129, 154, 114) Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0 1 of 7 (14.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 104, 95) --> (146, 163, 124) Brain_Stem: limiting intensities to 91.0 --> 132.0 33 of 59 (55.9%) samples deleted using 501 total control points for intensity normalization... bias field = 0.978 +- 0.054 1 of 329 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 53 seconds. #-------------------------------------- #@# CA Reg Sat Oct 7 17:26:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.29 (predicted orig area = 6.2) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.854, neg=0, invalid=762 0001: dt=210.138032, rms=0.750 (12.251%), neg=0, invalid=762 0002: dt=155.446894, rms=0.728 (2.929%), neg=0, invalid=762 0003: dt=221.952000, rms=0.716 (1.536%), neg=0, invalid=762 0004: dt=143.515152, rms=0.710 (0.897%), neg=0, invalid=762 0005: dt=369.920000, rms=0.703 (0.929%), neg=0, invalid=762 0006: dt=110.976000, rms=0.699 (0.622%), neg=0, invalid=762 0007: dt=1183.744000, rms=0.690 (1.250%), neg=0, invalid=762 0008: dt=92.480000, rms=0.685 (0.700%), neg=0, invalid=762 0009: dt=517.888000, rms=0.684 (0.266%), neg=0, invalid=762 0010: dt=129.472000, rms=0.682 (0.225%), neg=0, invalid=762 0011: dt=129.472000, rms=0.682 (0.080%), neg=0, invalid=762 0012: dt=129.472000, rms=0.681 (0.133%), neg=0, invalid=762 0013: dt=129.472000, rms=0.679 (0.210%), neg=0, invalid=762 0014: dt=129.472000, rms=0.678 (0.244%), neg=0, invalid=762 0015: dt=129.472000, rms=0.676 (0.248%), neg=0, invalid=762 0016: dt=129.472000, rms=0.674 (0.241%), neg=0, invalid=762 0017: dt=129.472000, rms=0.673 (0.222%), neg=0, invalid=762 0018: dt=129.472000, rms=0.671 (0.223%), neg=0, invalid=762 0019: dt=129.472000, rms=0.670 (0.221%), neg=0, invalid=762 0020: dt=129.472000, rms=0.668 (0.188%), neg=0, invalid=762 0021: dt=129.472000, rms=0.667 (0.168%), neg=0, invalid=762 0022: dt=129.472000, rms=0.666 (0.166%), neg=0, invalid=762 0023: dt=129.472000, rms=0.665 (0.175%), neg=0, invalid=762 0024: dt=129.472000, rms=0.664 (0.158%), neg=0, invalid=762 0025: dt=129.472000, rms=0.663 (0.134%), neg=0, invalid=762 0026: dt=129.472000, rms=0.662 (0.121%), neg=0, invalid=762 0027: dt=129.472000, rms=0.662 (0.111%), neg=0, invalid=762 0028: dt=1183.744000, rms=0.661 (0.094%), neg=0, invalid=762 0029: dt=1183.744000, rms=0.661 (-5.946%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.661, neg=0, invalid=762 0030: dt=129.472000, rms=0.660 (0.213%), neg=0, invalid=762 0031: dt=517.888000, rms=0.659 (0.208%), neg=0, invalid=762 0032: dt=517.888000, rms=0.659 (-0.066%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.664, neg=0, invalid=762 0033: dt=136.982456, rms=0.658 (0.879%), neg=0, invalid=762 0034: dt=168.646240, rms=0.649 (1.407%), neg=0, invalid=762 0035: dt=82.666667, rms=0.645 (0.549%), neg=0, invalid=762 0036: dt=140.635193, rms=0.641 (0.678%), neg=0, invalid=762 0037: dt=36.288000, rms=0.639 (0.354%), neg=0, invalid=762 0038: dt=145.152000, rms=0.636 (0.398%), neg=0, invalid=762 0039: dt=112.746114, rms=0.633 (0.427%), neg=0, invalid=762 0040: dt=66.370370, rms=0.632 (0.277%), neg=0, invalid=762 0041: dt=145.152000, rms=0.630 (0.295%), neg=0, invalid=762 0042: dt=73.945946, rms=0.628 (0.277%), neg=0, invalid=762 0043: dt=82.944000, rms=0.627 (0.142%), neg=0, invalid=762 0044: dt=82.944000, rms=0.626 (0.235%), neg=0, invalid=762 0045: dt=82.944000, rms=0.624 (0.306%), neg=0, invalid=762 0046: dt=82.944000, rms=0.621 (0.389%), neg=0, invalid=762 0047: dt=82.944000, rms=0.618 (0.542%), neg=0, invalid=762 0048: dt=82.944000, rms=0.615 (0.551%), neg=0, invalid=762 0049: dt=82.944000, rms=0.612 (0.497%), neg=0, invalid=762 0050: dt=82.944000, rms=0.609 (0.423%), neg=0, invalid=762 0051: dt=82.944000, rms=0.606 (0.469%), neg=0, invalid=762 0052: dt=82.944000, rms=0.604 (0.394%), neg=0, invalid=762 0053: dt=82.944000, rms=0.602 (0.305%), neg=0, invalid=762 0054: dt=82.944000, rms=0.600 (0.222%), neg=0, invalid=762 0055: dt=82.944000, rms=0.599 (0.314%), neg=0, invalid=762 0056: dt=82.944000, rms=0.597 (0.223%), neg=0, invalid=762 0057: dt=82.944000, rms=0.596 (0.162%), neg=0, invalid=762 0058: dt=82.944000, rms=0.595 (0.147%), neg=0, invalid=762 0059: dt=82.944000, rms=0.594 (0.157%), neg=0, invalid=762 0060: dt=82.944000, rms=0.594 (0.126%), neg=0, invalid=762 0061: dt=82.944000, rms=0.593 (0.073%), neg=0, invalid=762 0062: dt=82.944000, rms=0.592 (0.145%), neg=0, invalid=762 0063: dt=82.944000, rms=0.592 (0.098%), neg=0, invalid=762 0064: dt=82.944000, rms=0.591 (0.074%), neg=0, invalid=762 0065: dt=124.416000, rms=0.591 (0.020%), neg=0, invalid=762 0066: dt=124.416000, rms=0.591 (-0.029%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=762 0067: dt=103.680000, rms=0.590 (0.328%), neg=0, invalid=762 0068: dt=62.208000, rms=0.590 (0.041%), neg=0, invalid=762 0069: dt=62.208000, rms=0.590 (0.026%), neg=0, invalid=762 0070: dt=62.208000, rms=0.589 (0.028%), neg=0, invalid=762 0071: dt=62.208000, rms=0.589 (0.016%), neg=0, invalid=762 0072: dt=62.208000, rms=0.589 (0.003%), neg=0, invalid=762 0073: dt=145.152000, rms=0.589 (0.040%), neg=0, invalid=762 0074: dt=36.288000, rms=0.589 (0.009%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.613, neg=0, invalid=762 0075: dt=0.000000, rms=0.612 (0.094%), neg=0, invalid=762 0076: dt=0.000000, rms=0.612 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.613, neg=0, invalid=762 0077: dt=0.000000, rms=0.612 (0.094%), neg=0, invalid=762 0078: dt=0.000000, rms=0.612 (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=0.683, neg=0, invalid=762 0079: dt=5.040816, rms=0.664 (2.895%), neg=0, invalid=762 0080: dt=2.000000, rms=0.663 (0.090%), neg=0, invalid=762 0081: dt=2.000000, rms=0.663 (-0.033%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.663, neg=0, invalid=762 0082: dt=0.015750, rms=0.663 (0.069%), neg=0, invalid=762 0083: dt=0.013500, rms=0.663 (0.000%), neg=0, invalid=762 0084: dt=0.013500, rms=0.663 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.733, neg=0, invalid=762 0085: dt=1.536000, rms=0.727 (0.835%), neg=0, invalid=762 0086: dt=1.809524, rms=0.722 (0.705%), neg=0, invalid=762 0087: dt=0.448000, rms=0.722 (0.052%), neg=0, invalid=762 0088: dt=0.448000, rms=0.721 (0.039%), neg=0, invalid=762 0089: dt=0.448000, rms=0.721 (0.031%), neg=0, invalid=762 0090: dt=0.448000, rms=0.721 (0.002%), neg=0, invalid=762 0091: dt=1.792000, rms=0.720 (0.146%), neg=0, invalid=762 0092: dt=0.192000, rms=0.720 (0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.721, neg=0, invalid=762 0093: dt=1.280000, rms=0.719 (0.174%), neg=0, invalid=762 0094: dt=0.448000, rms=0.719 (0.020%), neg=0, invalid=762 0095: dt=0.448000, rms=0.719 (0.010%), neg=0, invalid=762 0096: dt=0.448000, rms=0.719 (0.007%), neg=0, invalid=762 0097: dt=0.448000, rms=0.719 (-0.002%), 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=0.676, neg=0, invalid=762 0098: dt=0.906929, rms=0.655 (3.093%), neg=0, invalid=762 0099: dt=0.080000, rms=0.654 (0.162%), neg=0, invalid=762 0100: dt=0.080000, rms=0.654 (-0.083%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.654, neg=0, invalid=762 0101: dt=0.028000, rms=0.654 (0.084%), neg=0, invalid=762 0102: dt=0.016000, rms=0.654 (0.009%), neg=0, invalid=762 0103: dt=0.016000, rms=0.654 (-0.008%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.10309 (17) Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (1093 voxels, overlap=0.746) Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (1093 voxels, peak = 16), gca=16.3 gca peak = 0.15565 (16) mri peak = 0.07792 (17) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (541 voxels, overlap=0.819) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (541 voxels, peak = 16), gca=15.6 gca peak = 0.26829 (96) mri peak = 0.08821 (95) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (486 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (486 voxels, peak = 96), gca=96.0 gca peak = 0.20183 (93) mri peak = 0.10406 (94) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (392 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (392 voxels, peak = 96), gca=96.3 gca peak = 0.21683 (55) mri peak = 0.08895 (63) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (398 voxels, overlap=0.992) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (398 voxels, peak = 57), gca=57.5 gca peak = 0.30730 (58) mri peak = 0.08092 (66) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (315 voxels, overlap=0.996) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (315 voxels, peak = 64), gca=63.5 gca peak = 0.11430 (101) mri peak = 0.08453 (104) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (42748 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (42748 voxels, peak = 104), gca=103.5 gca peak = 0.12076 (102) mri peak = 0.07521 (99) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (38468 voxels, overlap=0.914) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (38468 voxels, peak = 104), gca=103.5 gca peak = 0.14995 (59) mri peak = 0.03507 (62) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (9456 voxels, overlap=0.944) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (9456 voxels, peak = 60), gca=60.5 gca peak = 0.15082 (58) mri peak = 0.03608 (68) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (11623 voxels, overlap=0.862) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (11623 voxels, peak = 62), gca=62.4 gca peak = 0.14161 (67) mri peak = 0.09308 (74) Right_Caudate (50): linear fit = 1.10 x + 0.0 (431 voxels, overlap=0.757) Right_Caudate (50): linear fit = 1.10 x + 0.0 (431 voxels, peak = 73), gca=73.4 gca peak = 0.15243 (71) mri peak = 0.09483 (79) Left_Caudate (11): linear fit = 1.08 x + 0.0 (580 voxels, overlap=0.805) Left_Caudate (11): linear fit = 1.08 x + 0.0 (580 voxels, peak = 76), gca=76.3 gca peak = 0.13336 (57) mri peak = 0.03681 (61) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (6437 voxels, overlap=0.711) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (6437 voxels, peak = 64), gca=63.6 gca peak = 0.13252 (56) mri peak = 0.04315 (68) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (7439 voxels, overlap=0.182) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (7439 voxels, peak = 67), gca=67.5 gca peak = 0.18181 (84) mri peak = 0.06479 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (3222 voxels, overlap=0.784) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (3222 voxels, peak = 89), gca=89.5 gca peak = 0.20573 (83) mri peak = 0.07157 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (3527 voxels, overlap=0.750) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (3527 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.09125 (63) Left_Amygdala (18): linear fit = 1.08 x + 0.0 (126 voxels, overlap=0.838) Left_Amygdala (18): linear fit = 1.08 x + 0.0 (126 voxels, peak = 61), gca=61.3 gca peak = 0.39313 (56) mri peak = 0.09524 (64) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (314 voxels, overlap=0.565) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (314 voxels, peak = 64), gca=63.6 gca peak = 0.14181 (85) mri peak = 0.06368 (87) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2776 voxels, overlap=0.980) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2776 voxels, peak = 85), gca=84.6 gca peak = 0.11978 (83) mri peak = 0.07083 (85) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (2471 voxels, overlap=0.885) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (2471 voxels, peak = 84), gca=84.2 gca peak = 0.13399 (79) mri peak = 0.06972 (85) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1363 voxels, overlap=0.774) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1363 voxels, peak = 87), gca=86.5 gca peak = 0.14159 (79) mri peak = 0.05882 (82) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1464 voxels, overlap=0.999) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1464 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.09181 (84) Brain_Stem (16): linear fit = 1.10 x + 0.0 (5472 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (5472 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.08096 (92) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (658 voxels, overlap=0.619) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (658 voxels, peak = 94), gca=94.2 gca peak = 0.12801 (89) mri peak = 0.07407 (89) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (804 voxels, overlap=0.686) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (804 voxels, peak = 97), gca=96.6 gca peak = 0.20494 (23) mri peak = 0.13793 (17) gca peak = 0.15061 (21) mri peak = 0.13296 (19) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (209 voxels, overlap=0.861) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (209 voxels, peak = 18), gca=18.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.89 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=0.654, neg=0, invalid=762 0104: dt=110.976000, rms=0.646 (1.224%), neg=0, invalid=762 0105: dt=295.936000, rms=0.641 (0.735%), neg=0, invalid=762 0106: dt=129.472000, rms=0.639 (0.323%), neg=0, invalid=762 0107: dt=221.952000, rms=0.636 (0.379%), neg=0, invalid=762 0108: dt=92.480000, rms=0.636 (0.132%), neg=0, invalid=762 0109: dt=517.888000, rms=0.633 (0.353%), neg=0, invalid=762 0110: dt=92.480000, rms=0.633 (0.115%), neg=0, invalid=762 0111: dt=517.888000, rms=0.632 (0.165%), neg=0, invalid=762 0112: dt=92.480000, rms=0.631 (0.111%), neg=0, invalid=762 0113: dt=517.888000, rms=0.630 (0.146%), neg=0, invalid=762 0114: dt=92.480000, rms=0.630 (0.079%), neg=0, invalid=762 0115: dt=517.888000, rms=0.629 (0.102%), neg=0, invalid=762 0116: dt=110.976000, rms=0.628 (0.072%), neg=0, invalid=762 0117: dt=295.936000, rms=0.628 (0.059%), neg=0, invalid=762 0118: dt=110.976000, rms=0.628 (0.046%), neg=0, invalid=762 0119: dt=110.976000, rms=0.628 (0.028%), neg=0, invalid=762 0120: dt=110.976000, rms=0.627 (0.049%), neg=0, invalid=762 0121: dt=110.976000, rms=0.627 (0.068%), neg=0, invalid=762 0122: dt=110.976000, rms=0.626 (0.068%), neg=0, invalid=762 0123: dt=110.976000, rms=0.626 (0.079%), neg=0, invalid=762 0124: dt=110.976000, rms=0.625 (0.079%), neg=0, invalid=762 0125: dt=110.976000, rms=0.625 (0.074%), neg=0, invalid=762 0126: dt=110.976000, rms=0.625 (0.073%), neg=0, invalid=762 0127: dt=110.976000, rms=0.624 (0.068%), neg=0, invalid=762 0128: dt=110.976000, rms=0.624 (0.072%), neg=0, invalid=762 0129: dt=110.976000, rms=0.623 (0.069%), neg=0, invalid=762 0130: dt=110.976000, rms=0.623 (0.062%), neg=0, invalid=762 0131: dt=110.976000, rms=0.622 (0.061%), neg=0, invalid=762 0132: dt=110.976000, rms=0.622 (0.056%), neg=0, invalid=762 0133: dt=110.976000, rms=0.622 (0.056%), neg=0, invalid=762 0134: dt=110.976000, rms=0.621 (0.050%), neg=0, invalid=762 0135: dt=110.976000, rms=0.621 (0.053%), neg=0, invalid=762 0136: dt=110.976000, rms=0.621 (0.049%), neg=0, invalid=762 0137: dt=110.976000, rms=0.620 (0.048%), neg=0, invalid=762 0138: dt=110.976000, rms=0.620 (0.047%), neg=0, invalid=762 0139: dt=110.976000, rms=0.620 (0.043%), neg=0, invalid=762 0140: dt=110.976000, rms=0.620 (0.043%), neg=0, invalid=762 0141: dt=110.976000, rms=0.619 (0.043%), neg=0, invalid=762 0142: dt=110.976000, rms=0.619 (0.046%), neg=0, invalid=762 0143: dt=110.976000, rms=0.619 (0.045%), neg=0, invalid=762 0144: dt=110.976000, rms=0.619 (0.043%), neg=0, invalid=762 0145: dt=110.976000, rms=0.618 (0.045%), neg=0, invalid=762 0146: dt=110.976000, rms=0.618 (0.044%), neg=0, invalid=762 0147: dt=110.976000, rms=0.618 (0.041%), neg=0, invalid=762 0148: dt=110.976000, rms=0.618 (0.035%), neg=0, invalid=762 0149: dt=110.976000, rms=0.617 (0.037%), neg=0, invalid=762 0150: dt=110.976000, rms=0.617 (0.036%), neg=0, invalid=762 0151: dt=110.976000, rms=0.617 (0.042%), neg=0, invalid=762 0152: dt=110.976000, rms=0.617 (0.043%), neg=0, invalid=762 0153: dt=110.976000, rms=0.616 (0.043%), neg=0, invalid=762 0154: dt=110.976000, rms=0.616 (0.037%), neg=0, invalid=762 0155: dt=110.976000, rms=0.616 (0.036%), neg=0, invalid=762 0156: dt=110.976000, rms=0.616 (0.032%), neg=0, invalid=762 0157: dt=110.976000, rms=0.615 (0.032%), neg=0, invalid=762 0158: dt=110.976000, rms=0.615 (0.029%), neg=0, invalid=762 0159: dt=110.976000, rms=0.615 (0.034%), neg=0, invalid=762 0160: dt=110.976000, rms=0.615 (0.034%), neg=0, invalid=762 0161: dt=110.976000, rms=0.615 (0.035%), neg=0, invalid=762 0162: dt=110.976000, rms=0.614 (0.033%), neg=0, invalid=762 0163: dt=110.976000, rms=0.614 (0.028%), neg=0, invalid=762 0164: dt=110.976000, rms=0.614 (0.022%), neg=0, invalid=762 0165: dt=110.976000, rms=0.614 (0.026%), neg=0, invalid=762 0166: dt=110.976000, rms=0.614 (0.022%), neg=0, invalid=762 0167: dt=110.976000, rms=0.614 (0.024%), neg=0, invalid=762 0168: dt=110.976000, rms=0.614 (0.030%), neg=0, invalid=762 0169: dt=110.976000, rms=0.613 (0.030%), neg=0, invalid=762 0170: dt=110.976000, rms=0.613 (0.025%), neg=0, invalid=762 0171: dt=110.976000, rms=0.613 (0.023%), neg=0, invalid=762 0172: dt=887.808000, rms=0.613 (0.016%), neg=0, invalid=762 0173: dt=887.808000, rms=0.613 (-0.640%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.613, neg=0, invalid=762 0174: dt=221.952000, rms=0.612 (0.226%), neg=0, invalid=762 0175: dt=129.472000, rms=0.612 (0.066%), neg=0, invalid=762 0176: dt=295.936000, rms=0.611 (0.023%), neg=0, invalid=762 0177: dt=295.936000, rms=0.611 (-0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.613, neg=0, invalid=762 0178: dt=111.157895, rms=0.610 (0.539%), neg=0, invalid=762 0179: dt=123.914894, rms=0.605 (0.709%), neg=0, invalid=762 0180: dt=67.918367, rms=0.602 (0.448%), neg=0, invalid=762 0181: dt=74.982249, rms=0.600 (0.392%), neg=0, invalid=762 0182: dt=70.846512, rms=0.598 (0.339%), neg=0, invalid=762 0183: dt=87.843137, rms=0.596 (0.296%), neg=0, invalid=762 0184: dt=62.208000, rms=0.595 (0.306%), neg=0, invalid=762 0185: dt=103.680000, rms=0.593 (0.280%), neg=0, invalid=762 0186: dt=36.288000, rms=0.591 (0.229%), neg=0, invalid=762 0187: dt=580.608000, rms=0.582 (1.529%), neg=0, invalid=762 0188: dt=82.944000, rms=0.581 (0.172%), neg=0, invalid=762 0189: dt=64.000000, rms=0.581 (0.142%), neg=0, invalid=762 0190: dt=82.944000, rms=0.580 (0.113%), neg=0, invalid=762 0191: dt=62.208000, rms=0.579 (0.141%), neg=0, invalid=762 0192: dt=82.944000, rms=0.579 (0.100%), neg=0, invalid=762 0193: dt=62.208000, rms=0.578 (0.127%), neg=0, invalid=762 0194: dt=82.944000, rms=0.577 (0.089%), neg=0, invalid=762 0195: dt=62.208000, rms=0.577 (0.122%), neg=0, invalid=762 0196: dt=82.944000, rms=0.576 (0.090%), neg=0, invalid=762 0197: dt=36.288000, rms=0.576 (0.096%), neg=0, invalid=762 0198: dt=580.608000, rms=0.571 (0.757%), neg=0, invalid=762 0199: dt=145.152000, rms=0.570 (0.163%), neg=0, invalid=762 0200: dt=36.288000, rms=0.570 (0.065%), neg=0, invalid=762 0201: dt=580.608000, rms=0.568 (0.405%), neg=0, invalid=762 0202: dt=81.351111, rms=0.566 (0.255%), neg=0, invalid=762 0203: dt=124.416000, rms=0.566 (0.082%), neg=0, invalid=762 0204: dt=82.944000, rms=0.565 (0.086%), neg=0, invalid=762 0205: dt=124.416000, rms=0.565 (0.069%), neg=0, invalid=762 0206: dt=82.944000, rms=0.564 (0.080%), neg=0, invalid=762 0207: dt=103.680000, rms=0.564 (0.074%), neg=0, invalid=762 0208: dt=62.208000, rms=0.564 (0.053%), neg=0, invalid=762 0209: dt=36.288000, rms=0.563 (0.031%), neg=0, invalid=762 0210: dt=36.288000, rms=0.563 (0.024%), neg=0, invalid=762 0211: dt=9.072000, rms=0.563 (0.009%), neg=0, invalid=762 0212: dt=1.134000, rms=0.563 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.564, neg=0, invalid=762 0213: dt=2.268000, rms=0.563 (0.105%), neg=0, invalid=762 0214: dt=2.268000, rms=0.563 (0.012%), neg=0, invalid=762 0215: dt=1.134000, rms=0.563 (0.005%), neg=0, invalid=762 0216: dt=0.070875, rms=0.563 (-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=0.569, neg=0, invalid=762 0217: dt=0.002734, rms=0.569 (0.088%), neg=0, invalid=762 0218: dt=0.001750, rms=0.569 (0.000%), neg=0, invalid=762 0219: dt=0.000109, rms=0.569 (0.000%), neg=0, invalid=762 0220: dt=0.000055, rms=0.569 (0.000%), neg=0, invalid=762 0221: dt=0.000014, rms=0.569 (0.000%), neg=0, invalid=762 0222: dt=0.000000, rms=0.569 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.569, neg=0, invalid=762 0223: dt=0.000000, rms=0.569 (0.087%), neg=0, invalid=762 0224: dt=0.000000, rms=0.569 (0.000%), neg=0, invalid=762 0225: dt=0.000015, rms=0.569 (0.000%), neg=0, invalid=762 0226: dt=0.000008, rms=0.569 (0.000%), neg=0, invalid=762 0227: dt=0.000004, rms=0.569 (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=0.588, neg=0, invalid=762 0228: dt=11.520000, rms=0.558 (5.156%), neg=0, invalid=762 0229: dt=4.032000, rms=0.553 (0.745%), neg=0, invalid=762 0230: dt=4.032000, rms=0.550 (0.601%), neg=0, invalid=762 0231: dt=0.180000, rms=0.550 (0.025%), neg=0, invalid=762 0232: dt=0.011250, rms=0.550 (0.001%), neg=0, invalid=762 0233: dt=0.005625, rms=0.550 (0.001%), neg=0, invalid=762 0234: dt=0.000703, rms=0.550 (0.000%), neg=0, invalid=762 0235: dt=0.000540, rms=0.550 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.550, neg=0, invalid=762 0236: dt=16.128000, rms=0.540 (1.819%), neg=0, invalid=762 0237: dt=11.520000, rms=0.538 (0.527%), neg=0, invalid=762 0238: dt=11.520000, rms=0.536 (0.335%), neg=0, invalid=762 0239: dt=2.880000, rms=0.535 (0.073%), neg=0, invalid=762 0240: dt=0.252000, rms=0.535 (0.004%), neg=0, invalid=762 0241: dt=0.252000, rms=0.535 (0.008%), neg=0, invalid=762 0242: dt=0.031500, rms=0.535 (0.003%), neg=0, invalid=762 0243: dt=0.007875, rms=0.535 (-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=0.560, neg=0, invalid=762 0244: dt=0.000000, rms=0.559 (0.095%), neg=0, invalid=762 0245: dt=0.000000, rms=0.559 (0.000%), neg=0, invalid=762 0246: dt=0.100000, rms=0.559 (-0.066%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.560, neg=0, invalid=762 0247: dt=0.000000, rms=0.559 (0.095%), neg=0, invalid=762 0248: dt=0.000000, rms=0.559 (0.000%), neg=0, invalid=762 0249: dt=0.100000, rms=0.559 (-0.044%), 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=0.519, neg=0, invalid=762 0250: dt=0.448000, rms=0.505 (2.848%), neg=0, invalid=762 0251: dt=0.448000, rms=0.501 (0.603%), neg=0, invalid=762 0252: dt=0.384000, rms=0.500 (0.308%), neg=0, invalid=762 0253: dt=0.384000, rms=0.499 (0.217%), neg=0, invalid=762 0254: dt=0.384000, rms=0.498 (0.164%), neg=0, invalid=762 0255: dt=0.384000, rms=0.497 (0.126%), neg=0, invalid=762 0256: dt=0.384000, rms=0.497 (0.101%), neg=0, invalid=762 0257: dt=0.384000, rms=0.496 (0.086%), neg=0, invalid=762 0258: dt=0.384000, rms=0.496 (0.073%), neg=0, invalid=762 0259: dt=0.384000, rms=0.496 (0.059%), neg=0, invalid=762 0260: dt=0.384000, rms=0.496 (0.057%), neg=0, invalid=762 0261: dt=0.384000, rms=0.495 (0.044%), neg=0, invalid=762 0262: dt=0.384000, rms=0.495 (0.044%), neg=0, invalid=762 0263: dt=0.384000, rms=0.495 (0.070%), neg=0, invalid=762 0264: dt=0.384000, rms=0.495 (0.034%), neg=0, invalid=762 0265: dt=0.384000, rms=0.494 (0.049%), neg=0, invalid=762 0266: dt=0.384000, rms=0.494 (0.065%), neg=0, invalid=762 0267: dt=0.384000, rms=0.494 (0.016%), neg=0, invalid=762 0268: dt=0.384000, rms=0.494 (0.015%), neg=0, invalid=762 0269: dt=0.448000, rms=0.494 (0.012%), neg=0, invalid=762 0270: dt=0.448000, rms=0.494 (0.011%), neg=0, invalid=762 0271: dt=0.448000, rms=0.494 (0.030%), neg=0, invalid=762 0272: dt=0.448000, rms=0.494 (0.008%), neg=0, invalid=762 0273: dt=0.448000, rms=0.493 (0.024%), neg=0, invalid=762 0274: dt=0.448000, rms=0.493 (0.009%), neg=0, invalid=762 0275: dt=0.384000, rms=0.493 (0.005%), neg=0, invalid=762 0276: dt=0.384000, rms=0.493 (0.010%), neg=0, invalid=762 0277: dt=0.384000, rms=0.493 (0.008%), neg=0, invalid=762 0278: dt=0.384000, rms=0.493 (0.018%), neg=0, invalid=762 0279: dt=0.384000, rms=0.493 (0.020%), neg=0, invalid=762 0280: dt=0.384000, rms=0.493 (0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.494, neg=0, invalid=762 0281: dt=0.384000, rms=0.488 (1.160%), neg=0, invalid=762 0282: dt=0.448000, rms=0.487 (0.262%), neg=0, invalid=762 0283: dt=0.448000, rms=0.487 (0.034%), neg=0, invalid=762 0284: dt=0.448000, rms=0.486 (0.007%), neg=0, invalid=762 0285: dt=0.448000, rms=0.486 (0.001%), neg=0, invalid=762 0286: dt=0.448000, rms=0.486 (-0.011%), 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=0.485, neg=0, invalid=762 0287: dt=0.000000, rms=0.484 (0.126%), neg=0, invalid=762 0288: dt=0.000000, rms=0.484 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.485, neg=0, invalid=762 0289: dt=129.472000, rms=0.484 (0.176%), neg=0, invalid=762 0290: dt=129.472000, rms=0.484 (0.025%), neg=0, invalid=762 0291: dt=129.472000, rms=0.484 (-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=0.485, neg=0, invalid=762 0292: dt=36.288000, rms=0.484 (0.204%), neg=0, invalid=762 0293: dt=36.288000, rms=0.483 (0.037%), neg=0, invalid=762 0294: dt=36.288000, rms=0.483 (0.018%), neg=0, invalid=762 0295: dt=36.288000, rms=0.483 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.484, neg=0, invalid=762 0296: dt=104.594286, rms=0.481 (0.533%), neg=0, invalid=762 0297: dt=36.288000, rms=0.481 (0.118%), neg=0, invalid=762 0298: dt=36.288000, rms=0.481 (0.051%), neg=0, invalid=762 0299: dt=36.288000, rms=0.480 (0.077%), neg=0, invalid=762 0300: dt=36.288000, rms=0.480 (0.106%), neg=0, invalid=762 0301: dt=36.288000, rms=0.479 (0.122%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0302: dt=36.288000, rms=0.478 (0.120%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0303: dt=36.288000, rms=0.478 (0.108%), neg=0, invalid=762 0304: dt=145.152000, rms=0.478 (0.040%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.479, neg=0, invalid=762 iter 0, gcam->neg = 8 after 2 iterations, nbhd size=0, neg = 0 0305: dt=38.400000, rms=0.475 (0.702%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 10 iterations, nbhd size=1, neg = 0 0306: dt=38.400000, rms=0.474 (0.351%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0307: dt=25.600000, rms=0.472 (0.345%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0308: dt=25.600000, rms=0.471 (0.173%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0309: dt=25.600000, rms=0.470 (0.169%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0310: dt=25.600000, rms=0.469 (0.223%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0311: dt=25.600000, rms=0.468 (0.234%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0312: dt=25.600000, rms=0.467 (0.201%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0313: dt=25.600000, rms=0.466 (0.177%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 9 iterations, nbhd size=1, neg = 0 0314: dt=25.600000, rms=0.465 (0.208%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=1, neg = 0 0315: dt=25.600000, rms=0.465 (0.163%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 11 iterations, nbhd size=1, neg = 0 0316: dt=25.600000, rms=0.464 (0.164%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 5 iterations, nbhd size=0, neg = 0 0317: dt=25.600000, rms=0.463 (0.176%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0318: dt=25.600000, rms=0.462 (0.170%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0319: dt=25.600000, rms=0.462 (0.151%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 10 iterations, nbhd size=1, neg = 0 0320: dt=25.600000, rms=0.461 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 2 iterations, nbhd size=0, neg = 0 0321: dt=25.600000, rms=0.461 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 16 iterations, nbhd size=1, neg = 0 0322: dt=25.600000, rms=0.460 (0.079%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0323: dt=25.600000, rms=0.460 (0.077%), neg=0, invalid=762 0324: dt=25.600000, rms=0.460 (0.028%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0325: dt=25.600000, rms=0.459 (0.059%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0326: dt=25.600000, rms=0.459 (0.049%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0327: dt=25.600000, rms=0.459 (0.047%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.460, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0328: dt=72.220183, rms=0.455 (0.937%), neg=0, invalid=762 0329: dt=25.600000, rms=0.454 (0.301%), neg=0, invalid=762 0330: dt=44.800000, rms=0.453 (0.133%), neg=0, invalid=762 0331: dt=44.800000, rms=0.453 (0.016%), neg=0, invalid=762 0332: dt=44.800000, rms=0.452 (0.269%), neg=0, invalid=762 0333: dt=44.800000, rms=0.452 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0334: dt=44.800000, rms=0.451 (0.096%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0335: dt=44.800000, rms=0.451 (-0.069%), neg=0, invalid=762 0336: dt=23.500000, rms=0.451 (0.138%), neg=0, invalid=762 0337: dt=19.200000, rms=0.450 (0.047%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.457, neg=0, invalid=762 0338: dt=0.252000, rms=0.457 (0.119%), neg=0, invalid=762 0339: dt=0.108000, rms=0.457 (0.001%), neg=0, invalid=762 0340: dt=0.108000, rms=0.457 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.457, neg=0, invalid=762 0341: dt=3.047619, rms=0.457 (0.159%), neg=0, invalid=762 0342: dt=1.008000, rms=0.457 (0.005%), neg=0, invalid=762 0343: dt=1.008000, rms=0.457 (0.008%), neg=0, invalid=762 0344: dt=1.008000, rms=0.457 (-0.010%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.468, neg=0, invalid=762 0345: dt=1.024000, rms=0.467 (0.241%), neg=0, invalid=762 0346: dt=0.112000, rms=0.467 (0.006%), neg=0, invalid=762 0347: dt=0.112000, rms=0.467 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=762 0348: dt=1.792000, rms=0.465 (0.394%), neg=0, invalid=762 0349: dt=1.024000, rms=0.465 (0.043%), neg=0, invalid=762 0350: dt=1.024000, rms=0.465 (-0.002%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.457, neg=0, invalid=762 iter 0, gcam->neg = 901 after 13 iterations, nbhd size=1, neg = 0 0351: dt=2.271322, rms=0.424 (7.224%), neg=0, invalid=762 0352: dt=0.080000, rms=0.424 (0.060%), neg=0, invalid=762 0353: dt=0.080000, rms=0.424 (-0.066%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.425, neg=0, invalid=762 0354: dt=0.096000, rms=0.424 (0.239%), neg=0, invalid=762 0355: dt=0.000000, rms=0.424 (0.005%), neg=0, invalid=762 0356: dt=0.050000, rms=0.424 (-0.023%), 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=0.409, neg=0, invalid=762 0357: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0358: dt=32.368000, rms=0.409 (0.003%), neg=0, invalid=762 0359: dt=23.120000, rms=0.409 (0.000%), neg=0, invalid=762 0360: dt=23.120000, rms=0.409 (-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=0.409, neg=0, invalid=762 0361: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0362: dt=62.208000, rms=0.409 (0.040%), neg=0, invalid=762 0363: dt=145.152000, rms=0.409 (0.057%), neg=0, invalid=762 0364: dt=36.288000, rms=0.409 (0.010%), neg=0, invalid=762 0365: dt=36.288000, rms=0.409 (0.010%), neg=0, invalid=762 0366: dt=36.288000, rms=0.409 (0.016%), neg=0, invalid=762 0367: dt=36.288000, rms=0.409 (0.020%), neg=0, invalid=762 0368: dt=36.288000, rms=0.409 (0.020%), neg=0, invalid=762 0369: dt=36.288000, rms=0.409 (0.017%), neg=0, invalid=762 0370: dt=36.288000, rms=0.409 (0.014%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0371: dt=11.200000, rms=0.409 (0.060%), neg=0, invalid=762 0372: dt=8.000000, rms=0.409 (0.012%), neg=0, invalid=762 0373: dt=8.000000, rms=0.409 (0.001%), neg=0, invalid=762 0374: dt=8.000000, rms=0.409 (-0.036%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0375: dt=75.397260, rms=0.407 (0.605%), neg=0, invalid=762 0376: dt=25.600000, rms=0.405 (0.313%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0377: dt=44.800000, rms=0.405 (0.136%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0378: dt=44.800000, rms=0.404 (0.115%), neg=0, invalid=762 0379: dt=44.800000, rms=0.403 (0.235%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0380: dt=44.800000, rms=0.402 (0.202%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0381: dt=44.800000, rms=0.402 (0.236%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0382: dt=44.800000, rms=0.401 (0.186%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0383: dt=44.800000, rms=0.400 (0.178%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0384: dt=44.800000, rms=0.399 (0.149%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0385: dt=44.800000, rms=0.399 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0386: dt=44.800000, rms=0.399 (0.097%), neg=0, invalid=762 0387: dt=32.000000, rms=0.399 (0.019%), neg=0, invalid=762 0388: dt=32.000000, rms=0.399 (0.009%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0389: dt=32.000000, rms=0.399 (0.008%), neg=0, invalid=762 0390: dt=32.000000, rms=0.398 (0.013%), neg=0, invalid=762 0391: dt=32.000000, rms=0.398 (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=0.403, neg=0, invalid=762 0392: dt=0.000000, rms=0.403 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=762 0393: dt=2.304000, rms=0.403 (0.013%), neg=0, invalid=762 0394: dt=1.008000, rms=0.403 (0.002%), neg=0, invalid=762 0395: dt=1.008000, rms=0.403 (-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=0.411, neg=0, invalid=762 0396: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 0397: dt=0.000000, rms=0.411 (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=0.397, neg=0, invalid=762 iter 0, gcam->neg = 579 after 14 iterations, nbhd size=1, neg = 0 0398: dt=1.280000, rms=0.388 (2.352%), neg=0, invalid=762 0399: dt=0.000015, rms=0.388 (0.000%), neg=0, invalid=762 0400: dt=0.000015, rms=0.388 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=762 0401: dt=0.112000, rms=0.387 (0.074%), neg=0, invalid=762 0402: dt=0.080000, rms=0.387 (0.019%), neg=0, invalid=762 0403: dt=0.080000, rms=0.387 (0.010%), neg=0, invalid=762 0404: dt=0.080000, rms=0.387 (-0.025%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 1 minutes and 51 seconds. mri_ca_register utimesec 8244.543638 mri_ca_register stimesec 9.166606 mri_ca_register ru_maxrss 1338304 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4529199 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63472 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 4230 mri_ca_register ru_nivcsw 35293 FSRUNTIME@ mri_ca_register 2.0309 hours 2 threads #-------------------------------------- #@# SubCort Seg Sat Oct 7 19:28:48 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-382 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-6.0.0/0051362/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 2 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.21 Atlas used for the 3D morph was /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.09804 (17) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (1417 voxels, overlap=0.811) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (1417 voxels, peak = 17), gca=17.3 gca peak = 0.17677 (13) mri peak = 0.08616 (17) Right_Lateral_Ventricle (43): linear fit = 1.20 x + 0.0 (1306 voxels, overlap=0.892) Right_Lateral_Ventricle (43): linear fit = 1.20 x + 0.0 (1306 voxels, peak = 16), gca=15.5 gca peak = 0.28129 (95) mri peak = 0.10183 (95) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (382 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (382 voxels, peak = 96), gca=96.4 gca peak = 0.16930 (96) mri peak = 0.11983 (94) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (349 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (349 voxels, peak = 98), gca=98.4 gca peak = 0.24553 (55) mri peak = 0.07905 (63) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (509 voxels, overlap=0.962) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (509 voxels, peak = 62), gca=62.4 gca peak = 0.30264 (59) mri peak = 0.07713 (62) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (470 voxels, overlap=1.015) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (470 voxels, peak = 63), gca=63.4 gca peak = 0.07580 (103) mri peak = 0.08934 (104) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31460 voxels, overlap=0.784) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31460 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.07237 (99) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30742 voxels, overlap=0.835) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30742 voxels, peak = 104), gca=104.0 gca peak = 0.09712 (58) mri peak = 0.04272 (64) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (10203 voxels, overlap=0.946) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (10203 voxels, peak = 61), gca=60.6 gca peak = 0.11620 (58) mri peak = 0.04483 (63) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (10917 voxels, overlap=0.806) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (10917 voxels, peak = 64), gca=63.5 gca peak = 0.30970 (66) mri peak = 0.07820 (79) Right_Caudate (50): linear fit = 1.14 x + 0.0 (844 voxels, overlap=0.377) Right_Caudate (50): linear fit = 1.14 x + 0.0 (844 voxels, peak = 76), gca=75.6 gca peak = 0.15280 (69) mri peak = 0.08963 (79) Left_Caudate (11): linear fit = 1.07 x + 0.0 (904 voxels, overlap=1.004) Left_Caudate (11): linear fit = 1.07 x + 0.0 (904 voxels, peak = 73), gca=73.5 gca peak = 0.13902 (56) mri peak = 0.05161 (63) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (5123 voxels, overlap=0.864) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (5123 voxels, peak = 62), gca=62.4 gca peak = 0.14777 (55) mri peak = 0.05681 (68) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (6423 voxels, overlap=0.227) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (6423 voxels, peak = 66), gca=65.7 gca peak = 0.16765 (84) mri peak = 0.07499 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (2421 voxels, overlap=0.865) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (2421 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.08716 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (2944 voxels, overlap=0.743) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (2944 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.10451 (67) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (266 voxels, overlap=0.817) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (266 voxels, peak = 64), gca=63.6 gca peak = 0.33601 (57) mri peak = 0.08961 (65) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (243 voxels, overlap=1.005) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (243 voxels, peak = 64), gca=63.6 gca peak = 0.11131 (90) mri peak = 0.06785 (86) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (2474 voxels, overlap=0.992) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (2474 voxels, peak = 88), gca=87.8 gca peak = 0.11793 (83) mri peak = 0.07065 (85) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (2597 voxels, overlap=0.950) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (2597 voxels, peak = 87), gca=86.7 gca peak = 0.08324 (81) mri peak = 0.06699 (81) Left_Putamen (12): linear fit = 1.07 x + 0.0 (1357 voxels, overlap=0.759) Left_Putamen (12): linear fit = 1.07 x + 0.0 (1357 voxels, peak = 86), gca=86.3 gca peak = 0.10360 (77) mri peak = 0.06001 (82) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1309 voxels, overlap=0.883) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1309 voxels, peak = 81), gca=81.2 gca peak = 0.08424 (78) mri peak = 0.09242 (84) Brain_Stem (16): linear fit = 1.07 x + 0.0 (5773 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.07 x + 0.0 (5773 voxels, peak = 83), gca=83.1 gca peak = 0.12631 (89) mri peak = 0.07270 (92) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (678 voxels, overlap=0.760) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (678 voxels, peak = 95), gca=94.8 gca peak = 0.14500 (87) mri peak = 0.07380 (96) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (714 voxels, overlap=0.813) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (714 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) mri peak = 0.10010 (15) gca peak = 0.19357 (14) mri peak = 0.13450 (20) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (225 voxels, overlap=0.887) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (225 voxels, peak = 18), gca=17.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.10 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.11 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.17218 (16) mri peak = 0.09804 (17) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (1417 voxels, overlap=0.921) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (1417 voxels, peak = 16), gca=16.0 gca peak = 0.16342 (15) mri peak = 0.08616 (17) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (1306 voxels, overlap=0.743) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (1306 voxels, peak = 16), gca=16.4 gca peak = 0.25981 (97) mri peak = 0.10183 (95) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (382 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (382 voxels, peak = 97), gca=96.5 gca peak = 0.16584 (97) mri peak = 0.11983 (94) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (349 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (349 voxels, peak = 97), gca=97.5 gca peak = 0.26963 (63) mri peak = 0.07905 (63) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (509 voxels, overlap=1.004) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (509 voxels, peak = 62), gca=62.1 gca peak = 0.24587 (64) mri peak = 0.07713 (62) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (470 voxels, overlap=1.013) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (470 voxels, peak = 64), gca=64.0 gca peak = 0.07772 (104) mri peak = 0.08934 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31460 voxels, overlap=0.833) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31460 voxels, peak = 103), gca=103.5 gca peak = 0.07714 (104) mri peak = 0.07237 (99) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30742 voxels, overlap=0.835) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30742 voxels, peak = 104), gca=104.0 gca peak = 0.09252 (61) mri peak = 0.04272 (64) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (10203 voxels, overlap=0.979) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (10203 voxels, peak = 63), gca=62.5 gca peak = 0.10558 (64) mri peak = 0.04483 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (10917 voxels, overlap=0.965) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (10917 voxels, peak = 66), gca=65.6 gca peak = 0.24443 (76) mri peak = 0.07820 (79) Right_Caudate (50): linear fit = 0.99 x + 0.0 (844 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.99 x + 0.0 (844 voxels, peak = 75), gca=74.9 gca peak = 0.12679 (73) mri peak = 0.08963 (79) Left_Caudate (11): linear fit = 0.99 x + 0.0 (904 voxels, overlap=1.005) Left_Caudate (11): linear fit = 0.99 x + 0.0 (904 voxels, peak = 72), gca=71.9 gca peak = 0.12455 (62) mri peak = 0.05161 (63) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (5123 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (5123 voxels, peak = 61), gca=61.1 gca peak = 0.12176 (66) mri peak = 0.05681 (68) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (6423 voxels, overlap=0.991) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (6423 voxels, peak = 66), gca=66.0 gca peak = 0.15873 (90) mri peak = 0.07499 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (2421 voxels, overlap=0.985) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (2421 voxels, peak = 90), gca=89.6 gca peak = 0.15153 (90) mri peak = 0.08716 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (2944 voxels, overlap=0.967) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (2944 voxels, peak = 90), gca=89.6 gca peak = 0.24255 (65) mri peak = 0.10451 (67) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (266 voxels, overlap=1.020) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (266 voxels, peak = 65), gca=65.0 gca peak = 0.30515 (64) mri peak = 0.08961 (65) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (243 voxels, overlap=1.021) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (243 voxels, peak = 64), gca=64.0 gca peak = 0.11020 (86) mri peak = 0.06785 (86) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2474 voxels, overlap=0.952) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2474 voxels, peak = 86), gca=85.6 gca peak = 0.09848 (90) mri peak = 0.07065 (85) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (2597 voxels, overlap=0.982) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (2597 voxels, peak = 89), gca=88.7 gca peak = 0.08936 (88) mri peak = 0.06699 (81) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1357 voxels, overlap=0.939) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1357 voxels, peak = 87), gca=86.7 gca peak = 0.08162 (81) mri peak = 0.06001 (82) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1309 voxels, overlap=0.999) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1309 voxels, peak = 81), gca=80.6 gca peak = 0.07305 (83) mri peak = 0.09242 (84) Brain_Stem (16): linear fit = 0.99 x + 0.0 (5773 voxels, overlap=0.727) Brain_Stem (16): linear fit = 0.99 x + 0.0 (5773 voxels, peak = 82), gca=81.8 gca peak = 0.11574 (95) mri peak = 0.07270 (92) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (678 voxels, overlap=0.846) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (678 voxels, peak = 93), gca=92.6 gca peak = 0.16271 (92) mri peak = 0.07380 (96) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (714 voxels, overlap=0.951) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (714 voxels, peak = 94), gca=94.3 gca peak = 0.17034 (28) mri peak = 0.10010 (15) gca peak = 0.16541 (20) mri peak = 0.13450 (20) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (225 voxels, overlap=0.744) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (225 voxels, peak = 20), gca=20.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.15020 (36) gca peak Left_Thalamus = 0.64095 (101) gca peak Third_Ventricle = 0.17034 (28) gca peak CSF = 0.21662 (40) gca peak Left_Accumbens_area = 0.64436 (66) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11917 (35) gca peak Right_Inf_Lat_Vent = 0.21972 (26) gca peak Right_Accumbens_area = 0.29834 (74) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65358 (35) gca peak WM_hypointensities = 0.07609 (77) gca peak non_WM_hypointensities = 0.10019 (77) gca peak Optic_Chiasm = 0.70601 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 77226 voxels changed in iteration 0 of unlikely voxel relabeling 258 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 42922 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 477 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 74328 changed. image ll: -2.098, PF=0.500 pass 2: 19205 changed. image ll: -2.097, PF=0.500 pass 3: 4935 changed. 42630 voxels changed in iteration 0 of unlikely voxel relabeling 261 voxels changed in iteration 1 of unlikely voxel relabeling 18 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6819 voxels changed in iteration 0 of unlikely voxel relabeling 96 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5863 voxels changed in iteration 0 of unlikely voxel relabeling 54 voxels changed in iteration 1 of unlikely voxel relabeling 24 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 1 voxels changed in iteration 4 of unlikely voxel relabeling 4175 voxels changed in iteration 0 of unlikely voxel relabeling 15 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3342.971791 mri_ca_label stimesec 1.430782 mri_ca_label ru_maxrss 2096384 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 711771 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 63464 mri_ca_label ru_oublock 464 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 315 mri_ca_label ru_nivcsw 4504 auto-labeling took 54 minutes and 58 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/transforms/cc_up.lta 0051362 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-6.0.0/0051362/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/norm.mgz 33968 voxels in left wm, 36272 in right wm, xrange [123, 132] searching rotation angles z=[-3 11], y=[-7 7] searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.7 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.5 searching scale 1 Z rot 8.7 searching scale 1 Z rot 9.0 searching scale 1 Z rot 9.2 searching scale 1 Z rot 9.5 searching scale 1 Z rot 9.7 searching scale 1 Z rot 10.0 searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.5 global minimum found at slice 127.3, rotations (-0.25, 3.72) final transformation (x=127.3, yr=-0.254, zr=3.722): 0.99788 -0.06492 -0.00443 6.58695; 0.06492 0.99789 -0.00029 40.93382; 0.00444 -0.00000 0.99999 24.43588; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 79 103 eigenvectors: 0.00036 0.00494 0.99999; -0.20476 -0.97880 0.00491; 0.97881 -0.20476 0.00066; error in mid anterior detected - correcting... writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aseg.auto.mgz... corpus callosum segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Sat Oct 7 20:24:31 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Oct 7 20:24:31 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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... 931 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 103 gm peak at 69 (69), valley at 29 (29) csf peak at 10, 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 109 gm peak at 69 (69), valley at 25 (25) csf peak at 10, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 27 seconds. #-------------------------------------------- #@# Mask BFS Sat Oct 7 20:27:59 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1436288 voxels in mask (pct= 8.56) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Oct 7 20:28:01 CEST 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 106.1 +- 5.5 [79.0 --> 125.0] GM (69.0) : 67.3 +- 9.7 [30.0 --> 95.0] setting bottom of white matter range to 77.0 setting top of gray matter range to 86.7 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 16029 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4230 filled 2011 bright non-wm voxels segmented. 8181 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 0.50 minutes reading wm segmentation from wm.seg.mgz... 62 voxels added to wm to prevent paths from MTL structures to cortex 2599 additional wm voxels added 0 additional wm voxels added SEG EDIT: 49350 voxels turned on, 37268 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+): 27 found - 27 modified | TOTAL: 27 pass 2 (xy+): 0 found - 27 modified | TOTAL: 27 pass 1 (xy-): 28 found - 28 modified | TOTAL: 55 pass 2 (xy-): 0 found - 28 modified | TOTAL: 55 pass 1 (yz+): 35 found - 35 modified | TOTAL: 90 pass 2 (yz+): 0 found - 35 modified | TOTAL: 90 pass 1 (yz-): 20 found - 20 modified | TOTAL: 110 pass 2 (yz-): 0 found - 20 modified | TOTAL: 110 pass 1 (xz+): 22 found - 22 modified | TOTAL: 132 pass 2 (xz+): 0 found - 22 modified | TOTAL: 132 pass 1 (xz-): 24 found - 24 modified | TOTAL: 156 pass 2 (xz-): 0 found - 24 modified | TOTAL: 156 Iteration Number : 1 pass 1 (+++): 32 found - 32 modified | TOTAL: 32 pass 2 (+++): 0 found - 32 modified | TOTAL: 32 pass 1 (+++): 12 found - 12 modified | TOTAL: 44 pass 2 (+++): 0 found - 12 modified | TOTAL: 44 pass 1 (+++): 17 found - 17 modified | TOTAL: 61 pass 2 (+++): 0 found - 17 modified | TOTAL: 61 pass 1 (+++): 25 found - 25 modified | TOTAL: 86 pass 2 (+++): 0 found - 25 modified | TOTAL: 86 Iteration Number : 1 pass 1 (++): 186 found - 186 modified | TOTAL: 186 pass 2 (++): 0 found - 186 modified | TOTAL: 186 pass 1 (+-): 161 found - 161 modified | TOTAL: 347 pass 2 (+-): 0 found - 161 modified | TOTAL: 347 pass 1 (--): 146 found - 146 modified | TOTAL: 493 pass 2 (--): 0 found - 146 modified | TOTAL: 493 pass 1 (-+): 148 found - 148 modified | TOTAL: 641 pass 2 (-+): 0 found - 148 modified | TOTAL: 641 Iteration Number : 2 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 10 found - 10 modified | TOTAL: 16 pass 2 (xy-): 0 found - 10 modified | TOTAL: 16 pass 1 (yz+): 9 found - 9 modified | TOTAL: 25 pass 2 (yz+): 0 found - 9 modified | TOTAL: 25 pass 1 (yz-): 14 found - 14 modified | TOTAL: 39 pass 2 (yz-): 0 found - 14 modified | TOTAL: 39 pass 1 (xz+): 11 found - 11 modified | TOTAL: 50 pass 2 (xz+): 0 found - 11 modified | TOTAL: 50 pass 1 (xz-): 8 found - 8 modified | TOTAL: 58 pass 2 (xz-): 0 found - 8 modified | TOTAL: 58 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 3 found - 3 modified | TOTAL: 7 pass 2 (+++): 0 found - 3 modified | TOTAL: 7 Iteration Number : 2 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 8 found - 8 modified | TOTAL: 13 pass 2 (+-): 0 found - 8 modified | TOTAL: 13 pass 1 (--): 5 found - 5 modified | TOTAL: 18 pass 2 (--): 0 found - 5 modified | TOTAL: 18 pass 1 (-+): 3 found - 3 modified | TOTAL: 21 pass 2 (-+): 0 found - 3 modified | TOTAL: 21 Iteration Number : 3 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+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 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 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 972 (out of 550200: 0.176663) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Oct 7 20:30:13 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 1.05525 -0.01208 0.00471 -8.93146; 0.00855 1.11986 0.37860 -26.39128; -0.00847 -0.35063 0.97219 39.08955; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.05525 -0.01208 0.00471 -8.93146; 0.00855 1.11986 0.37860 -26.39128; -0.00847 -0.35063 0.97219 39.08955; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1479 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75) need search nearby using seed (125, 120, 154), TAL = (3.0, 26.0, 8.0) talairach voxel to voxel transform 0.94752 0.00782 -0.00764 8.96793; -0.00894 0.79585 -0.30988 33.03664; 0.00503 0.28710 0.91677 -28.21438; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 120, 154) --> (3.0, 26.0, 8.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (3.00, 26.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 26.00, 8.00) SRC: (110.11, 79.86, 147.96) search lh wm seed point around talairach space (-15.00, 26.00, 8.00), SRC: (144.22, 79.54, 148.14) 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 20:31:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 1 found - 1 modified | TOTAL: 5 pass 2 (xz+): 0 found - 1 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 6 (out of 262326: 0.002287) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 986 vertices, 1093 faces slice 50: 6772 vertices, 7029 faces slice 60: 16201 vertices, 16598 faces slice 70: 27815 vertices, 28233 faces slice 80: 39674 vertices, 40149 faces slice 90: 51788 vertices, 52210 faces slice 100: 63920 vertices, 64361 faces slice 110: 75793 vertices, 76244 faces slice 120: 87301 vertices, 87756 faces slice 130: 98558 vertices, 98983 faces slice 140: 108849 vertices, 109274 faces slice 150: 117696 vertices, 118067 faces slice 160: 125736 vertices, 126037 faces slice 170: 131774 vertices, 132052 faces slice 180: 136714 vertices, 136940 faces slice 190: 139470 vertices, 139584 faces slice 200: 139540 vertices, 139630 faces slice 210: 139540 vertices, 139630 faces slice 220: 139540 vertices, 139630 faces slice 230: 139540 vertices, 139630 faces slice 240: 139540 vertices, 139630 faces slice 250: 139540 vertices, 139630 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... 139540 voxel in cpt #1: X=-90 [v=139540,e=418890,f=279260] located at (-26.377993, -22.056107, 41.319027) For the whole surface: X=-90 [v=139540,e=418890,f=279260] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat Oct 7 20:31:07 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 4 found - 4 modified | TOTAL: 4 pass 2 (yz+): 0 found - 4 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 2 found - 2 modified | TOTAL: 7 pass 2 (xz+): 0 found - 2 modified | TOTAL: 7 pass 1 (xz-): 0 found - 0 modified | TOTAL: 7 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 = 8 (out of 271031: 0.002952) 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: 2086 vertices, 2272 faces slice 50: 10639 vertices, 11008 faces slice 60: 22283 vertices, 22706 faces slice 70: 34252 vertices, 34680 faces slice 80: 46088 vertices, 46527 faces slice 90: 58181 vertices, 58626 faces slice 100: 70753 vertices, 71195 faces slice 110: 82778 vertices, 83214 faces slice 120: 94244 vertices, 94716 faces slice 130: 105086 vertices, 105505 faces slice 140: 115466 vertices, 115848 faces slice 150: 123939 vertices, 124300 faces slice 160: 131098 vertices, 131382 faces slice 170: 136552 vertices, 136815 faces slice 180: 140723 vertices, 140934 faces slice 190: 142742 vertices, 142838 faces slice 200: 142742 vertices, 142838 faces slice 210: 142742 vertices, 142838 faces slice 220: 142742 vertices, 142838 faces slice 230: 142742 vertices, 142838 faces slice 240: 142742 vertices, 142838 faces slice 250: 142742 vertices, 142838 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... 142742 voxel in cpt #1: X=-96 [v=142742,e=428514,f=285676] located at (27.824986, -26.274376, 39.041965) For the whole surface: X=-96 [v=142742,e=428514,f=285676] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Oct 7 20:31:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sat Oct 7 20:31:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 9697 of (9697 9700) to complete... Waiting for PID 9700 of (9697 9700) 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 (9697 9700) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sat Oct 7 20:31:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sat Oct 7 20:31:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 9744 of (9744 9747) to complete... Waiting for PID 9747 of (9744 9747) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 45.9 mm, total surface area = 70309 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.163 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.048 (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=0.039 (target=0.015) step 060: RMS=0.039 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 42.089601 mris_inflate stimesec 0.093985 mris_inflate ru_maxrss 206844 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29675 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9840 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1977 mris_inflate ru_nivcsw 3253 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.5 mm, total surface area = 72131 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.160 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.065 (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 43.002462 mris_inflate stimesec 0.097985 mris_inflate ru_maxrss 209472 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30331 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10064 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2299 mris_inflate ru_nivcsw 3284 PIDs (9744 9747) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sat Oct 7 20:32:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sat Oct 7 20:32:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 9811 of (9811 9814) to complete... Waiting for PID 9814 of (9811 9814) 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 0.98 +- 0.57 (0.00-->6.39) (max @ vno 56216 --> 57424) face area 0.03 +- 0.03 (-0.10-->0.68) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.325... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.043, avgs=0 005/300: dt: 0.9000, rms radial error=175.784, avgs=0 010/300: dt: 0.9000, rms radial error=175.228, avgs=0 015/300: dt: 0.9000, rms radial error=174.498, avgs=0 020/300: dt: 0.9000, rms radial error=173.666, avgs=0 025/300: dt: 0.9000, rms radial error=172.776, avgs=0 030/300: dt: 0.9000, rms radial error=171.852, avgs=0 035/300: dt: 0.9000, rms radial error=170.912, avgs=0 040/300: dt: 0.9000, rms radial error=169.967, avgs=0 045/300: dt: 0.9000, rms radial error=169.024, avgs=0 050/300: dt: 0.9000, rms radial error=168.082, avgs=0 055/300: dt: 0.9000, rms radial error=167.143, avgs=0 060/300: dt: 0.9000, rms radial error=166.207, avgs=0 065/300: dt: 0.9000, rms radial error=165.275, avgs=0 070/300: dt: 0.9000, rms radial error=164.348, avgs=0 075/300: dt: 0.9000, rms radial error=163.425, avgs=0 080/300: dt: 0.9000, rms radial error=162.506, avgs=0 085/300: dt: 0.9000, rms radial error=161.593, avgs=0 090/300: dt: 0.9000, rms radial error=160.684, avgs=0 095/300: dt: 0.9000, rms radial error=159.780, avgs=0 100/300: dt: 0.9000, rms radial error=158.881, avgs=0 105/300: dt: 0.9000, rms radial error=157.986, avgs=0 110/300: dt: 0.9000, rms radial error=157.096, avgs=0 115/300: dt: 0.9000, rms radial error=156.211, avgs=0 120/300: dt: 0.9000, rms radial error=155.331, avgs=0 125/300: dt: 0.9000, rms radial error=154.456, avgs=0 130/300: dt: 0.9000, rms radial error=153.585, avgs=0 135/300: dt: 0.9000, rms radial error=152.720, avgs=0 140/300: dt: 0.9000, rms radial error=151.860, avgs=0 145/300: dt: 0.9000, rms radial error=151.004, avgs=0 150/300: dt: 0.9000, rms radial error=150.153, avgs=0 155/300: dt: 0.9000, rms radial error=149.307, avgs=0 160/300: dt: 0.9000, rms radial error=148.465, avgs=0 165/300: dt: 0.9000, rms radial error=147.627, avgs=0 170/300: dt: 0.9000, rms radial error=146.795, avgs=0 175/300: dt: 0.9000, rms radial error=145.967, avgs=0 180/300: dt: 0.9000, rms radial error=145.143, avgs=0 185/300: dt: 0.9000, rms radial error=144.324, avgs=0 190/300: dt: 0.9000, rms radial error=143.509, avgs=0 195/300: dt: 0.9000, rms radial error=142.699, avgs=0 200/300: dt: 0.9000, rms radial error=141.893, avgs=0 205/300: dt: 0.9000, rms radial error=141.092, avgs=0 210/300: dt: 0.9000, rms radial error=140.295, avgs=0 215/300: dt: 0.9000, rms radial error=139.503, avgs=0 220/300: dt: 0.9000, rms radial error=138.714, avgs=0 225/300: dt: 0.9000, rms radial error=137.931, avgs=0 230/300: dt: 0.9000, rms radial error=137.152, avgs=0 235/300: dt: 0.9000, rms radial error=136.377, avgs=0 240/300: dt: 0.9000, rms radial error=135.606, avgs=0 245/300: dt: 0.9000, rms radial error=134.840, avgs=0 250/300: dt: 0.9000, rms radial error=134.078, avgs=0 255/300: dt: 0.9000, rms radial error=133.320, avgs=0 260/300: dt: 0.9000, rms radial error=132.567, avgs=0 265/300: dt: 0.9000, rms radial error=131.817, avgs=0 270/300: dt: 0.9000, rms radial error=131.072, avgs=0 275/300: dt: 0.9000, rms radial error=130.332, avgs=0 280/300: dt: 0.9000, rms radial error=129.595, avgs=0 285/300: dt: 0.9000, rms radial error=128.862, avgs=0 290/300: dt: 0.9000, rms radial error=128.134, avgs=0 295/300: dt: 0.9000, rms radial error=127.409, avgs=0 300/300: dt: 0.9000, rms radial error=126.689, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16231.40 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 = 2691.40 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 = 277.13 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00625 epoch 4 (K=640.0), pass 1, starting sse = 19.46 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/13 = 0.00584 final distance error %26.05 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 250.569907 mris_sphere stimesec 0.179972 mris_sphere ru_maxrss 205012 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 29731 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9864 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 11404 mris_sphere ru_nivcsw 20389 FSRUNTIME@ mris_sphere 0.0697 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 0.96 +- 0.56 (0.00-->8.10) (max @ vno 109163 --> 109164) face area 0.03 +- 0.03 (-0.22-->0.71) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.323... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.717, avgs=0 005/300: dt: 0.9000, rms radial error=175.458, avgs=0 010/300: dt: 0.9000, rms radial error=174.902, avgs=0 015/300: dt: 0.9000, rms radial error=174.171, avgs=0 020/300: dt: 0.9000, rms radial error=173.340, avgs=0 025/300: dt: 0.9000, rms radial error=172.452, avgs=0 030/300: dt: 0.9000, rms radial error=171.535, avgs=0 035/300: dt: 0.9000, rms radial error=170.600, avgs=0 040/300: dt: 0.9000, rms radial error=169.658, avgs=0 045/300: dt: 0.9000, rms radial error=168.713, avgs=0 050/300: dt: 0.9000, rms radial error=167.769, avgs=0 055/300: dt: 0.9000, rms radial error=166.827, avgs=0 060/300: dt: 0.9000, rms radial error=165.889, avgs=0 065/300: dt: 0.9000, rms radial error=164.956, avgs=0 070/300: dt: 0.9000, rms radial error=164.026, avgs=0 075/300: dt: 0.9000, rms radial error=163.102, avgs=0 080/300: dt: 0.9000, rms radial error=162.182, avgs=0 085/300: dt: 0.9000, rms radial error=161.267, avgs=0 090/300: dt: 0.9000, rms radial error=160.357, avgs=0 095/300: dt: 0.9000, rms radial error=159.452, avgs=0 100/300: dt: 0.9000, rms radial error=158.553, avgs=0 105/300: dt: 0.9000, rms radial error=157.658, avgs=0 110/300: dt: 0.9000, rms radial error=156.768, avgs=0 115/300: dt: 0.9000, rms radial error=155.883, avgs=0 120/300: dt: 0.9000, rms radial error=155.004, avgs=0 125/300: dt: 0.9000, rms radial error=154.132, avgs=0 130/300: dt: 0.9000, rms radial error=153.264, avgs=0 135/300: dt: 0.9000, rms radial error=152.401, avgs=0 140/300: dt: 0.9000, rms radial error=151.543, avgs=0 145/300: dt: 0.9000, rms radial error=150.690, avgs=0 150/300: dt: 0.9000, rms radial error=149.842, avgs=0 155/300: dt: 0.9000, rms radial error=148.998, avgs=0 160/300: dt: 0.9000, rms radial error=148.159, avgs=0 165/300: dt: 0.9000, rms radial error=147.324, avgs=0 170/300: dt: 0.9000, rms radial error=146.494, avgs=0 175/300: dt: 0.9000, rms radial error=145.669, avgs=0 180/300: dt: 0.9000, rms radial error=144.848, avgs=0 185/300: dt: 0.9000, rms radial error=144.032, avgs=0 190/300: dt: 0.9000, rms radial error=143.220, avgs=0 195/300: dt: 0.9000, rms radial error=142.413, avgs=0 200/300: dt: 0.9000, rms radial error=141.610, avgs=0 205/300: dt: 0.9000, rms radial error=140.812, avgs=0 210/300: dt: 0.9000, rms radial error=140.018, avgs=0 215/300: dt: 0.9000, rms radial error=139.228, avgs=0 220/300: dt: 0.9000, rms radial error=138.443, avgs=0 225/300: dt: 0.9000, rms radial error=137.662, avgs=0 230/300: dt: 0.9000, rms radial error=136.885, avgs=0 235/300: dt: 0.9000, rms radial error=136.113, avgs=0 240/300: dt: 0.9000, rms radial error=135.346, avgs=0 245/300: dt: 0.9000, rms radial error=134.583, avgs=0 250/300: dt: 0.9000, rms radial error=133.824, avgs=0 255/300: dt: 0.9000, rms radial error=133.070, avgs=0 260/300: dt: 0.9000, rms radial error=132.320, avgs=0 265/300: dt: 0.9000, rms radial error=131.575, avgs=0 270/300: dt: 0.9000, rms radial error=130.834, avgs=0 275/300: dt: 0.9000, rms radial error=130.097, avgs=0 280/300: dt: 0.9000, rms radial error=129.364, avgs=0 285/300: dt: 0.9000, rms radial error=128.635, avgs=0 290/300: dt: 0.9000, rms radial error=127.910, avgs=0 295/300: dt: 0.9000, rms radial error=127.189, avgs=0 300/300: dt: 0.9000, rms radial error=126.472, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16617.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2743.07 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 277.88 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00735 epoch 4 (K=640.0), pass 1, starting sse = 17.79 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/13 = 0.00721 final distance error %25.80 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 255.821109 mris_sphere stimesec 0.194970 mris_sphere ru_maxrss 209680 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 30386 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 10048 mris_sphere ru_oublock 10088 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 11510 mris_sphere ru_nivcsw 20663 FSRUNTIME@ mris_sphere 0.0706 hours 1 threads PIDs (9811 9814) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sat Oct 7 20:36:16 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat Oct 7 20:36:16 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat Oct 7 20:36:16 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051362 lh #@# Fix Topology rh Sat Oct 7 20:36:16 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051362 rh Waiting for PID 10068 of (10068 10071) to complete... Waiting for PID 10071 of (10068 10071) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051362 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=-90 (nv=139540, nf=279260, ne=418890, g=46) 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... 4961 ambiguous faces found in tessellation segmenting defects... 53 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 8 into 10 -merging segment 26 into 25 -merging segment 33 into 31 -merging segment 43 into 40 49 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7351 (-4.8676) -vertex loglikelihood: -6.6003 (-3.3002) -normal dot loglikelihood: -3.5944 (-3.5944) -quad curv loglikelihood: -6.6237 (-3.3118) Total Loglikelihood : -26.5536 CORRECTING DEFECT 0 (vertices=151, convex hull=184, v0=317) After retessellation of defect 0 (v0=317), euler #=-48 (136430,407816,271338) : difference with theory (-46) = 2 CORRECTING DEFECT 1 (vertices=22, convex hull=63, v0=2270) After retessellation of defect 1 (v0=2270), euler #=-47 (136439,407868,271382) : difference with theory (-45) = 2 CORRECTING DEFECT 2 (vertices=24, convex hull=61, v0=9370) After retessellation of defect 2 (v0=9370), euler #=-46 (136454,407940,271440) : difference with theory (-44) = 2 CORRECTING DEFECT 3 (vertices=29, convex hull=44, v0=10793) After retessellation of defect 3 (v0=10793), euler #=-45 (136463,407983,271475) : difference with theory (-43) = 2 CORRECTING DEFECT 4 (vertices=99, convex hull=84, v0=14776) After retessellation of defect 4 (v0=14776), euler #=-44 (136480,408064,271540) : difference with theory (-42) = 2 CORRECTING DEFECT 5 (vertices=22, convex hull=43, v0=15817) After retessellation of defect 5 (v0=15817), euler #=-43 (136484,408090,271563) : difference with theory (-41) = 2 CORRECTING DEFECT 6 (vertices=6, convex hull=21, v0=19198) After retessellation of defect 6 (v0=19198), euler #=-42 (136484,408096,271570) : difference with theory (-40) = 2 CORRECTING DEFECT 7 (vertices=100, convex hull=125, v0=19356) After retessellation of defect 7 (v0=19356), euler #=-41 (136528,408285,271716) : difference with theory (-39) = 2 CORRECTING DEFECT 8 (vertices=12, convex hull=26, v0=26227) After retessellation of defect 8 (v0=26227), euler #=-40 (136529,408294,271725) : difference with theory (-38) = 2 CORRECTING DEFECT 9 (vertices=579, convex hull=457, v0=28697) After retessellation of defect 9 (v0=28697), euler #=-38 (136756,409203,272409) : difference with theory (-37) = 1 CORRECTING DEFECT 10 (vertices=24, convex hull=60, v0=30580) After retessellation of defect 10 (v0=30580), euler #=-37 (136770,409270,272463) : difference with theory (-36) = 1 CORRECTING DEFECT 11 (vertices=35, convex hull=48, v0=34972) After retessellation of defect 11 (v0=34972), euler #=-36 (136792,409354,272526) : difference with theory (-35) = 1 CORRECTING DEFECT 12 (vertices=36, convex hull=55, v0=37108) After retessellation of defect 12 (v0=37108), euler #=-35 (136804,409411,272572) : difference with theory (-34) = 1 CORRECTING DEFECT 13 (vertices=72, convex hull=109, v0=44035) After retessellation of defect 13 (v0=44035), euler #=-34 (136839,409559,272686) : difference with theory (-33) = 1 CORRECTING DEFECT 14 (vertices=5, convex hull=22, v0=51377) After retessellation of defect 14 (v0=51377), euler #=-33 (136841,409572,272698) : difference with theory (-32) = 1 CORRECTING DEFECT 15 (vertices=25, convex hull=55, v0=52421) After retessellation of defect 15 (v0=52421), euler #=-32 (136852,409627,272743) : difference with theory (-31) = 1 CORRECTING DEFECT 16 (vertices=31, convex hull=33, v0=58546) After retessellation of defect 16 (v0=58546), euler #=-31 (136861,409665,272773) : difference with theory (-30) = 1 CORRECTING DEFECT 17 (vertices=40, convex hull=46, v0=70995) After retessellation of defect 17 (v0=70995), euler #=-30 (136874,409722,272818) : difference with theory (-29) = 1 CORRECTING DEFECT 18 (vertices=520, convex hull=175, v0=71918) After retessellation of defect 18 (v0=71918), euler #=-30 (136935,409997,273032) : difference with theory (-28) = 2 CORRECTING DEFECT 19 (vertices=17, convex hull=30, v0=79301) After retessellation of defect 19 (v0=79301), euler #=-29 (136936,410009,273044) : difference with theory (-27) = 2 CORRECTING DEFECT 20 (vertices=31, convex hull=51, v0=80095) After retessellation of defect 20 (v0=80095), euler #=-28 (136947,410058,273083) : difference with theory (-26) = 2 CORRECTING DEFECT 21 (vertices=28, convex hull=62, v0=86157) After retessellation of defect 21 (v0=86157), euler #=-27 (136959,410117,273131) : difference with theory (-25) = 2 CORRECTING DEFECT 22 (vertices=9, convex hull=14, v0=89379) After retessellation of defect 22 (v0=89379), euler #=-26 (136960,410122,273136) : difference with theory (-24) = 2 CORRECTING DEFECT 23 (vertices=14, convex hull=23, v0=91068) After retessellation of defect 23 (v0=91068), euler #=-25 (136963,410137,273149) : difference with theory (-23) = 2 CORRECTING DEFECT 24 (vertices=38, convex hull=73, v0=93619) After retessellation of defect 24 (v0=93619), euler #=-24 (136978,410224,273222) : difference with theory (-22) = 2 CORRECTING DEFECT 25 (vertices=14, convex hull=21, v0=95774) After retessellation of defect 25 (v0=95774), euler #=-23 (136981,410238,273234) : difference with theory (-21) = 2 CORRECTING DEFECT 26 (vertices=6, convex hull=14, v0=98166) After retessellation of defect 26 (v0=98166), euler #=-22 (136981,410242,273239) : difference with theory (-20) = 2 CORRECTING DEFECT 27 (vertices=10, convex hull=20, v0=98358) After retessellation of defect 27 (v0=98358), euler #=-21 (136982,410253,273250) : difference with theory (-19) = 2 CORRECTING DEFECT 28 (vertices=34, convex hull=49, v0=100153) After retessellation of defect 28 (v0=100153), euler #=-20 (136991,410298,273287) : difference with theory (-18) = 2 CORRECTING DEFECT 29 (vertices=50, convex hull=76, v0=100269) After retessellation of defect 29 (v0=100269), euler #=-18 (137024,410433,273391) : difference with theory (-17) = 1 CORRECTING DEFECT 30 (vertices=51, convex hull=33, v0=102089) After retessellation of defect 30 (v0=102089), euler #=-17 (137029,410455,273409) : difference with theory (-16) = 1 CORRECTING DEFECT 31 (vertices=66, convex hull=101, v0=102406) After retessellation of defect 31 (v0=102406), euler #=-16 (137038,410522,273468) : difference with theory (-15) = 1 CORRECTING DEFECT 32 (vertices=6, convex hull=43, v0=103153) After retessellation of defect 32 (v0=103153), euler #=-15 (137041,410542,273486) : difference with theory (-14) = 1 CORRECTING DEFECT 33 (vertices=137, convex hull=137, v0=103184) After retessellation of defect 33 (v0=103184), euler #=-14 (137065,410676,273597) : difference with theory (-13) = 1 CORRECTING DEFECT 34 (vertices=60, convex hull=66, v0=104221) After retessellation of defect 34 (v0=104221), euler #=-13 (137067,410711,273631) : difference with theory (-12) = 1 CORRECTING DEFECT 35 (vertices=6, convex hull=27, v0=104323) After retessellation of defect 35 (v0=104323), euler #=-12 (137068,410720,273640) : difference with theory (-11) = 1 CORRECTING DEFECT 36 (vertices=19, convex hull=22, v0=107310) After retessellation of defect 36 (v0=107310), euler #=-11 (137072,410740,273657) : difference with theory (-10) = 1 CORRECTING DEFECT 37 (vertices=218, convex hull=243, v0=108766) After retessellation of defect 37 (v0=108766), euler #=-9 (137184,411203,274010) : difference with theory (-9) = 0 CORRECTING DEFECT 38 (vertices=24, convex hull=38, v0=112299) After retessellation of defect 38 (v0=112299), euler #=-8 (137186,411223,274029) : difference with theory (-8) = 0 CORRECTING DEFECT 39 (vertices=54, convex hull=98, v0=113157) After retessellation of defect 39 (v0=113157), euler #=-7 (137209,411331,274115) : difference with theory (-7) = 0 CORRECTING DEFECT 40 (vertices=24, convex hull=55, v0=113403) After retessellation of defect 40 (v0=113403), euler #=-6 (137222,411391,274163) : difference with theory (-6) = 0 CORRECTING DEFECT 41 (vertices=22, convex hull=49, v0=115546) After retessellation of defect 41 (v0=115546), euler #=-5 (137231,411432,274196) : difference with theory (-5) = 0 CORRECTING DEFECT 42 (vertices=40, convex hull=78, v0=115699) After retessellation of defect 42 (v0=115699), euler #=-4 (137257,411543,274282) : difference with theory (-4) = 0 CORRECTING DEFECT 43 (vertices=33, convex hull=50, v0=118325) After retessellation of defect 43 (v0=118325), euler #=-3 (137266,411588,274319) : difference with theory (-3) = 0 CORRECTING DEFECT 44 (vertices=173, convex hull=193, v0=118397) After retessellation of defect 44 (v0=118397), euler #=-2 (137362,411971,274607) : difference with theory (-2) = 0 CORRECTING DEFECT 45 (vertices=58, convex hull=115, v0=126950) After retessellation of defect 45 (v0=126950), euler #=-1 (137404,412141,274736) : difference with theory (-1) = 0 CORRECTING DEFECT 46 (vertices=23, convex hull=58, v0=131740) After retessellation of defect 46 (v0=131740), euler #=0 (137412,412184,274772) : difference with theory (0) = 0 CORRECTING DEFECT 47 (vertices=28, convex hull=71, v0=134411) After retessellation of defect 47 (v0=134411), euler #=1 (137421,412237,274817) : difference with theory (1) = 0 CORRECTING DEFECT 48 (vertices=30, convex hull=50, v0=134887) After retessellation of defect 48 (v0=134887), euler #=2 (137434,412296,274864) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.87 +- 0.24 (0.08-->9.94) (max @ vno 31249 --> 33498) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.87 +- 0.24 (0.08-->9.94) (max @ vno 31249 --> 33498) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 190 mutations (36.3%), 334 crossovers (63.7%), 157 vertices were eliminated building final representation... 2106 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=137434, nf=274864, ne=412296, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 28.6 minutes 0 defective edges removing intersecting faces 000: 369 intersecting 001: 13 intersecting mris_fix_topology utimesec 1713.312536 mris_fix_topology stimesec 0.224965 mris_fix_topology ru_maxrss 436676 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 56235 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 9824 mris_fix_topology ru_oublock 13208 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 403 mris_fix_topology ru_nivcsw 4363 FSRUNTIME@ mris_fix_topology lh 0.4759 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051362 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=-96 (nv=142742, nf=285676, ne=428514, g=49) 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 6 iterations marking ambiguous vertices... 5332 ambiguous faces found in tessellation segmenting defects... 49 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 49 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.6576 (-4.8288) -vertex loglikelihood: -6.5775 (-3.2887) -normal dot loglikelihood: -3.4957 (-3.4957) -quad curv loglikelihood: -6.6309 (-3.3154) Total Loglikelihood : -26.3616 CORRECTING DEFECT 0 (vertices=17, convex hull=51, v0=278) After retessellation of defect 0 (v0=278), euler #=-43 (139505,417196,277648) : difference with theory (-46) = -3 CORRECTING DEFECT 1 (vertices=28, convex hull=73, v0=3964) After retessellation of defect 1 (v0=3964), euler #=-42 (139514,417253,277697) : difference with theory (-45) = -3 CORRECTING DEFECT 2 (vertices=33, convex hull=72, v0=4905) After retessellation of defect 2 (v0=4905), euler #=-41 (139530,417332,277761) : difference with theory (-44) = -3 CORRECTING DEFECT 3 (vertices=31, convex hull=68, v0=17019) After retessellation of defect 3 (v0=17019), euler #=-40 (139549,417416,277827) : difference with theory (-43) = -3 CORRECTING DEFECT 4 (vertices=27, convex hull=50, v0=30576) After retessellation of defect 4 (v0=30576), euler #=-39 (139560,417468,277869) : difference with theory (-42) = -3 CORRECTING DEFECT 5 (vertices=23, convex hull=66, v0=31763) After retessellation of defect 5 (v0=31763), euler #=-38 (139569,417519,277912) : difference with theory (-41) = -3 CORRECTING DEFECT 6 (vertices=23, convex hull=52, v0=52266) After retessellation of defect 6 (v0=52266), euler #=-37 (139579,417568,277952) : difference with theory (-40) = -3 CORRECTING DEFECT 7 (vertices=62, convex hull=62, v0=57596) After retessellation of defect 7 (v0=57596), euler #=-36 (139588,417621,277997) : difference with theory (-39) = -3 CORRECTING DEFECT 8 (vertices=25, convex hull=30, v0=57964) After retessellation of defect 8 (v0=57964), euler #=-35 (139593,417651,278023) : difference with theory (-38) = -3 CORRECTING DEFECT 9 (vertices=46, convex hull=58, v0=60159) After retessellation of defect 9 (v0=60159), euler #=-34 (139616,417745,278095) : difference with theory (-37) = -3 CORRECTING DEFECT 10 (vertices=25, convex hull=34, v0=60882) After retessellation of defect 10 (v0=60882), euler #=-33 (139624,417781,278124) : difference with theory (-36) = -3 CORRECTING DEFECT 11 (vertices=19, convex hull=22, v0=64261) After retessellation of defect 11 (v0=64261), euler #=-32 (139628,417798,278138) : difference with theory (-35) = -3 CORRECTING DEFECT 12 (vertices=24, convex hull=52, v0=65357) After retessellation of defect 12 (v0=65357), euler #=-31 (139642,417858,278185) : difference with theory (-34) = -3 CORRECTING DEFECT 13 (vertices=29, convex hull=44, v0=67242) After retessellation of defect 13 (v0=67242), euler #=-30 (139655,417912,278227) : difference with theory (-33) = -3 CORRECTING DEFECT 14 (vertices=17, convex hull=47, v0=70931) After retessellation of defect 14 (v0=70931), euler #=-29 (139665,417960,278266) : difference with theory (-32) = -3 CORRECTING DEFECT 15 (vertices=475, convex hull=203, v0=73007) After retessellation of defect 15 (v0=73007), euler #=-28 (139676,418090,278386) : difference with theory (-31) = -3 CORRECTING DEFECT 16 (vertices=35, convex hull=46, v0=75172) After retessellation of defect 16 (v0=75172), euler #=-27 (139688,418143,278428) : difference with theory (-30) = -3 CORRECTING DEFECT 17 (vertices=31, convex hull=59, v0=79717) After retessellation of defect 17 (v0=79717), euler #=-26 (139706,418218,278486) : difference with theory (-29) = -3 CORRECTING DEFECT 18 (vertices=33, convex hull=58, v0=84174) After retessellation of defect 18 (v0=84174), euler #=-25 (139716,418269,278528) : difference with theory (-28) = -3 CORRECTING DEFECT 19 (vertices=19, convex hull=30, v0=84669) After retessellation of defect 19 (v0=84669), euler #=-24 (139721,418293,278548) : difference with theory (-27) = -3 CORRECTING DEFECT 20 (vertices=29, convex hull=47, v0=89740) After retessellation of defect 20 (v0=89740), euler #=-23 (139733,418351,278595) : difference with theory (-26) = -3 CORRECTING DEFECT 21 (vertices=194, convex hull=192, v0=90782) After retessellation of defect 21 (v0=90782), euler #=-22 (139807,418669,278840) : difference with theory (-25) = -3 CORRECTING DEFECT 22 (vertices=30, convex hull=58, v0=92544) After retessellation of defect 22 (v0=92544), euler #=-21 (139823,418741,278897) : difference with theory (-24) = -3 CORRECTING DEFECT 23 (vertices=901, convex hull=252, v0=99871) After retessellation of defect 23 (v0=99871), euler #=-21 (139964,419289,279304) : difference with theory (-23) = -2 CORRECTING DEFECT 24 (vertices=22, convex hull=31, v0=102615) After retessellation of defect 24 (v0=102615), euler #=-21 (139969,419319,279329) : difference with theory (-22) = -1 CORRECTING DEFECT 25 (vertices=6, convex hull=33, v0=102730) After retessellation of defect 25 (v0=102730), euler #=-20 (139972,419337,279345) : difference with theory (-21) = -1 CORRECTING DEFECT 26 (vertices=235, convex hull=151, v0=104701) After retessellation of defect 26 (v0=104701), euler #=-19 (140030,419585,279536) : difference with theory (-20) = -1 CORRECTING DEFECT 27 (vertices=56, convex hull=100, v0=104938) After retessellation of defect 27 (v0=104938), euler #=-18 (140064,419728,279646) : difference with theory (-19) = -1 CORRECTING DEFECT 28 (vertices=27, convex hull=66, v0=108370) After retessellation of defect 28 (v0=108370), euler #=-17 (140075,419786,279694) : difference with theory (-18) = -1 CORRECTING DEFECT 29 (vertices=65, convex hull=72, v0=109020) After retessellation of defect 29 (v0=109020), euler #=-16 (140112,419929,279801) : difference with theory (-17) = -1 CORRECTING DEFECT 30 (vertices=24, convex hull=52, v0=111451) After retessellation of defect 30 (v0=111451), euler #=-15 (140126,419990,279849) : difference with theory (-16) = -1 CORRECTING DEFECT 31 (vertices=9, convex hull=19, v0=112632) After retessellation of defect 31 (v0=112632), euler #=-14 (140128,420001,279859) : difference with theory (-15) = -1 CORRECTING DEFECT 32 (vertices=10, convex hull=21, v0=113288) After retessellation of defect 32 (v0=113288), euler #=-13 (140130,420011,279868) : difference with theory (-14) = -1 CORRECTING DEFECT 33 (vertices=13, convex hull=22, v0=113314) After retessellation of defect 33 (v0=113314), euler #=-12 (140134,420032,279886) : difference with theory (-13) = -1 CORRECTING DEFECT 34 (vertices=13, convex hull=36, v0=113471) After retessellation of defect 34 (v0=113471), euler #=-11 (140136,420050,279903) : difference with theory (-12) = -1 CORRECTING DEFECT 35 (vertices=60, convex hull=82, v0=116269) After retessellation of defect 35 (v0=116269), euler #=-10 (140163,420163,279990) : difference with theory (-11) = -1 CORRECTING DEFECT 36 (vertices=67, convex hull=41, v0=118698) After retessellation of defect 36 (v0=118698), euler #=-9 (140172,420206,280025) : difference with theory (-10) = -1 CORRECTING DEFECT 37 (vertices=11, convex hull=29, v0=121145) After retessellation of defect 37 (v0=121145), euler #=-8 (140174,420225,280043) : difference with theory (-9) = -1 CORRECTING DEFECT 38 (vertices=86, convex hull=128, v0=121294) After retessellation of defect 38 (v0=121294), euler #=-8 (140222,420427,280197) : difference with theory (-8) = 0 CORRECTING DEFECT 39 (vertices=38, convex hull=65, v0=124465) After retessellation of defect 39 (v0=124465), euler #=-7 (140243,420515,280265) : difference with theory (-7) = 0 CORRECTING DEFECT 40 (vertices=57, convex hull=100, v0=126189) After retessellation of defect 40 (v0=126189), euler #=-6 (140283,420677,280388) : difference with theory (-6) = 0 CORRECTING DEFECT 41 (vertices=18, convex hull=55, v0=126471) After retessellation of defect 41 (v0=126471), euler #=-5 (140293,420726,280428) : difference with theory (-5) = 0 CORRECTING DEFECT 42 (vertices=17, convex hull=44, v0=128489) After retessellation of defect 42 (v0=128489), euler #=-4 (140300,420762,280458) : difference with theory (-4) = 0 CORRECTING DEFECT 43 (vertices=29, convex hull=35, v0=129786) After retessellation of defect 43 (v0=129786), euler #=-3 (140309,420803,280491) : difference with theory (-3) = 0 CORRECTING DEFECT 44 (vertices=43, convex hull=66, v0=131542) After retessellation of defect 44 (v0=131542), euler #=-2 (140324,420870,280544) : difference with theory (-2) = 0 CORRECTING DEFECT 45 (vertices=46, convex hull=65, v0=134176) After retessellation of defect 45 (v0=134176), euler #=-1 (140347,420966,280618) : difference with theory (-1) = 0 CORRECTING DEFECT 46 (vertices=62, convex hull=94, v0=139255) After retessellation of defect 46 (v0=139255), euler #=0 (140371,421076,280705) : difference with theory (0) = 0 CORRECTING DEFECT 47 (vertices=33, convex hull=55, v0=141021) After retessellation of defect 47 (v0=141021), euler #=1 (140377,421119,280743) : difference with theory (1) = 0 CORRECTING DEFECT 48 (vertices=18, convex hull=17, v0=142099) After retessellation of defect 48 (v0=142099), euler #=2 (140379,421131,280754) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.87 +- 0.24 (0.05-->17.56) (max @ vno 112535 --> 140946) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.87 +- 0.24 (0.05-->17.56) (max @ vno 112535 --> 140946) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 168 mutations (36.4%), 293 crossovers (63.6%), 210 vertices were eliminated building final representation... 2363 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=140379, nf=280754, ne=421131, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 31.9 minutes 0 defective edges removing intersecting faces 000: 400 intersecting 001: 16 intersecting mris_fix_topology utimesec 1911.850354 mris_fix_topology stimesec 0.165974 mris_fix_topology ru_maxrss 445440 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 56784 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 10048 mris_fix_topology ru_oublock 13464 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 582 mris_fix_topology ru_nivcsw 2812 FSRUNTIME@ mris_fix_topology rh 0.5309 hours 1 threads PIDs (10068 10071) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 137434 - 412296 + 274864 = 2 --> 0 holes F =2V-4: 274864 = 274868-4 (0) 2E=3F: 824592 = 824592 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 140379 - 421131 + 280754 = 2 --> 0 holes F =2V-4: 280754 = 280758-4 (0) 2E=3F: 842262 = 842262 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 27 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 96 intersecting 001: 3 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Oct 7 21:08:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051362 lh #-------------------------------------------- #@# Make White Surf rh Sat Oct 7 21:08:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051362 rh Waiting for PID 11960 of (11960 11963) to complete... Waiting for PID 11963 of (11960 11963) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051362 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-6.0.0/0051362/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... 50338 bright wm thresholded. 2140 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.orig... computing class statistics... border white: 271136 voxels (1.62%) border gray 285350 voxels (1.70%) WM (96.0): 96.3 +- 9.1 [70.0 --> 110.0] GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.9 (was 70) setting MAX_BORDER_WHITE to 110.1 (was 105) setting MIN_BORDER_WHITE to 66.0 (was 85) setting MAX_CSF to 43.7 (was 40) setting MAX_GRAY to 91.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.23 (0.01-->4.67) (max @ vno 31249 --> 33498) face area 0.27 +- 0.13 (0.00-->4.60) mean absolute distance = 0.75 +- 1.01 3335 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-8.7, GM=66+-7.8 mean inside = 91.4, mean outside = 71.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=77.7, 66 (66) missing vertices, mean dist 0.1 [0.8 (%38.8)->0.7 (%61.2))] %59 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.26 (0.07-->4.56) (max @ vno 31249 --> 33498) face area 0.27 +- 0.13 (0.00-->4.09) mean absolute distance = 0.39 +- 0.68 4065 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3540618.0, rms=10.660 001: dt: 0.5000, sse=1974268.2, rms=7.457 (30.049%) 002: dt: 0.5000, sse=1323784.0, rms=5.562 (25.410%) 003: dt: 0.5000, sse=1051489.0, rms=4.531 (18.539%) 004: dt: 0.5000, sse=939244.1, rms=4.041 (10.804%) 005: dt: 0.5000, sse=901497.8, rms=3.862 (4.446%) 006: dt: 0.5000, sse=884533.2, rms=3.775 (2.247%) rms = 3.75, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=880084.5, rms=3.747 (0.727%) 008: dt: 0.2500, sse=699975.3, rms=2.580 (31.144%) 009: dt: 0.2500, sse=652385.3, rms=2.196 (14.898%) 010: dt: 0.2500, sse=644630.6, rms=2.119 (3.518%) 011: dt: 0.2500, sse=638828.5, rms=2.056 (2.933%) rms = 2.04, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=636563.9, rms=2.038 (0.909%) 013: dt: 0.1250, sse=626355.0, rms=1.928 (5.409%) rms = 1.92, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=624691.9, rms=1.919 (0.438%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=80.9, 58 (12) missing vertices, mean dist -0.2 [0.5 (%68.5)->0.2 (%31.5))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.88 +- 0.25 (0.09-->4.47) (max @ vno 31249 --> 33498) face area 0.34 +- 0.16 (0.00-->5.15) mean absolute distance = 0.29 +- 0.43 3983 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1225869.4, rms=4.651 015: dt: 0.5000, sse=952791.0, rms=3.309 (28.851%) rms = 3.59, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=813511.2, rms=2.426 (26.691%) 017: dt: 0.2500, sse=761862.9, rms=1.973 (18.662%) 018: dt: 0.2500, sse=743503.1, rms=1.784 (9.597%) rms = 1.73, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=738622.4, rms=1.734 (2.778%) 020: dt: 0.1250, sse=730369.2, rms=1.626 (6.219%) rms = 1.62, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=728975.1, rms=1.618 (0.503%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... mean border=83.4, 60 (8) missing vertices, mean dist -0.2 [0.3 (%68.1)->0.2 (%31.9))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.25 (0.06-->4.38) (max @ vno 31249 --> 33498) face area 0.33 +- 0.16 (0.00-->4.96) mean absolute distance = 0.24 +- 0.35 3719 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=958960.1, rms=3.462 022: dt: 0.5000, sse=928767.7, rms=3.254 (6.005%) rms = 3.54, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=777139.0, rms=2.213 (31.984%) 024: dt: 0.2500, sse=734648.7, rms=1.762 (20.376%) 025: dt: 0.2500, sse=719216.9, rms=1.625 (7.767%) rms = 1.62, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=716656.9, rms=1.620 (0.338%) 027: dt: 0.1250, sse=704146.0, rms=1.482 (8.542%) rms = 1.48, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=704427.9, rms=1.478 (0.240%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.3, 89 (7) missing vertices, mean dist -0.1 [0.3 (%55.2)->0.2 (%44.8))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=729573.2, rms=1.869 rms = 2.22, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=681402.6, rms=1.305 (30.188%) 030: dt: 0.2500, sse=669626.8, rms=1.073 (17.754%) rms = 1.09, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=668227.1, rms=1.068 (0.499%) positioning took 0.4 minutes generating cortex label... 13 non-cortical segments detected only using segment with 7611 vertices erasing segment 1 (vno[0] = 58612) erasing segment 2 (vno[0] = 88117) erasing segment 3 (vno[0] = 89101) erasing segment 4 (vno[0] = 93875) erasing segment 5 (vno[0] = 100044) erasing segment 6 (vno[0] = 100985) erasing segment 7 (vno[0] = 101104) erasing segment 8 (vno[0] = 102956) erasing segment 9 (vno[0] = 103883) erasing segment 10 (vno[0] = 103989) erasing segment 11 (vno[0] = 136981) erasing segment 12 (vno[0] = 136984) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.area vertex spacing 0.88 +- 0.26 (0.04-->4.36) (max @ vno 31249 --> 33498) face area 0.32 +- 0.16 (0.00-->4.95) refinement took 5.1 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051362 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-6.0.0/0051362/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... 50338 bright wm thresholded. 2140 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.orig... computing class statistics... border white: 271136 voxels (1.62%) border gray 285350 voxels (1.70%) WM (96.0): 96.3 +- 9.1 [70.0 --> 110.0] GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.9 (was 70) setting MAX_BORDER_WHITE to 109.1 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 46.7 (was 40) setting MAX_GRAY to 90.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 57.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.23 (0.02-->3.81) (max @ vno 76035 --> 81853) face area 0.27 +- 0.13 (0.00-->2.73) mean absolute distance = 0.77 +- 1.07 4154 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=100+-7.0, GM=69+-7.8 mean inside = 91.4, mean outside = 72.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=79.9, 33 (33) missing vertices, mean dist 0.0 [0.9 (%42.7)->0.7 (%57.3))] %54 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.06-->3.34) (max @ vno 121856 --> 124073) face area 0.27 +- 0.13 (0.00-->2.19) mean absolute distance = 0.43 +- 0.70 4655 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3318185.8, rms=10.113 001: dt: 0.5000, sse=1773009.0, rms=6.797 (32.789%) 002: dt: 0.5000, sse=1166424.5, rms=4.876 (28.267%) 003: dt: 0.5000, sse=958628.8, rms=4.016 (17.640%) 004: dt: 0.5000, sse=886030.7, rms=3.655 (8.985%) 005: dt: 0.5000, sse=862198.0, rms=3.534 (3.298%) 006: dt: 0.5000, sse=851194.4, rms=3.479 (1.562%) rms = 3.47, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=852315.2, rms=3.468 (0.315%) 008: dt: 0.2500, sse=690643.2, rms=2.375 (31.534%) 009: dt: 0.2500, sse=655425.1, rms=2.041 (14.041%) 010: dt: 0.2500, sse=647600.1, rms=1.976 (3.187%) rms = 1.93, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=641551.0, rms=1.930 (2.360%) 012: dt: 0.1250, sse=632027.6, rms=1.833 (4.996%) rms = 1.82, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=631298.5, rms=1.824 (0.521%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... mean border=83.2, 44 (3) missing vertices, mean dist -0.3 [0.5 (%68.8)->0.2 (%31.2))] %69 local maxima, %26 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 0.87 +- 0.25 (0.04-->3.23) (max @ vno 135724 --> 138129) face area 0.33 +- 0.16 (0.00-->2.99) mean absolute distance = 0.29 +- 0.43 3717 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1260292.9, rms=4.710 014: dt: 0.5000, sse=971364.9, rms=3.344 (28.994%) rms = 3.39, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=845562.2, rms=2.587 (22.649%) 016: dt: 0.2500, sse=781193.5, rms=2.064 (20.225%) 017: dt: 0.2500, sse=762217.8, rms=1.819 (11.848%) 018: dt: 0.2500, sse=746678.6, rms=1.718 (5.570%) 019: dt: 0.2500, sse=741627.4, rms=1.655 (3.655%) rms = 1.62, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=738555.7, rms=1.623 (1.917%) 021: dt: 0.1250, sse=733036.1, rms=1.546 (4.746%) rms = 1.54, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=731436.4, rms=1.542 (0.282%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... mean border=85.5, 59 (1) missing vertices, mean dist -0.2 [0.3 (%68.0)->0.2 (%32.0))] %82 local maxima, %14 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 0.87 +- 0.25 (0.07-->3.28) (max @ vno 96267 --> 139774) face area 0.32 +- 0.16 (0.00-->3.06) mean absolute distance = 0.24 +- 0.35 3979 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=947137.6, rms=3.330 023: dt: 0.5000, sse=897889.4, rms=2.902 (12.848%) rms = 3.23, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=763824.3, rms=2.019 (30.430%) 025: dt: 0.2500, sse=727612.6, rms=1.614 (20.051%) 026: dt: 0.2500, sse=714116.2, rms=1.515 (6.126%) rms = 1.50, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=711563.8, rms=1.502 (0.905%) 028: dt: 0.1250, sse=703371.6, rms=1.402 (6.601%) rms = 1.40, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=703526.3, rms=1.401 (0.070%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=86.4, 77 (1) missing vertices, mean dist -0.1 [0.3 (%54.8)->0.2 (%45.2))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=727127.6, rms=1.782 rms = 1.93, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=685293.9, rms=1.276 (28.403%) 031: dt: 0.2500, sse=671054.9, rms=1.028 (19.416%) rms = 1.04, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=671525.6, rms=1.024 (0.430%) positioning took 0.4 minutes generating cortex label... 13 non-cortical segments detected only using segment with 7527 vertices erasing segment 1 (vno[0] = 59957) erasing segment 2 (vno[0] = 101310) erasing segment 3 (vno[0] = 101335) erasing segment 4 (vno[0] = 102371) erasing segment 5 (vno[0] = 103368) erasing segment 6 (vno[0] = 103388) erasing segment 7 (vno[0] = 105428) erasing segment 8 (vno[0] = 108646) erasing segment 9 (vno[0] = 110616) erasing segment 10 (vno[0] = 110620) erasing segment 11 (vno[0] = 110634) erasing segment 12 (vno[0] = 115603) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.area vertex spacing 0.87 +- 0.26 (0.04-->3.81) (max @ vno 76035 --> 81853) face area 0.32 +- 0.16 (0.00-->3.08) refinement took 5.3 minutes PIDs (11960 11963) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sat Oct 7 21:13:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sat Oct 7 21:13:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 12501 of (12501 12504) to complete... Waiting for PID 12504 of (12501 12504) 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 (12501 12504) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sat Oct 7 21:13:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sat Oct 7 21:13:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 12548 of (12548 12551) to complete... Waiting for PID 12551 of (12548 12551) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.0 mm, total surface area = 79372 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.185 (target=0.015) step 005: RMS=0.128 (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=0.054 (target=0.015) step 030: RMS=0.046 (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=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 40.581830 mris_inflate stimesec 0.116982 mris_inflate ru_maxrss 201864 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29579 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10768 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5392 mris_inflate ru_nivcsw 4806 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 46.7 mm, total surface area = 79872 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.180 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 41.607674 mris_inflate stimesec 0.104984 mris_inflate ru_maxrss 206156 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30140 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11000 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5434 mris_inflate ru_nivcsw 4897 PIDs (12548 12551) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sat Oct 7 21:14:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 21:14:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 12778 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... Waiting for PID 12781 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... Waiting for PID 12784 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... Waiting for PID 12787 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... Waiting for PID 12790 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... Waiting for PID 12793 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... Waiting for PID 12796 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... Waiting for PID 12799 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... Waiting for PID 12802 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... Waiting for PID 12805 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... Waiting for PID 12809 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... Waiting for PID 12812 of (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = -7.994*4pi (-100.457) --> 9 handles ICI = 204.3, FI = 1905.5, variation=31116.489 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 147 vertices thresholded to be in k1 ~ [-0.20 0.47], k2 ~ [-0.13 0.08] total integrated curvature = 0.568*4pi (7.136) --> 0 handles ICI = 1.5, FI = 8.7, variation=149.913 134 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 128 vertices thresholded to be in [-0.11 0.22] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022 done. mris_curvature -w rh.white.preaparc total integrated curvature = -7.224*4pi (-90.773) --> 8 handles ICI = 193.9, FI = 1798.4, variation=29358.738 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 154 vertices thresholded to be in k1 ~ [-0.19 0.65], k2 ~ [-0.14 0.08] total integrated curvature = 0.559*4pi (7.027) --> 0 handles ICI = 1.5, FI = 9.1, variation=156.681 150 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 = 0.001 128 vertices thresholded to be in [-0.12 0.26] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023 done. PIDs (12778 12781 12784 12787 12790 12793 12796 12799 12802 12805 12809 12812) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sat Oct 7 21:15:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051362 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 [ 0051362/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 [ 253 ] Gb_filter = 0 WARN: S lookup min: -0.014552 WARN: S explicit min: 0.000000 vertex = 171 #----------------------------------------- #@# Curvature Stats rh Sat Oct 7 21:15:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051362 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 [ 0051362/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 254 ] Gb_filter = 0 WARN: S lookup min: -0.727026 WARN: S explicit min: 0.000000 vertex = 1478 WARN: C lookup max: 229.934219 WARN: C explicit max: 74.243919 vertex = 112340 #-------------------------------------------- #@# Sphere lh Sat Oct 7 21:15:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sat Oct 7 21:15:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 13159 of (13159 13163) to complete... Waiting for PID 13163 of (13159 13163) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.304... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.68 pass 1: epoch 2 of 3 starting distance error %19.45 unfolding complete - removing small folds... starting distance error %19.35 removing remaining folds... final distance error %19.37 MRISunfold() return, current seed 1234 -01: dt=0.0000, 159 negative triangles 276: dt=0.9900, 159 negative triangles 277: dt=0.9900, 72 negative triangles 278: dt=0.9900, 54 negative triangles 279: dt=0.9900, 50 negative triangles 280: dt=0.9900, 44 negative triangles 281: dt=0.9900, 46 negative triangles 282: dt=0.9900, 41 negative triangles 283: dt=0.9900, 43 negative triangles 284: dt=0.9900, 34 negative triangles 285: dt=0.9900, 32 negative triangles 286: dt=0.9900, 36 negative triangles 287: dt=0.9900, 30 negative triangles 288: dt=0.9900, 29 negative triangles 289: dt=0.9900, 28 negative triangles 290: dt=0.9900, 20 negative triangles 291: dt=0.9900, 27 negative triangles 292: dt=0.9900, 23 negative triangles 293: dt=0.9900, 27 negative triangles 294: dt=0.9900, 20 negative triangles 295: dt=0.9900, 25 negative triangles 296: dt=0.9900, 20 negative triangles 297: dt=0.9900, 25 negative triangles 298: dt=0.9900, 22 negative triangles 299: dt=0.9900, 24 negative triangles 300: dt=0.9900, 19 negative triangles 301: dt=0.9900, 22 negative triangles 302: dt=0.9900, 18 negative triangles 303: dt=0.9900, 24 negative triangles 304: dt=0.9900, 17 negative triangles 305: dt=0.9900, 23 negative triangles 306: dt=0.9900, 17 negative triangles 307: dt=0.9900, 23 negative triangles 308: dt=0.9900, 17 negative triangles 309: dt=0.9900, 22 negative triangles 310: dt=0.9900, 18 negative triangles 311: dt=0.9900, 23 negative triangles 312: dt=0.9900, 18 negative triangles 313: dt=0.9900, 23 negative triangles 314: dt=0.9405, 18 negative triangles 315: dt=0.9405, 23 negative triangles 316: dt=0.9405, 16 negative triangles 317: dt=0.9405, 19 negative triangles 318: dt=0.9405, 19 negative triangles 319: dt=0.9405, 19 negative triangles 320: dt=0.9405, 16 negative triangles 321: dt=0.9405, 21 negative triangles 322: dt=0.9405, 16 negative triangles 323: dt=0.9405, 19 negative triangles 324: dt=0.9405, 18 negative triangles 325: dt=0.9405, 20 negative triangles 326: dt=0.8935, 16 negative triangles 327: dt=0.8935, 22 negative triangles 328: dt=0.8935, 17 negative triangles 329: dt=0.8935, 17 negative triangles 330: dt=0.8935, 21 negative triangles 331: dt=0.8935, 18 negative triangles 332: dt=0.8935, 16 negative triangles 333: dt=0.8935, 23 negative triangles 334: dt=0.8935, 20 negative triangles 335: dt=0.8935, 15 negative triangles 336: dt=0.8935, 20 negative triangles 337: dt=0.8935, 16 negative triangles 338: dt=0.8935, 18 negative triangles 339: dt=0.8935, 18 negative triangles 340: dt=0.8935, 18 negative triangles 341: dt=0.8935, 15 negative triangles 342: dt=0.8935, 20 negative triangles 343: dt=0.8935, 15 negative triangles 344: dt=0.8935, 18 negative triangles 345: dt=0.8488, 17 negative triangles 346: dt=0.8488, 18 negative triangles 347: dt=0.8488, 16 negative triangles 348: dt=0.8488, 19 negative triangles 349: dt=0.8488, 15 negative triangles 350: dt=0.8488, 14 negative triangles 351: dt=0.8488, 19 negative triangles 352: dt=0.8488, 15 negative triangles 353: dt=0.8488, 15 negative triangles 354: dt=0.8488, 17 negative triangles 355: dt=0.8488, 12 negative triangles 356: dt=0.8488, 16 negative triangles 357: dt=0.8488, 13 negative triangles 358: dt=0.8488, 15 negative triangles 359: dt=0.8488, 10 negative triangles 360: dt=0.8488, 14 negative triangles 361: dt=0.8488, 10 negative triangles 362: dt=0.8488, 13 negative triangles 363: dt=0.8488, 10 negative triangles 364: dt=0.8488, 15 negative triangles 365: dt=0.8488, 9 negative triangles 366: dt=0.8488, 10 negative triangles 367: dt=0.8488, 8 negative triangles 368: dt=0.8488, 13 negative triangles 369: dt=0.8488, 8 negative triangles 370: dt=0.8488, 8 negative triangles 371: dt=0.8488, 8 negative triangles 372: dt=0.8488, 12 negative triangles 373: dt=0.8488, 7 negative triangles 374: dt=0.8488, 8 negative triangles 375: dt=0.8488, 6 negative triangles 376: dt=0.8488, 8 negative triangles 377: dt=0.8488, 5 negative triangles 378: dt=0.8488, 6 negative triangles 379: dt=0.8488, 6 negative triangles 380: dt=0.8488, 5 negative triangles 381: dt=0.8488, 4 negative triangles 382: dt=0.8488, 6 negative triangles 383: dt=0.8488, 4 negative triangles 384: dt=0.8488, 1 negative triangles 385: dt=0.8488, 1 negative triangles 386: dt=0.8488, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.12 hours mris_sphere utimesec 4031.630099 mris_sphere stimesec 1.484774 mris_sphere ru_maxrss 282980 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 49988 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9776 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 147514 mris_sphere ru_nivcsw 350615 FSRUNTIME@ mris_sphere 1.1207 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0.304... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.87 pass 1: epoch 2 of 3 starting distance error %19.77 unfolding complete - removing small folds... starting distance error %19.68 removing remaining folds... final distance error %19.69 MRISunfold() return, current seed 1234 -01: dt=0.0000, 240 negative triangles 176: dt=0.9900, 240 negative triangles 177: dt=0.9900, 147 negative triangles 178: dt=0.9900, 116 negative triangles 179: dt=0.9900, 116 negative triangles 180: dt=0.9900, 111 negative triangles 181: dt=0.9900, 105 negative triangles 182: dt=0.9900, 110 negative triangles 183: dt=0.9900, 106 negative triangles 184: dt=0.9900, 102 negative triangles 185: dt=0.9900, 99 negative triangles 186: dt=0.9900, 89 negative triangles 187: dt=0.9900, 93 negative triangles 188: dt=0.9900, 87 negative triangles 189: dt=0.9900, 83 negative triangles 190: dt=0.9900, 82 negative triangles 191: dt=0.9900, 76 negative triangles 192: dt=0.9900, 83 negative triangles 193: dt=0.9900, 73 negative triangles 194: dt=0.9900, 71 negative triangles 195: dt=0.9900, 66 negative triangles 196: dt=0.9900, 70 negative triangles 197: dt=0.9900, 62 negative triangles 198: dt=0.9900, 64 negative triangles 199: dt=0.9900, 60 negative triangles 200: dt=0.9900, 57 negative triangles 201: dt=0.9900, 55 negative triangles 202: dt=0.9900, 58 negative triangles 203: dt=0.9900, 54 negative triangles 204: dt=0.9900, 55 negative triangles 205: dt=0.9900, 49 negative triangles 206: dt=0.9900, 47 negative triangles 207: dt=0.9900, 43 negative triangles 208: dt=0.9900, 40 negative triangles 209: dt=0.9900, 40 negative triangles 210: dt=0.9900, 39 negative triangles 211: dt=0.9900, 42 negative triangles 212: dt=0.9900, 47 negative triangles 213: dt=0.9900, 41 negative triangles 214: dt=0.9900, 39 negative triangles 215: dt=0.9900, 46 negative triangles 216: dt=0.9900, 41 negative triangles 217: dt=0.9900, 43 negative triangles 218: dt=0.9900, 43 negative triangles 219: dt=0.9900, 42 negative triangles 220: dt=0.9405, 48 negative triangles 221: dt=0.9405, 45 negative triangles 222: dt=0.9405, 46 negative triangles 223: dt=0.9405, 50 negative triangles 224: dt=0.9405, 47 negative triangles 225: dt=0.9405, 45 negative triangles 226: dt=0.9405, 51 negative triangles 227: dt=0.9405, 48 negative triangles 228: dt=0.9405, 51 negative triangles 229: dt=0.9405, 51 negative triangles 230: dt=0.8935, 53 negative triangles 231: dt=0.8935, 55 negative triangles 232: dt=0.8935, 49 negative triangles 233: dt=0.8935, 54 negative triangles 234: dt=0.8935, 53 negative triangles 235: dt=0.8935, 53 negative triangles 236: dt=0.8935, 50 negative triangles 237: dt=0.8935, 62 negative triangles 238: dt=0.8935, 57 negative triangles 239: dt=0.8935, 54 negative triangles 240: dt=0.8488, 56 negative triangles 241: dt=0.8488, 56 negative triangles 242: dt=0.8488, 58 negative triangles 243: dt=0.8488, 56 negative triangles 244: dt=0.8488, 61 negative triangles 245: dt=0.8488, 63 negative triangles 246: dt=0.8488, 57 negative triangles 247: dt=0.8488, 57 negative triangles 248: dt=0.8488, 65 negative triangles 249: dt=0.8488, 60 negative triangles 250: dt=0.8064, 61 negative triangles 251: dt=0.8064, 66 negative triangles 252: dt=0.8064, 60 negative triangles 253: dt=0.8064, 66 negative triangles 254: dt=0.8064, 68 negative triangles 255: dt=0.8064, 63 negative triangles 256: dt=0.8064, 65 negative triangles 257: dt=0.8064, 59 negative triangles 258: dt=0.8064, 63 negative triangles 259: dt=0.8064, 67 negative triangles 260: dt=0.7660, 57 negative triangles expanding nbhd size to 1 261: dt=0.9900, 62 negative triangles 262: dt=0.9900, 58 negative triangles 263: dt=0.9900, 56 negative triangles 264: dt=0.9900, 52 negative triangles 265: dt=0.9900, 51 negative triangles 266: dt=0.9900, 49 negative triangles 267: dt=0.9900, 52 negative triangles 268: dt=0.9900, 53 negative triangles 269: dt=0.9900, 50 negative triangles 270: dt=0.9405, 48 negative triangles 271: dt=0.9405, 45 negative triangles 272: dt=0.9405, 46 negative triangles 273: dt=0.9405, 47 negative triangles 274: dt=0.9405, 49 negative triangles 275: dt=0.9405, 49 negative triangles 276: dt=0.9405, 56 negative triangles 277: dt=0.9405, 54 negative triangles 278: dt=0.9405, 52 negative triangles 279: dt=0.9405, 51 negative triangles 280: dt=0.8935, 49 negative triangles 281: dt=0.8935, 48 negative triangles 282: dt=0.8935, 50 negative triangles 283: dt=0.8935, 51 negative triangles 284: dt=0.8935, 51 negative triangles 285: dt=0.8935, 49 negative triangles 286: dt=0.8935, 47 negative triangles 287: dt=0.8935, 46 negative triangles 288: dt=0.8935, 50 negative triangles 289: dt=0.8935, 50 negative triangles 290: dt=0.8488, 48 negative triangles 291: dt=0.8488, 50 negative triangles 292: dt=0.8488, 46 negative triangles 293: dt=0.8488, 45 negative triangles 294: dt=0.8488, 46 negative triangles 295: dt=0.8488, 46 negative triangles 296: dt=0.8488, 47 negative triangles 297: dt=0.8488, 49 negative triangles 298: dt=0.8488, 46 negative triangles 299: dt=0.8488, 46 negative triangles 300: dt=0.8064, 43 negative triangles 301: dt=0.8064, 43 negative triangles 302: dt=0.8064, 44 negative triangles 303: dt=0.8064, 48 negative triangles 304: dt=0.8064, 48 negative triangles 305: dt=0.8064, 47 negative triangles 306: dt=0.8064, 46 negative triangles 307: dt=0.8064, 44 negative triangles 308: dt=0.8064, 44 negative triangles 309: dt=0.8064, 43 negative triangles 310: dt=0.7660, 45 negative triangles 311: dt=0.7660, 48 negative triangles 312: dt=0.7660, 47 negative triangles 313: dt=0.7660, 46 negative triangles 314: dt=0.7660, 44 negative triangles 315: dt=0.7660, 43 negative triangles 316: dt=0.7660, 44 negative triangles 317: dt=0.7660, 43 negative triangles 318: dt=0.7660, 44 negative triangles 319: dt=0.7660, 42 negative triangles 320: dt=0.7277, 41 negative triangles 321: dt=0.7277, 41 negative triangles 322: dt=0.7277, 42 negative triangles 323: dt=0.7277, 42 negative triangles 324: dt=0.7277, 41 negative triangles 325: dt=0.7277, 39 negative triangles 326: dt=0.7277, 39 negative triangles 327: dt=0.7277, 39 negative triangles 328: dt=0.7277, 40 negative triangles 329: dt=0.7277, 42 negative triangles 330: dt=0.6914, 41 negative triangles 331: dt=0.6914, 41 negative triangles 332: dt=0.6914, 39 negative triangles 333: dt=0.6914, 38 negative triangles 334: dt=0.6914, 38 negative triangles 335: dt=0.6914, 41 negative triangles 336: dt=0.6914, 39 negative triangles 337: dt=0.6914, 37 negative triangles 338: dt=0.6914, 36 negative triangles 339: dt=0.6914, 35 negative triangles 340: dt=0.6914, 35 negative triangles 341: dt=0.6914, 37 negative triangles 342: dt=0.6914, 38 negative triangles 343: dt=0.6914, 38 negative triangles 344: dt=0.6914, 36 negative triangles 345: dt=0.6914, 35 negative triangles 346: dt=0.6914, 36 negative triangles 347: dt=0.6914, 36 negative triangles 348: dt=0.6914, 36 negative triangles 349: dt=0.6568, 36 negative triangles 350: dt=0.6568, 35 negative triangles 351: dt=0.6568, 32 negative triangles 352: dt=0.6568, 31 negative triangles 353: dt=0.6568, 30 negative triangles 354: dt=0.6568, 31 negative triangles 355: dt=0.6568, 30 negative triangles 356: dt=0.6568, 30 negative triangles 357: dt=0.6568, 29 negative triangles 358: dt=0.6568, 30 negative triangles 359: dt=0.6568, 29 negative triangles 360: dt=0.6568, 30 negative triangles 361: dt=0.6568, 31 negative triangles 362: dt=0.6568, 31 negative triangles 363: dt=0.6568, 29 negative triangles 364: dt=0.6568, 27 negative triangles 365: dt=0.6568, 29 negative triangles 366: dt=0.6568, 27 negative triangles 367: dt=0.6568, 28 negative triangles 368: dt=0.6568, 29 negative triangles 369: dt=0.6568, 27 negative triangles 370: dt=0.6568, 28 negative triangles 371: dt=0.6568, 26 negative triangles 372: dt=0.6568, 27 negative triangles 373: dt=0.6568, 28 negative triangles 374: dt=0.6568, 26 negative triangles 375: dt=0.6568, 26 negative triangles 376: dt=0.6568, 25 negative triangles 377: dt=0.6568, 26 negative triangles 378: dt=0.6568, 22 negative triangles 379: dt=0.6568, 24 negative triangles 380: dt=0.6568, 23 negative triangles 381: dt=0.6568, 24 negative triangles 382: dt=0.6568, 26 negative triangles 383: dt=0.6568, 23 negative triangles 384: dt=0.6568, 24 negative triangles 385: dt=0.6568, 21 negative triangles 386: dt=0.6568, 22 negative triangles 387: dt=0.6568, 20 negative triangles 388: dt=0.6568, 23 negative triangles 389: dt=0.6568, 24 negative triangles 390: dt=0.6568, 22 negative triangles 391: dt=0.6568, 21 negative triangles 392: dt=0.6568, 20 negative triangles 393: dt=0.6568, 20 negative triangles 394: dt=0.6568, 20 negative triangles 395: dt=0.6568, 20 negative triangles 396: dt=0.6568, 20 negative triangles 397: dt=0.6568, 18 negative triangles 398: dt=0.6568, 20 negative triangles 399: dt=0.6568, 19 negative triangles 400: dt=0.6568, 19 negative triangles 401: dt=0.6568, 18 negative triangles 402: dt=0.6568, 20 negative triangles 403: dt=0.6568, 18 negative triangles 404: dt=0.6568, 17 negative triangles 405: dt=0.6568, 15 negative triangles 406: dt=0.6568, 17 negative triangles 407: dt=0.6568, 16 negative triangles 408: dt=0.6568, 15 negative triangles 409: dt=0.6568, 13 negative triangles 410: dt=0.6568, 14 negative triangles 411: dt=0.6568, 13 negative triangles 412: dt=0.6568, 14 negative triangles 413: dt=0.6568, 13 negative triangles 414: dt=0.6568, 13 negative triangles 415: dt=0.6568, 13 negative triangles 416: dt=0.6568, 13 negative triangles 417: dt=0.6568, 13 negative triangles 418: dt=0.6568, 14 negative triangles 419: dt=0.6239, 14 negative triangles 420: dt=0.6239, 13 negative triangles 421: dt=0.6239, 14 negative triangles 422: dt=0.6239, 13 negative triangles 423: dt=0.6239, 12 negative triangles 424: dt=0.6239, 12 negative triangles 425: dt=0.6239, 14 negative triangles 426: dt=0.6239, 12 negative triangles 427: dt=0.6239, 14 negative triangles 428: dt=0.6239, 12 negative triangles 429: dt=0.6239, 13 negative triangles 430: dt=0.6239, 12 negative triangles 431: dt=0.6239, 12 negative triangles 432: dt=0.6239, 13 negative triangles 433: dt=0.6239, 11 negative triangles 434: dt=0.6239, 11 negative triangles 435: dt=0.6239, 9 negative triangles 436: dt=0.6239, 9 negative triangles 437: dt=0.6239, 9 negative triangles 438: dt=0.6239, 9 negative triangles 439: dt=0.6239, 8 negative triangles 440: dt=0.6239, 8 negative triangles 441: dt=0.6239, 8 negative triangles 442: dt=0.6239, 8 negative triangles 443: dt=0.6239, 8 negative triangles 444: dt=0.6239, 9 negative triangles 445: dt=0.6239, 8 negative triangles 446: dt=0.6239, 8 negative triangles 447: dt=0.6239, 8 negative triangles 448: dt=0.6239, 8 negative triangles 449: dt=0.5927, 8 negative triangles 450: dt=0.5927, 8 negative triangles 451: dt=0.5927, 8 negative triangles 452: dt=0.5927, 8 negative triangles 453: dt=0.5927, 9 negative triangles 454: dt=0.5927, 9 negative triangles 455: dt=0.5927, 10 negative triangles 456: dt=0.5927, 9 negative triangles 457: dt=0.5927, 9 negative triangles 458: dt=0.5927, 7 negative triangles 459: dt=0.5927, 7 negative triangles 460: dt=0.5927, 7 negative triangles 461: dt=0.5927, 5 negative triangles 462: dt=0.5927, 5 negative triangles 463: dt=0.5927, 5 negative triangles 464: dt=0.5927, 5 negative triangles 465: dt=0.5927, 5 negative triangles 466: dt=0.5927, 5 negative triangles 467: dt=0.5927, 5 negative triangles 468: dt=0.5927, 5 negative triangles 469: dt=0.5927, 5 negative triangles 470: dt=0.5927, 5 negative triangles 471: dt=0.5631, 5 negative triangles 472: dt=0.5631, 5 negative triangles 473: dt=0.5631, 5 negative triangles 474: dt=0.5631, 5 negative triangles 475: dt=0.5631, 5 negative triangles 476: dt=0.5631, 5 negative triangles 477: dt=0.5631, 4 negative triangles 478: dt=0.5631, 4 negative triangles 479: dt=0.5631, 4 negative triangles 480: dt=0.5631, 4 negative triangles 481: dt=0.5631, 4 negative triangles 482: dt=0.5631, 4 negative triangles 483: dt=0.5631, 4 negative triangles 484: dt=0.5631, 4 negative triangles 485: dt=0.5631, 3 negative triangles 486: dt=0.5631, 3 negative triangles 487: dt=0.5631, 2 negative triangles 488: dt=0.5631, 2 negative triangles 489: dt=0.5631, 2 negative triangles 490: dt=0.5631, 1 negative triangles 491: dt=0.5631, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.13 hours mris_sphere utimesec 4066.987723 mris_sphere stimesec 1.503771 mris_sphere ru_maxrss 289064 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 50989 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10144 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 136147 mris_sphere ru_nivcsw 351069 FSRUNTIME@ mris_sphere 1.1254 hours 1 threads PIDs (13159 13163) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sat Oct 7 22:23:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 22:23:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 16948 of (16948 16951) to complete... Waiting for PID 16951 of (16948 16951) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 5.239 curvature mean = 0.043, std = 0.822 curvature mean = 0.023, std = 0.854 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 371200.3, tmin=1.0119 d=32.00 min @ (0.00, 8.00, -8.00) sse = 227945.4, tmin=2.0409 d=16.00 min @ (4.00, 0.00, 0.00) sse = 214262.2, tmin=3.0815 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 214118.2, tmin=4.1268 d=4.00 min @ (1.00, 0.00, -1.00) sse = 211599.5, tmin=5.1804 d=2.00 min @ (0.00, 0.00, 0.50) sse = 211414.9, tmin=6.2412 d=1.00 min @ (-0.25, 0.25, -0.25) sse = 211170.0, tmin=7.3011 d=0.50 min @ (0.12, 0.00, 0.00) sse = 211164.3, tmin=8.3732 tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.37 min curvature mean = 0.005, std = 0.833 curvature mean = 0.008, std = 0.944 curvature mean = 0.001, std = 0.843 curvature mean = 0.003, std = 0.977 curvature mean = -0.002, std = 0.844 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.025, std = 0.306 curvature mean = 0.040, std = 0.250 curvature mean = 0.063, std = 0.324 curvature mean = 0.035, std = 0.308 curvature mean = 0.032, std = 0.510 curvature mean = 0.035, std = 0.336 curvature mean = 0.018, std = 0.651 curvature mean = 0.035, std = 0.347 curvature mean = 0.007, std = 0.762 MRISregister() return, current seed 0 -01: dt=0.0000, 167 negative triangles 113: dt=0.9900, 167 negative triangles expanding nbhd size to 1 114: dt=0.9900, 204 negative triangles 115: dt=0.9900, 157 negative triangles 116: dt=0.9900, 148 negative triangles 117: dt=0.9900, 140 negative triangles 118: dt=0.9900, 132 negative triangles 119: dt=0.9900, 127 negative triangles 120: dt=0.9900, 116 negative triangles 121: dt=0.9900, 112 negative triangles 122: dt=0.9900, 101 negative triangles 123: dt=0.9900, 94 negative triangles 124: dt=0.9900, 87 negative triangles 125: dt=0.9900, 82 negative triangles 126: dt=0.9900, 80 negative triangles 127: dt=0.9900, 73 negative triangles 128: dt=0.9900, 74 negative triangles 129: dt=0.9900, 65 negative triangles 130: dt=0.9900, 62 negative triangles 131: dt=0.9900, 55 negative triangles 132: dt=0.9900, 48 negative triangles 133: dt=0.9900, 40 negative triangles 134: dt=0.9900, 33 negative triangles 135: dt=0.9900, 28 negative triangles 136: dt=0.9900, 27 negative triangles 137: dt=0.9900, 25 negative triangles 138: dt=0.9900, 27 negative triangles 139: dt=0.9900, 27 negative triangles 140: dt=0.9900, 25 negative triangles 141: dt=0.9900, 21 negative triangles 142: dt=0.9900, 20 negative triangles 143: dt=0.9900, 15 negative triangles 144: dt=0.9900, 17 negative triangles 145: dt=0.9900, 16 negative triangles 146: dt=0.9900, 15 negative triangles 147: dt=0.9900, 14 negative triangles 148: dt=0.9900, 15 negative triangles 149: dt=0.9900, 13 negative triangles 150: dt=0.9900, 14 negative triangles 151: dt=0.9900, 13 negative triangles 152: dt=0.9900, 14 negative triangles 153: dt=0.9900, 13 negative triangles 154: dt=0.9900, 12 negative triangles 155: dt=0.9900, 13 negative triangles 156: dt=0.9900, 12 negative triangles 157: dt=0.9900, 10 negative triangles 158: dt=0.9900, 10 negative triangles 159: dt=0.9900, 10 negative triangles 160: dt=0.9900, 10 negative triangles 161: dt=0.9900, 11 negative triangles 162: dt=0.9900, 9 negative triangles 163: dt=0.9900, 10 negative triangles 164: dt=0.9900, 8 negative triangles 165: dt=0.9900, 7 negative triangles 166: dt=0.9900, 7 negative triangles 167: dt=0.9900, 5 negative triangles 168: dt=0.9900, 4 negative triangles 169: dt=0.9900, 6 negative triangles 170: dt=0.9900, 3 negative triangles 171: dt=0.9900, 3 negative triangles 172: dt=0.9900, 3 negative triangles 173: dt=0.9900, 6 negative triangles 174: dt=0.9900, 2 negative triangles 175: dt=0.9900, 2 negative triangles 176: dt=0.9900, 2 negative triangles 177: dt=0.9900, 3 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.22 hours mris_register utimesec 4379.367234 mris_register stimesec 3.831417 mris_register ru_maxrss 254388 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 36389 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 9776 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 394593 mris_register ru_nivcsw 241377 FSRUNTIME@ mris_register 1.2174 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 5.407 curvature mean = 0.012, std = 0.817 curvature mean = 0.028, std = 0.862 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 349887.2, tmin=1.0592 d=32.00 min @ (-8.00, -8.00, -8.00) sse = 281110.0, tmin=2.1353 d=16.00 min @ (0.00, 4.00, 4.00) sse = 235459.6, tmin=3.2279 d=4.00 min @ (0.00, -1.00, 0.00) sse = 233899.3, tmin=5.4301 d=2.00 min @ (0.50, 0.00, 0.00) sse = 233664.9, tmin=6.5381 d=1.00 min @ (0.00, 0.25, 0.00) sse = 233574.2, tmin=7.6445 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 233554.8, tmin=8.7600 tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.76 min curvature mean = -0.001, std = 0.827 curvature mean = 0.010, std = 0.949 curvature mean = -0.003, std = 0.836 curvature mean = 0.004, std = 0.980 curvature mean = -0.004, std = 0.838 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.028, std = 0.316 curvature mean = 0.033, std = 0.244 curvature mean = 0.067, std = 0.318 curvature mean = 0.029, std = 0.301 curvature mean = 0.032, std = 0.495 curvature mean = 0.028, std = 0.328 curvature mean = 0.017, std = 0.629 curvature mean = 0.028, std = 0.339 curvature mean = 0.006, std = 0.733 MRISregister() return, current seed 0 -01: dt=0.0000, 112 negative triangles 112: dt=0.9900, 112 negative triangles expanding nbhd size to 1 113: dt=0.9900, 131 negative triangles 114: dt=0.9900, 109 negative triangles 115: dt=0.9900, 107 negative triangles 116: dt=0.9900, 102 negative triangles 117: dt=0.9900, 101 negative triangles 118: dt=0.9900, 92 negative triangles 119: dt=0.9900, 89 negative triangles 120: dt=0.9900, 80 negative triangles 121: dt=0.9900, 70 negative triangles 122: dt=0.9900, 59 negative triangles 123: dt=0.9900, 59 negative triangles 124: dt=0.9900, 58 negative triangles 125: dt=0.9900, 56 negative triangles 126: dt=0.9900, 57 negative triangles 127: dt=0.9900, 56 negative triangles 128: dt=0.9900, 60 negative triangles 129: dt=0.9900, 60 negative triangles 130: dt=0.9900, 61 negative triangles 131: dt=0.9900, 60 negative triangles 132: dt=0.9900, 60 negative triangles 133: dt=0.9900, 60 negative triangles 134: dt=0.9900, 60 negative triangles 135: dt=0.9405, 62 negative triangles 136: dt=0.9405, 61 negative triangles 137: dt=0.9405, 61 negative triangles 138: dt=0.9405, 61 negative triangles 139: dt=0.9405, 60 negative triangles 140: dt=0.9405, 64 negative triangles 141: dt=0.9405, 62 negative triangles 142: dt=0.9405, 61 negative triangles 143: dt=0.9405, 62 negative triangles 144: dt=0.9405, 62 negative triangles 145: dt=0.8935, 67 negative triangles 146: dt=0.8935, 68 negative triangles 147: dt=0.8935, 67 negative triangles 148: dt=0.8935, 65 negative triangles 149: dt=0.8935, 65 negative triangles 150: dt=0.8935, 65 negative triangles 151: dt=0.8935, 66 negative triangles 152: dt=0.8935, 65 negative triangles 153: dt=0.8935, 64 negative triangles 154: dt=0.8935, 63 negative triangles 155: dt=0.8488, 64 negative triangles 156: dt=0.8488, 63 negative triangles 157: dt=0.8488, 62 negative triangles 158: dt=0.8488, 62 negative triangles 159: dt=0.8488, 64 negative triangles 160: dt=0.8488, 62 negative triangles 161: dt=0.8488, 62 negative triangles 162: dt=0.8488, 64 negative triangles 163: dt=0.8488, 63 negative triangles 164: dt=0.8488, 62 negative triangles 165: dt=0.8064, 62 negative triangles 166: dt=0.8064, 59 negative triangles 167: dt=0.8064, 59 negative triangles 168: dt=0.8064, 62 negative triangles 169: dt=0.8064, 63 negative triangles 170: dt=0.8064, 61 negative triangles 171: dt=0.8064, 59 negative triangles 172: dt=0.8064, 58 negative triangles 173: dt=0.8064, 59 negative triangles 174: dt=0.8064, 60 negative triangles 175: dt=0.7660, 59 negative triangles 176: dt=0.7660, 60 negative triangles 177: dt=0.7660, 60 negative triangles 178: dt=0.7660, 60 negative triangles 179: dt=0.7660, 58 negative triangles 180: dt=0.7660, 57 negative triangles 181: dt=0.7660, 66 negative triangles 182: dt=0.7660, 61 negative triangles 183: dt=0.7660, 60 negative triangles 184: dt=0.7660, 58 negative triangles 185: dt=0.7277, 58 negative triangles 186: dt=0.7277, 58 negative triangles 187: dt=0.7277, 59 negative triangles 188: dt=0.7277, 58 negative triangles 189: dt=0.7277, 56 negative triangles 190: dt=0.7277, 58 negative triangles 191: dt=0.7277, 56 negative triangles 192: dt=0.7277, 56 negative triangles 193: dt=0.7277, 54 negative triangles 194: dt=0.7277, 57 negative triangles 195: dt=0.7277, 54 negative triangles 196: dt=0.7277, 57 negative triangles 197: dt=0.7277, 54 negative triangles 198: dt=0.7277, 56 negative triangles 199: dt=0.7277, 55 negative triangles 200: dt=0.7277, 53 negative triangles 201: dt=0.7277, 53 negative triangles 202: dt=0.7277, 50 negative triangles 203: dt=0.7277, 50 negative triangles 204: dt=0.7277, 50 negative triangles 205: dt=0.7277, 50 negative triangles 206: dt=0.7277, 50 negative triangles 207: dt=0.7277, 48 negative triangles 208: dt=0.7277, 47 negative triangles 209: dt=0.7277, 53 negative triangles 210: dt=0.7277, 51 negative triangles 211: dt=0.7277, 47 negative triangles 212: dt=0.7277, 49 negative triangles 213: dt=0.7277, 47 negative triangles 214: dt=0.7277, 48 negative triangles 215: dt=0.7277, 47 negative triangles 216: dt=0.7277, 46 negative triangles 217: dt=0.7277, 45 negative triangles 218: dt=0.7277, 48 negative triangles 219: dt=0.7277, 46 negative triangles 220: dt=0.7277, 46 negative triangles 221: dt=0.7277, 45 negative triangles 222: dt=0.7277, 47 negative triangles 223: dt=0.7277, 44 negative triangles 224: dt=0.7277, 49 negative triangles 225: dt=0.7277, 47 negative triangles 226: dt=0.7277, 44 negative triangles 227: dt=0.7277, 46 negative triangles 228: dt=0.7277, 43 negative triangles 229: dt=0.7277, 45 negative triangles 230: dt=0.7277, 46 negative triangles 231: dt=0.7277, 46 negative triangles 232: dt=0.7277, 44 negative triangles 233: dt=0.7277, 45 negative triangles 234: dt=0.7277, 43 negative triangles 235: dt=0.7277, 45 negative triangles 236: dt=0.7277, 44 negative triangles 237: dt=0.7277, 44 negative triangles 238: dt=0.6914, 45 negative triangles 239: dt=0.6914, 44 negative triangles 240: dt=0.6914, 43 negative triangles 241: dt=0.6914, 42 negative triangles 242: dt=0.6914, 44 negative triangles 243: dt=0.6914, 43 negative triangles 244: dt=0.6914, 44 negative triangles 245: dt=0.6914, 41 negative triangles 246: dt=0.6914, 45 negative triangles 247: dt=0.6914, 46 negative triangles 248: dt=0.6914, 44 negative triangles 249: dt=0.6914, 42 negative triangles 250: dt=0.6914, 42 negative triangles 251: dt=0.6914, 43 negative triangles 252: dt=0.6914, 42 negative triangles 253: dt=0.6914, 43 negative triangles 254: dt=0.6914, 44 negative triangles 255: dt=0.6568, 45 negative triangles 256: dt=0.6568, 42 negative triangles 257: dt=0.6568, 43 negative triangles 258: dt=0.6568, 44 negative triangles 259: dt=0.6568, 41 negative triangles 260: dt=0.6568, 44 negative triangles 261: dt=0.6568, 45 negative triangles 262: dt=0.6568, 42 negative triangles 263: dt=0.6568, 42 negative triangles 264: dt=0.6568, 40 negative triangles 265: dt=0.6568, 42 negative triangles 266: dt=0.6568, 42 negative triangles 267: dt=0.6568, 40 negative triangles 268: dt=0.6568, 41 negative triangles 269: dt=0.6568, 42 negative triangles 270: dt=0.6568, 40 negative triangles 271: dt=0.6568, 42 negative triangles 272: dt=0.6568, 39 negative triangles 273: dt=0.6568, 39 negative triangles 274: dt=0.6568, 40 negative triangles 275: dt=0.6568, 39 negative triangles 276: dt=0.6568, 38 negative triangles 277: dt=0.6568, 41 negative triangles 278: dt=0.6568, 40 negative triangles 279: dt=0.6568, 38 negative triangles 280: dt=0.6568, 39 negative triangles 281: dt=0.6568, 39 negative triangles 282: dt=0.6568, 39 negative triangles 283: dt=0.6568, 39 negative triangles 284: dt=0.6568, 39 negative triangles 285: dt=0.6568, 39 negative triangles 286: dt=0.6239, 39 negative triangles 287: dt=0.6239, 36 negative triangles 288: dt=0.6239, 39 negative triangles 289: dt=0.6239, 37 negative triangles 290: dt=0.6239, 37 negative triangles 291: dt=0.6239, 35 negative triangles 292: dt=0.6239, 36 negative triangles 293: dt=0.6239, 33 negative triangles 294: dt=0.6239, 34 negative triangles 295: dt=0.6239, 32 negative triangles 296: dt=0.6239, 33 negative triangles 297: dt=0.6239, 32 negative triangles 298: dt=0.6239, 34 negative triangles 299: dt=0.6239, 33 negative triangles 300: dt=0.6239, 32 negative triangles 301: dt=0.6239, 31 negative triangles 302: dt=0.6239, 33 negative triangles 303: dt=0.6239, 30 negative triangles 304: dt=0.6239, 32 negative triangles 305: dt=0.6239, 33 negative triangles 306: dt=0.6239, 30 negative triangles 307: dt=0.6239, 31 negative triangles 308: dt=0.6239, 28 negative triangles 309: dt=0.6239, 30 negative triangles 310: dt=0.6239, 28 negative triangles 311: dt=0.6239, 29 negative triangles 312: dt=0.6239, 29 negative triangles 313: dt=0.6239, 29 negative triangles 314: dt=0.6239, 27 negative triangles 315: dt=0.6239, 28 negative triangles 316: dt=0.6239, 28 negative triangles 317: dt=0.6239, 27 negative triangles 318: dt=0.6239, 25 negative triangles 319: dt=0.6239, 27 negative triangles 320: dt=0.6239, 26 negative triangles 321: dt=0.6239, 25 negative triangles 322: dt=0.6239, 27 negative triangles 323: dt=0.6239, 25 negative triangles 324: dt=0.6239, 23 negative triangles 325: dt=0.6239, 23 negative triangles 326: dt=0.6239, 24 negative triangles 327: dt=0.6239, 24 negative triangles 328: dt=0.6239, 25 negative triangles 329: dt=0.6239, 24 negative triangles 330: dt=0.6239, 23 negative triangles 331: dt=0.6239, 22 negative triangles 332: dt=0.6239, 23 negative triangles 333: dt=0.6239, 23 negative triangles 334: dt=0.6239, 22 negative triangles 335: dt=0.6239, 23 negative triangles 336: dt=0.6239, 23 negative triangles 337: dt=0.6239, 23 negative triangles 338: dt=0.6239, 23 negative triangles 339: dt=0.6239, 25 negative triangles 340: dt=0.6239, 22 negative triangles 341: dt=0.5927, 23 negative triangles 342: dt=0.5927, 23 negative triangles 343: dt=0.5927, 23 negative triangles 344: dt=0.5927, 24 negative triangles 345: dt=0.5927, 22 negative triangles 346: dt=0.5927, 22 negative triangles 347: dt=0.5927, 22 negative triangles 348: dt=0.5927, 25 negative triangles 349: dt=0.5927, 22 negative triangles 350: dt=0.5927, 23 negative triangles 351: dt=0.5631, 23 negative triangles 352: dt=0.5631, 21 negative triangles 353: dt=0.5631, 21 negative triangles 354: dt=0.5631, 20 negative triangles 355: dt=0.5631, 19 negative triangles 356: dt=0.5631, 18 negative triangles 357: dt=0.5631, 19 negative triangles 358: dt=0.5631, 18 negative triangles 359: dt=0.5631, 15 negative triangles 360: dt=0.5631, 15 negative triangles 361: dt=0.5631, 17 negative triangles 362: dt=0.5631, 15 negative triangles 363: dt=0.5631, 14 negative triangles 364: dt=0.5631, 12 negative triangles 365: dt=0.5631, 14 negative triangles 366: dt=0.5631, 13 negative triangles 367: dt=0.5631, 12 negative triangles 368: dt=0.5631, 12 negative triangles 369: dt=0.5631, 13 negative triangles 370: dt=0.5631, 12 negative triangles 371: dt=0.5631, 12 negative triangles 372: dt=0.5631, 14 negative triangles 373: dt=0.5631, 15 negative triangles 374: dt=0.5350, 14 negative triangles 375: dt=0.5350, 13 negative triangles 376: dt=0.5350, 15 negative triangles 377: dt=0.5350, 15 negative triangles 378: dt=0.5350, 13 negative triangles 379: dt=0.5350, 13 negative triangles 380: dt=0.5350, 11 negative triangles 381: dt=0.5350, 14 negative triangles 382: dt=0.5350, 13 negative triangles 383: dt=0.5350, 10 negative triangles 384: dt=0.5350, 14 negative triangles 385: dt=0.5350, 11 negative triangles 386: dt=0.5350, 11 negative triangles 387: dt=0.5350, 13 negative triangles 388: dt=0.5350, 10 negative triangles 389: dt=0.5350, 14 negative triangles 390: dt=0.5350, 11 negative triangles 391: dt=0.5350, 13 negative triangles 392: dt=0.5350, 12 negative triangles 393: dt=0.5082, 11 negative triangles 394: dt=0.5082, 13 negative triangles 395: dt=0.5082, 11 negative triangles 396: dt=0.5082, 13 negative triangles 397: dt=0.5082, 10 negative triangles 398: dt=0.5082, 13 negative triangles 399: dt=0.5082, 10 negative triangles 400: dt=0.5082, 13 negative triangles 401: dt=0.5082, 12 negative triangles 402: dt=0.5082, 11 negative triangles 403: dt=0.4828, 10 negative triangles 404: dt=0.4828, 11 negative triangles 405: dt=0.4828, 10 negative triangles 406: dt=0.4828, 13 negative triangles 407: dt=0.4828, 11 negative triangles 408: dt=0.4828, 10 negative triangles 409: dt=0.4828, 11 negative triangles 410: dt=0.4828, 10 negative triangles 411: dt=0.4828, 11 negative triangles 412: dt=0.4828, 11 negative triangles 413: dt=0.4587, 11 negative triangles 414: dt=0.4587, 10 negative triangles 415: dt=0.4587, 11 negative triangles 416: dt=0.4587, 13 negative triangles 417: dt=0.4587, 10 negative triangles 418: dt=0.4587, 9 negative triangles 419: dt=0.4587, 9 negative triangles 420: dt=0.4587, 10 negative triangles 421: dt=0.4587, 9 negative triangles 422: dt=0.4587, 9 negative triangles 423: dt=0.4587, 11 negative triangles 424: dt=0.4587, 9 negative triangles 425: dt=0.4587, 9 negative triangles 426: dt=0.4587, 9 negative triangles 427: dt=0.4587, 9 negative triangles 428: dt=0.4587, 7 negative triangles 429: dt=0.4587, 7 negative triangles 430: dt=0.4587, 7 negative triangles 431: dt=0.4587, 7 negative triangles 432: dt=0.4587, 7 negative triangles 433: dt=0.4587, 7 negative triangles 434: dt=0.4587, 8 negative triangles 435: dt=0.4587, 7 negative triangles 436: dt=0.4587, 7 negative triangles 437: dt=0.4587, 7 negative triangles 438: dt=0.4357, 7 negative triangles 439: dt=0.4357, 7 negative triangles 440: dt=0.4357, 8 negative triangles 441: dt=0.4357, 8 negative triangles 442: dt=0.4357, 9 negative triangles 443: dt=0.4357, 7 negative triangles 444: dt=0.4357, 7 negative triangles 445: dt=0.4357, 7 negative triangles 446: dt=0.4357, 7 negative triangles 447: dt=0.4357, 7 negative triangles 448: dt=0.4139, 7 negative triangles 449: dt=0.4139, 7 negative triangles 450: dt=0.4139, 7 negative triangles 451: dt=0.4139, 8 negative triangles 452: dt=0.4139, 7 negative triangles 453: dt=0.4139, 7 negative triangles 454: dt=0.4139, 7 negative triangles 455: dt=0.4139, 7 negative triangles 456: dt=0.4139, 7 negative triangles 457: dt=0.4139, 8 negative triangles 458: dt=0.3932, 8 negative triangles 459: dt=0.3932, 7 negative triangles 460: dt=0.3932, 8 negative triangles 461: dt=0.3932, 8 negative triangles 462: dt=0.3932, 7 negative triangles 463: dt=0.3932, 7 negative triangles 464: dt=0.3932, 7 negative triangles 465: dt=0.3932, 7 negative triangles 466: dt=0.3932, 7 negative triangles 467: dt=0.3932, 6 negative triangles 468: dt=0.3932, 6 negative triangles 469: dt=0.3932, 6 negative triangles 470: dt=0.3932, 6 negative triangles 471: dt=0.3932, 6 negative triangles 472: dt=0.3932, 6 negative triangles 473: dt=0.3932, 6 negative triangles 474: dt=0.3932, 6 negative triangles 475: dt=0.3932, 7 negative triangles 476: dt=0.3932, 6 negative triangles 477: dt=0.3736, 6 negative triangles 478: dt=0.3736, 6 negative triangles 479: dt=0.3736, 6 negative triangles 480: dt=0.3736, 6 negative triangles 481: dt=0.3736, 5 negative triangles 482: dt=0.3736, 5 negative triangles 483: dt=0.3736, 5 negative triangles 484: dt=0.3736, 6 negative triangles 485: dt=0.3736, 5 negative triangles 486: dt=0.3736, 5 negative triangles 487: dt=0.3736, 5 negative triangles 488: dt=0.3736, 4 negative triangles 489: dt=0.3736, 4 negative triangles 490: dt=0.3736, 4 negative triangles 491: dt=0.3736, 4 negative triangles 492: dt=0.3736, 4 negative triangles 493: dt=0.3736, 4 negative triangles 494: dt=0.3736, 5 negative triangles 495: dt=0.3736, 4 negative triangles 496: dt=0.3736, 4 negative triangles 497: dt=0.3736, 4 negative triangles 498: dt=0.3549, 4 negative triangles 499: dt=0.3549, 4 negative triangles 500: dt=0.3549, 4 negative triangles 501: dt=0.3549, 5 negative triangles 502: dt=0.3549, 5 negative triangles 503: dt=0.3549, 6 negative triangles 504: dt=0.3549, 7 negative triangles 505: dt=0.3549, 5 negative triangles 506: dt=0.3549, 5 negative triangles 507: dt=0.3549, 6 negative triangles 508: dt=0.3372, 5 negative triangles 509: dt=0.3372, 4 negative triangles 510: dt=0.3372, 4 negative triangles 511: dt=0.3372, 4 negative triangles 512: dt=0.3372, 4 negative triangles 513: dt=0.3372, 4 negative triangles 514: dt=0.3372, 4 negative triangles 515: dt=0.3372, 4 negative triangles 516: dt=0.3372, 4 negative triangles 517: dt=0.3372, 4 negative triangles 518: dt=0.3203, 4 negative triangles 519: dt=0.3203, 4 negative triangles 520: dt=0.3203, 4 negative triangles 521: dt=0.3203, 4 negative triangles 522: dt=0.3203, 5 negative triangles 523: dt=0.3203, 4 negative triangles 524: dt=0.3203, 4 negative triangles 525: dt=0.3203, 4 negative triangles 526: dt=0.3203, 4 negative triangles 527: dt=0.3203, 4 negative triangles 528: dt=0.3043, 4 negative triangles 529: dt=0.3043, 4 negative triangles 530: dt=0.3043, 4 negative triangles 531: dt=0.3043, 4 negative triangles 532: dt=0.3043, 4 negative triangles 533: dt=0.3043, 4 negative triangles 534: dt=0.3043, 4 negative triangles 535: dt=0.3043, 4 negative triangles 536: dt=0.3043, 3 negative triangles 537: dt=0.3043, 3 negative triangles 538: dt=0.3043, 3 negative triangles 539: dt=0.3043, 4 negative triangles 540: dt=0.3043, 3 negative triangles 541: dt=0.3043, 3 negative triangles 542: dt=0.3043, 3 negative triangles 543: dt=0.3043, 3 negative triangles 544: dt=0.3043, 3 negative triangles 545: dt=0.3043, 3 negative triangles 546: dt=0.2891, 3 negative triangles 547: dt=0.2891, 3 negative triangles 548: dt=0.2891, 3 negative triangles 549: dt=0.2891, 3 negative triangles 550: dt=0.2891, 2 negative triangles 551: dt=0.2891, 2 negative triangles 552: dt=0.2891, 2 negative triangles 553: dt=0.2891, 2 negative triangles 554: dt=0.2891, 2 negative triangles 555: dt=0.2891, 2 negative triangles 556: dt=0.2891, 1 negative triangles 557: dt=0.2891, 1 negative triangles 558: dt=0.2891, 1 negative triangles 559: dt=0.2891, 1 negative triangles 560: dt=0.2891, 1 negative triangles 561: dt=0.2891, 1 negative triangles 562: dt=0.2891, 2 negative triangles 563: dt=0.2891, 1 negative triangles 564: dt=0.2891, 1 negative triangles 565: dt=0.2891, 1 negative triangles 566: dt=0.2746, 1 negative triangles 567: dt=0.2746, 1 negative triangles 568: dt=0.2746, 1 negative triangles 569: dt=0.2746, 1 negative triangles 570: dt=0.2746, 1 negative triangles 571: dt=0.2746, 1 negative triangles 572: dt=0.2746, 1 negative triangles 573: dt=0.2746, 1 negative triangles 574: dt=0.2746, 1 negative triangles 575: dt=0.2746, 1 negative triangles 576: dt=0.2609, 1 negative triangles 577: dt=0.2609, 1 negative triangles 578: dt=0.2609, 1 negative triangles 579: dt=0.2609, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.28 hours mris_register utimesec 4781.612084 mris_register stimesec 4.023388 mris_register ru_maxrss 261864 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 37847 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10040 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 398217 mris_register ru_nivcsw 237851 FSRUNTIME@ mris_register 1.2827 hours 1 threads PIDs (16948 16951) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sat Oct 7 23:40:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sat Oct 7 23:40:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 20550 of (20550 20553) to complete... Waiting for PID 20553 of (20550 20553) 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 (20550 20553) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sat Oct 7 23:40:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 Sat Oct 7 23:40:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 20595 of (20595 20598) to complete... Waiting for PID 20598 of (20595 20598) 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 (20595 20598) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sat Oct 7 23:40:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 Sat Oct 7 23:40:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 20641 of (20641 20644) to complete... Waiting for PID 20644 of (20641 20644) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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... 1025 labels changed using aseg relabeling using gibbs priors... 000: 3102 changed, 137434 examined... 001: 723 changed, 12957 examined... 002: 192 changed, 4027 examined... 003: 66 changed, 1136 examined... 004: 25 changed, 378 examined... 005: 15 changed, 138 examined... 006: 7 changed, 78 examined... 007: 0 changed, 46 examined... 263 labels changed using aseg 000: 118 total segments, 74 labels (390 vertices) changed 001: 43 total segments, 2 labels (5 vertices) changed 002: 41 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... 1565 vertices marked for relabeling... 1565 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 15 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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... 954 labels changed using aseg relabeling using gibbs priors... 000: 2782 changed, 140379 examined... 001: 630 changed, 11948 examined... 002: 136 changed, 3502 examined... 003: 27 changed, 844 examined... 004: 10 changed, 172 examined... 005: 2 changed, 61 examined... 006: 2 changed, 16 examined... 007: 2 changed, 11 examined... 008: 0 changed, 12 examined... 192 labels changed using aseg 000: 93 total segments, 56 labels (287 vertices) changed 001: 38 total segments, 1 labels (1 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1647 vertices marked for relabeling... 1647 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 15 seconds. PIDs (20641 20644) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sat Oct 7 23:40:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051362 lh #-------------------------------------------- #@# Make Pial Surf rh Sat Oct 7 23:40:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051362 rh Waiting for PID 20700 of (20700 20703) to complete... Waiting for PID 20703 of (20700 20703) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051362 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-6.0.0/0051362/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... 50338 bright wm thresholded. 2140 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.orig... computing class statistics... border white: 271136 voxels (1.62%) border gray 285350 voxels (1.70%) WM (96.0): 96.3 +- 9.1 [70.0 --> 110.0] GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.9 (was 70) setting MAX_BORDER_WHITE to 110.1 (was 105) setting MIN_BORDER_WHITE to 66.0 (was 85) setting MAX_CSF to 43.7 (was 40) setting MAX_GRAY to 91.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.6 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-8.7, GM=66+-7.8 mean inside = 91.4, mean outside = 71.3 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.26 (0.04-->4.36) (max @ vno 31249 --> 33498) face area 0.32 +- 0.16 (0.00-->4.95) mean absolute distance = 0.68 +- 0.95 3046 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 25 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 144 points - only 0.00% unknown deleting segment 4 with 25 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=77.7, 99 (96) missing vertices, mean dist 0.3 [1.4 (%13.8)->0.6 (%86.2))] %57 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.26 (0.05-->4.36) (max @ vno 31249 --> 33498) face area 0.32 +- 0.16 (0.00-->4.67) mean absolute distance = 0.39 +- 0.67 3940 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2317248.0, rms=8.009 001: dt: 0.5000, sse=1207218.9, rms=4.673 (41.656%) 002: dt: 0.5000, sse=988920.8, rms=3.714 (20.508%) rms = 3.74, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=842465.0, rms=2.840 (23.550%) 004: dt: 0.2500, sse=783684.7, rms=2.387 (15.928%) 005: dt: 0.2500, sse=756921.8, rms=2.166 (9.252%) 006: dt: 0.2500, sse=746998.6, rms=2.079 (4.032%) 007: dt: 0.2500, sse=741460.3, rms=2.023 (2.716%) rms = 1.98, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=738319.6, rms=1.985 (1.862%) 009: dt: 0.1250, sse=730242.0, rms=1.903 (4.132%) rms = 1.89, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=731588.4, rms=1.893 (0.520%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 21 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 70 points - only 0.00% unknown deleting segment 3 with 18 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 19 points - only 0.00% unknown mean border=80.8, 65 (24) missing vertices, mean dist -0.2 [0.5 (%67.4)->0.2 (%32.6))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.88 +- 0.26 (0.05-->4.29) (max @ vno 31249 --> 33498) face area 0.34 +- 0.17 (0.00-->4.97) mean absolute distance = 0.29 +- 0.43 4006 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1181128.1, rms=4.435 011: dt: 0.5000, sse=934197.2, rms=3.209 (27.644%) rms = 3.51, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=806668.9, rms=2.331 (27.349%) 013: dt: 0.2500, sse=756890.9, rms=1.867 (19.925%) 014: dt: 0.2500, sse=743499.5, rms=1.702 (8.831%) rms = 1.66, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=738776.8, rms=1.660 (2.484%) 016: dt: 0.1250, sse=729700.2, rms=1.560 (5.978%) rms = 1.56, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=729772.9, rms=1.559 (0.084%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 78 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 19 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 27 points - only 0.00% unknown mean border=83.4, 67 (19) missing vertices, mean dist -0.2 [0.3 (%68.2)->0.2 (%31.8))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.26 (0.04-->4.29) (max @ vno 31249 --> 33498) face area 0.33 +- 0.17 (0.00-->4.81) mean absolute distance = 0.24 +- 0.35 3713 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=962354.9, rms=3.457 018: dt: 0.5000, sse=931446.5, rms=3.230 (6.586%) rms = 3.50, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=778940.1, rms=2.188 (32.257%) 020: dt: 0.2500, sse=730164.4, rms=1.731 (20.869%) 021: dt: 0.2500, sse=719627.9, rms=1.600 (7.604%) rms = 1.59, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=718016.0, rms=1.589 (0.689%) 023: dt: 0.1250, sse=706478.1, rms=1.453 (8.542%) rms = 1.45, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=706194.9, rms=1.451 (0.137%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 27 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 97 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 23 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown deleting segment 7 with 27 points - only 0.00% unknown mean border=84.3, 75 (12) missing vertices, mean dist -0.1 [0.3 (%55.6)->0.2 (%44.4))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=733117.8, rms=1.866 rms = 2.23, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=684842.8, rms=1.289 (30.930%) 026: dt: 0.2500, sse=671365.1, rms=1.053 (18.265%) rms = 1.07, time step reduction 2 of 3 to 0.125... rms = 1.05, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=669013.6, rms=1.048 (0.539%) positioning took 0.5 minutes generating cortex label... 12 non-cortical segments detected only using segment with 7623 vertices erasing segment 1 (vno[0] = 53747) erasing segment 2 (vno[0] = 87474) erasing segment 3 (vno[0] = 88117) erasing segment 4 (vno[0] = 89101) erasing segment 5 (vno[0] = 100985) erasing segment 6 (vno[0] = 101104) erasing segment 7 (vno[0] = 102956) erasing segment 8 (vno[0] = 103883) erasing segment 9 (vno[0] = 103989) erasing segment 10 (vno[0] = 136981) erasing segment 11 (vno[0] = 136984) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.area vertex spacing 0.88 +- 0.27 (0.04-->4.26) (max @ vno 31249 --> 33498) face area 0.32 +- 0.17 (0.00-->4.80) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=52.4, 121 (121) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.5 (%100.0))] %15 local maxima, %52 large gradients and %28 min vals, 146 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=28055384.0, rms=32.374 001: dt: 0.0500, sse=24604220.0, rms=30.268 (6.505%) 002: dt: 0.0500, sse=22135340.0, rms=28.666 (5.292%) 003: dt: 0.0500, sse=20263342.0, rms=27.389 (4.455%) 004: dt: 0.0500, sse=18772902.0, rms=26.328 (3.874%) 005: dt: 0.0500, sse=17538790.0, rms=25.416 (3.464%) 006: dt: 0.0500, sse=16485822.0, rms=24.611 (3.167%) 007: dt: 0.0500, sse=15568580.0, rms=23.887 (2.939%) 008: dt: 0.0500, sse=14757121.0, rms=23.229 (2.758%) 009: dt: 0.0500, sse=14029563.0, rms=22.622 (2.613%) 010: dt: 0.0500, sse=13370368.0, rms=22.057 (2.495%) positioning took 1.0 minutes mean border=52.3, 101 (58) missing vertices, mean dist 1.4 [0.1 (%0.1)->1.9 (%99.9))] %16 local maxima, %52 large gradients and %27 min vals, 139 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=14042560.0, rms=22.638 011: dt: 0.0500, sse=13435564.0, rms=22.119 (2.291%) 012: dt: 0.0500, sse=12877431.0, rms=21.631 (2.206%) 013: dt: 0.0500, sse=12361959.0, rms=21.170 (2.130%) 014: dt: 0.0500, sse=11884078.0, rms=20.734 (2.061%) 015: dt: 0.0500, sse=11439633.0, rms=20.320 (1.998%) 016: dt: 0.0500, sse=11025009.0, rms=19.926 (1.940%) 017: dt: 0.0500, sse=10636790.0, rms=19.549 (1.889%) 018: dt: 0.0500, sse=10272942.0, rms=19.190 (1.839%) 019: dt: 0.0500, sse=9930412.0, rms=18.845 (1.797%) 020: dt: 0.0500, sse=9606860.0, rms=18.513 (1.760%) positioning took 1.0 minutes mean border=52.2, 125 (45) missing vertices, mean dist 1.1 [0.1 (%1.0)->1.6 (%99.0))] %16 local maxima, %52 large gradients and %27 min vals, 132 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=9686495.0, rms=18.602 021: dt: 0.0500, sse=9371891.0, rms=18.276 (1.756%) 022: dt: 0.0500, sse=9073899.0, rms=17.961 (1.723%) 023: dt: 0.0500, sse=8788424.0, rms=17.654 (1.710%) 024: dt: 0.0500, sse=8516461.0, rms=17.356 (1.686%) 025: dt: 0.0500, sse=8256819.0, rms=17.067 (1.665%) 026: dt: 0.0500, sse=8008072.0, rms=16.785 (1.650%) 027: dt: 0.0500, sse=7767634.0, rms=16.508 (1.649%) 028: dt: 0.0500, sse=7532790.5, rms=16.233 (1.666%) 029: dt: 0.0500, sse=7303655.5, rms=15.960 (1.681%) 030: dt: 0.0500, sse=7080246.0, rms=15.690 (1.696%) positioning took 1.0 minutes mean border=52.0, 194 (40) missing vertices, mean dist 0.9 [0.1 (%7.3)->1.4 (%92.7))] %16 local maxima, %52 large gradients and %27 min vals, 101 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=7189676.0, rms=15.822 031: dt: 0.5000, sse=5544812.0, rms=13.688 (13.489%) 032: dt: 0.5000, sse=4331760.0, rms=11.864 (13.326%) 033: dt: 0.5000, sse=3425667.5, rms=10.299 (13.190%) 034: dt: 0.5000, sse=2761196.8, rms=8.969 (12.916%) 035: dt: 0.5000, sse=2311679.2, rms=7.950 (11.359%) 036: dt: 0.5000, sse=1984944.0, rms=7.109 (10.581%) 037: dt: 0.5000, sse=1772843.2, rms=6.512 (8.390%) 038: dt: 0.5000, sse=1630711.0, rms=6.071 (6.774%) 039: dt: 0.5000, sse=1552436.5, rms=5.820 (4.130%) 040: dt: 0.5000, sse=1497115.4, rms=5.627 (3.325%) 041: dt: 0.5000, sse=1468563.6, rms=5.531 (1.704%) 042: dt: 0.5000, sse=1441257.8, rms=5.428 (1.855%) rms = 5.40, time step reduction 1 of 3 to 0.250... 043: dt: 0.5000, sse=1433032.0, rms=5.401 (0.503%) 044: dt: 0.2500, sse=1248631.9, rms=4.640 (14.085%) 045: dt: 0.2500, sse=1189336.5, rms=4.390 (5.397%) rms = 4.40, time step reduction 2 of 3 to 0.125... 046: dt: 0.1250, sse=1170452.1, rms=4.302 (2.010%) 047: dt: 0.1250, sse=1146087.1, rms=4.183 (2.759%) rms = 4.17, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=1143226.6, rms=4.167 (0.392%) positioning took 2.3 minutes mean border=50.3, 1715 (21) missing vertices, mean dist 0.1 [0.2 (%45.8)->0.5 (%54.2))] %29 local maxima, %41 large gradients and %24 min vals, 75 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=1475723.0, rms=4.932 049: dt: 0.5000, sse=1446556.1, rms=4.830 (2.063%) 050: dt: 0.5000, sse=1417588.8, rms=4.753 (1.584%) rms = 4.89, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=1212061.9, rms=3.775 (20.578%) 052: dt: 0.2500, sse=1160343.6, rms=3.478 (7.879%) rms = 3.46, time step reduction 2 of 3 to 0.125... 053: dt: 0.2500, sse=1157887.4, rms=3.463 (0.437%) 054: dt: 0.1250, sse=1104117.4, rms=3.133 (9.516%) 055: dt: 0.1250, sse=1095801.1, rms=3.082 (1.641%) rms = 3.08, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1095614.5, rms=3.080 (0.041%) positioning took 1.2 minutes mean border=49.2, 1764 (18) missing vertices, mean dist 0.1 [0.1 (%47.3)->0.3 (%52.7))] %45 local maxima, %26 large gradients and %23 min vals, 54 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=1183838.0, rms=3.583 rms = 4.40, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1120580.6, rms=3.218 (10.182%) 058: dt: 0.2500, sse=1109509.1, rms=3.156 (1.930%) rms = 3.18, time step reduction 2 of 3 to 0.125... 059: dt: 0.1250, sse=1100569.2, rms=3.098 (1.842%) 060: dt: 0.1250, sse=1087803.5, rms=3.018 (2.602%) rms = 3.00, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1084016.1, rms=2.995 (0.740%) positioning took 0.9 minutes mean border=48.5, 3082 (17) missing vertices, mean dist 0.0 [0.2 (%49.4)->0.2 (%50.6))] %49 local maxima, %21 large gradients and %23 min vals, 58 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-6.0.0/0051362/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1112475.9, rms=3.175 rms = 3.99, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1086285.2, rms=3.008 (5.247%) rms = 2.97, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1077989.8, rms=2.974 (1.148%) 064: dt: 0.1250, sse=1064873.2, rms=2.881 (3.111%) rms = 2.85, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1059108.0, rms=2.848 (1.148%) positioning took 0.7 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.area.pial vertex spacing 0.97 +- 0.42 (0.07-->5.63) (max @ vno 94052 --> 92948) face area 0.38 +- 0.29 (0.00-->6.39) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 137434 vertices processed 25000 of 137434 vertices processed 50000 of 137434 vertices processed 75000 of 137434 vertices processed 100000 of 137434 vertices processed 125000 of 137434 vertices processed 0 of 137434 vertices processed 25000 of 137434 vertices processed 50000 of 137434 vertices processed 75000 of 137434 vertices processed 100000 of 137434 vertices processed 125000 of 137434 vertices processed thickness calculation complete, 69:267 truncations. 32657 vertices at 0 distance 105432 vertices at 1 distance 83777 vertices at 2 distance 29332 vertices at 3 distance 7719 vertices at 4 distance 1971 vertices at 5 distance 587 vertices at 6 distance 210 vertices at 7 distance 71 vertices at 8 distance 39 vertices at 9 distance 26 vertices at 10 distance 11 vertices at 11 distance 11 vertices at 12 distance 8 vertices at 13 distance 5 vertices at 14 distance 1 vertices at 15 distance 4 vertices at 16 distance 0 vertices at 17 distance 0 vertices at 18 distance 3 vertices at 19 distance 6 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.thickness positioning took 15.1 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051362 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-6.0.0/0051362/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... 50338 bright wm thresholded. 2140 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.orig... computing class statistics... border white: 271136 voxels (1.62%) border gray 285350 voxels (1.70%) WM (96.0): 96.3 +- 9.1 [70.0 --> 110.0] GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.9 (was 70) setting MAX_BORDER_WHITE to 109.1 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 46.7 (was 40) setting MAX_GRAY to 90.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 57.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.6 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=100+-7.0, GM=69+-7.8 mean inside = 91.4, mean outside = 72.3 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.87 +- 0.26 (0.04-->3.81) (max @ vno 76035 --> 81853) face area 0.32 +- 0.16 (0.00-->3.08) mean absolute distance = 0.72 +- 0.98 3589 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 3 with 50 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 42 points - only 0.00% unknown deleting segment 7 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown mean border=80.0, 97 (97) missing vertices, mean dist 0.3 [1.5 (%14.1)->0.6 (%85.9))] %53 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.26 (0.08-->3.48) (max @ vno 125094 --> 125095) face area 0.32 +- 0.16 (0.00-->3.28) mean absolute distance = 0.41 +- 0.69 4196 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2257621.8, rms=7.757 001: dt: 0.5000, sse=1202501.1, rms=4.581 (40.942%) 002: dt: 0.5000, sse=959514.8, rms=3.489 (23.831%) rms = 3.47, time step reduction 1 of 3 to 0.250... 003: dt: 0.5000, sse=962427.4, rms=3.465 (0.683%) 004: dt: 0.2500, sse=769587.2, rms=2.236 (35.485%) 005: dt: 0.2500, sse=748733.4, rms=1.948 (12.867%) 006: dt: 0.2500, sse=771115.4, rms=1.893 (2.828%) 007: dt: 0.2500, sse=726928.8, rms=1.835 (3.061%) rms = 1.82, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=726530.8, rms=1.824 (0.598%) 009: dt: 0.1250, sse=720156.5, rms=1.749 (4.121%) rms = 1.74, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=720314.9, rms=1.744 (0.252%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 39 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 6 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown mean border=83.1, 36 (15) missing vertices, mean dist -0.3 [0.5 (%67.9)->0.2 (%32.1))] %69 local maxima, %26 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 0.87 +- 0.26 (0.08-->3.56) (max @ vno 90286 --> 91306) face area 0.33 +- 0.17 (0.00-->3.62) mean absolute distance = 0.29 +- 0.43 3720 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1206303.4, rms=4.476 011: dt: 0.5000, sse=940498.1, rms=3.184 (28.857%) rms = 3.27, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=827395.2, rms=2.430 (23.698%) 013: dt: 0.2500, sse=764910.9, rms=1.887 (22.321%) 014: dt: 0.2500, sse=743948.0, rms=1.659 (12.088%) 015: dt: 0.2500, sse=737084.8, rms=1.578 (4.908%) rms = 1.55, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=735605.4, rms=1.553 (1.597%) 017: dt: 0.1250, sse=728928.6, rms=1.472 (5.176%) rms = 1.47, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=728401.2, rms=1.470 (0.140%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 41 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown mean border=85.5, 37 (6) missing vertices, mean dist -0.2 [0.3 (%68.0)->0.2 (%32.0))] %82 local maxima, %14 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 0.87 +- 0.26 (0.05-->3.71) (max @ vno 90286 --> 91306) face area 0.32 +- 0.16 (0.00-->3.66) mean absolute distance = 0.24 +- 0.35 3960 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=947343.6, rms=3.323 019: dt: 0.5000, sse=885537.2, rms=2.876 (13.442%) rms = 3.20, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=762906.6, rms=1.985 (30.981%) 021: dt: 0.2500, sse=726605.7, rms=1.571 (20.841%) 022: dt: 0.2500, sse=712995.9, rms=1.477 (5.977%) rms = 1.46, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=710802.4, rms=1.465 (0.854%) 024: dt: 0.1250, sse=703615.1, rms=1.362 (7.002%) rms = 1.36, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=704007.9, rms=1.362 (0.029%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 49 points - only 0.00% unknown deleting segment 1 with 15 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown mean border=86.3, 60 (4) missing vertices, mean dist -0.1 [0.3 (%54.7)->0.2 (%45.3))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=727711.0, rms=1.757 rms = 1.92, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=684951.9, rms=1.241 (29.346%) 027: dt: 0.2500, sse=678625.6, rms=1.000 (19.451%) rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 0.99, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=672004.1, rms=0.995 (0.497%) positioning took 0.5 minutes generating cortex label... 11 non-cortical segments detected only using segment with 7520 vertices erasing segment 1 (vno[0] = 92764) erasing segment 2 (vno[0] = 101310) erasing segment 3 (vno[0] = 101335) erasing segment 4 (vno[0] = 102389) erasing segment 5 (vno[0] = 105428) erasing segment 6 (vno[0] = 108646) erasing segment 7 (vno[0] = 110616) erasing segment 8 (vno[0] = 110620) erasing segment 9 (vno[0] = 110634) erasing segment 10 (vno[0] = 115603) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.area vertex spacing 0.87 +- 0.26 (0.04-->3.81) (max @ vno 76035 --> 81853) face area 0.32 +- 0.16 (0.00-->3.64) 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 4 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=55.1, 95 (95) missing vertices, mean dist 1.8 [0.9 (%0.0)->2.6 (%100.0))] %19 local maxima, %50 large gradients and %27 min vals, 142 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=27662052.0, rms=31.772 001: dt: 0.0500, sse=24292656.0, rms=29.725 (6.441%) 002: dt: 0.0500, sse=21921022.0, rms=28.196 (5.146%) 003: dt: 0.0500, sse=20127574.0, rms=26.981 (4.307%) 004: dt: 0.0500, sse=18702730.0, rms=25.976 (3.726%) 005: dt: 0.0500, sse=17523722.0, rms=25.113 (3.320%) 006: dt: 0.0500, sse=16519805.0, rms=24.355 (3.020%) 007: dt: 0.0500, sse=15645714.0, rms=23.675 (2.793%) 008: dt: 0.0500, sse=14871352.0, rms=23.055 (2.616%) 009: dt: 0.0500, sse=14175755.0, rms=22.484 (2.476%) 010: dt: 0.0500, sse=13545235.0, rms=21.954 (2.359%) positioning took 1.0 minutes mean border=55.0, 46 (29) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.0 (%100.0))] %20 local maxima, %50 large gradients and %26 min vals, 126 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=14265917.0, rms=22.562 011: dt: 0.0500, sse=13686088.0, rms=22.076 (2.151%) 012: dt: 0.0500, sse=13152846.0, rms=21.620 (2.066%) 013: dt: 0.0500, sse=12660011.0, rms=21.190 (1.990%) 014: dt: 0.0500, sse=12202967.0, rms=20.783 (1.921%) 015: dt: 0.0500, sse=11778816.0, rms=20.398 (1.853%) 016: dt: 0.0500, sse=11382946.0, rms=20.032 (1.795%) 017: dt: 0.0500, sse=11012960.0, rms=19.684 (1.739%) 018: dt: 0.0500, sse=10665669.0, rms=19.351 (1.690%) 019: dt: 0.0500, sse=10339025.0, rms=19.033 (1.645%) 020: dt: 0.0500, sse=10030674.0, rms=18.727 (1.605%) positioning took 1.0 minutes mean border=54.8, 57 (23) missing vertices, mean dist 1.2 [0.1 (%1.1)->1.6 (%98.9))] %20 local maxima, %50 large gradients and %26 min vals, 131 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=10129137.0, rms=18.831 021: dt: 0.0500, sse=9828544.0, rms=18.530 (1.599%) 022: dt: 0.0500, sse=9543594.0, rms=18.240 (1.565%) 023: dt: 0.0500, sse=9270789.0, rms=17.958 (1.546%) 024: dt: 0.0500, sse=9010455.0, rms=17.684 (1.523%) 025: dt: 0.0500, sse=8761519.0, rms=17.419 (1.501%) 026: dt: 0.0500, sse=8521556.0, rms=17.159 (1.492%) 027: dt: 0.0500, sse=8288179.0, rms=16.902 (1.496%) 028: dt: 0.0500, sse=8059451.0, rms=16.647 (1.511%) 029: dt: 0.0500, sse=7834830.5, rms=16.392 (1.530%) 030: dt: 0.0500, sse=7613388.5, rms=16.137 (1.556%) positioning took 1.0 minutes mean border=54.7, 93 (18) missing vertices, mean dist 0.9 [0.1 (%7.5)->1.4 (%92.5))] %20 local maxima, %50 large gradients and %25 min vals, 119 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=7719835.5, rms=16.259 031: dt: 0.5000, sse=6042261.5, rms=14.198 (12.673%) 032: dt: 0.5000, sse=4712188.5, rms=12.315 (13.262%) 033: dt: 0.5000, sse=3666560.2, rms=10.609 (13.857%) 034: dt: 0.5000, sse=2888434.2, rms=9.125 (13.985%) 035: dt: 0.5000, sse=2371557.2, rms=7.993 (12.402%) 036: dt: 0.5000, sse=2016408.0, rms=7.104 (11.125%) 037: dt: 0.5000, sse=1803989.9, rms=6.520 (8.223%) 038: dt: 0.5000, sse=1654930.1, rms=6.069 (6.916%) 039: dt: 0.5000, sse=1577672.4, rms=5.826 (4.006%) 040: dt: 0.5000, sse=1510126.4, rms=5.597 (3.923%) 041: dt: 0.5000, sse=1482742.4, rms=5.505 (1.650%) 042: dt: 0.5000, sse=1445740.5, rms=5.372 (2.415%) rms = 5.37, time step reduction 1 of 3 to 0.250... 043: dt: 0.5000, sse=1443392.0, rms=5.365 (0.126%) 044: dt: 0.2500, sse=1239160.5, rms=4.535 (15.480%) 045: dt: 0.2500, sse=1181597.1, rms=4.291 (5.376%) rms = 4.30, time step reduction 2 of 3 to 0.125... 046: dt: 0.1250, sse=1160428.4, rms=4.192 (2.303%) 047: dt: 0.1250, sse=1132128.1, rms=4.054 (3.287%) rms = 4.03, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=1127881.6, rms=4.032 (0.552%) positioning took 2.3 minutes mean border=52.9, 1453 (7) missing vertices, mean dist 0.1 [0.2 (%42.8)->0.4 (%57.2))] %34 local maxima, %38 large gradients and %23 min vals, 66 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=1504454.8, rms=4.989 049: dt: 0.5000, sse=1478473.9, rms=4.903 (1.722%) 050: dt: 0.5000, sse=1422375.5, rms=4.719 (3.747%) rms = 4.89, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=1206137.0, rms=3.706 (21.479%) 052: dt: 0.2500, sse=1149790.5, rms=3.385 (8.646%) rms = 3.36, time step reduction 2 of 3 to 0.125... 053: dt: 0.2500, sse=1145203.4, rms=3.359 (0.784%) 054: dt: 0.1250, sse=1087957.0, rms=3.004 (10.570%) 055: dt: 0.1250, sse=1078533.0, rms=2.944 (1.987%) rms = 2.93, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1076756.9, rms=2.933 (0.370%) positioning took 1.2 minutes mean border=51.6, 1668 (7) missing vertices, mean dist 0.1 [0.2 (%44.5)->0.3 (%55.5))] %49 local maxima, %23 large gradients and %22 min vals, 50 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=1177186.4, rms=3.523 rms = 4.37, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1108495.4, rms=3.127 (11.240%) 058: dt: 0.2500, sse=1093491.8, rms=3.038 (2.841%) rms = 3.05, time step reduction 2 of 3 to 0.125... 059: dt: 0.1250, sse=1084917.4, rms=2.981 (1.857%) 060: dt: 0.1250, sse=1072459.1, rms=2.902 (2.662%) rms = 2.87, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1067705.2, rms=2.873 (1.000%) positioning took 0.9 minutes mean border=50.9, 2958 (7) missing vertices, mean dist 0.0 [0.2 (%47.6)->0.2 (%52.4))] %53 local maxima, %19 large gradients and %22 min vals, 52 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-6.0.0/0051362/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1095686.0, rms=3.055 rms = 3.80, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1069292.0, rms=2.884 (5.605%) rms = 2.84, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1059952.1, rms=2.840 (1.514%) 064: dt: 0.1250, sse=1047086.4, rms=2.748 (3.251%) rms = 2.72, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1041974.0, rms=2.718 (1.106%) positioning took 0.7 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.area.pial vertex spacing 0.96 +- 0.40 (0.07-->5.59) (max @ vno 99312 --> 98230) face area 0.37 +- 0.28 (0.00-->4.18) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 140379 vertices processed 25000 of 140379 vertices processed 50000 of 140379 vertices processed 75000 of 140379 vertices processed 100000 of 140379 vertices processed 125000 of 140379 vertices processed 0 of 140379 vertices processed 25000 of 140379 vertices processed 50000 of 140379 vertices processed 75000 of 140379 vertices processed 100000 of 140379 vertices processed 125000 of 140379 vertices processed thickness calculation complete, 83:339 truncations. 33728 vertices at 0 distance 107234 vertices at 1 distance 84835 vertices at 2 distance 30392 vertices at 3 distance 8329 vertices at 4 distance 2269 vertices at 5 distance 688 vertices at 6 distance 205 vertices at 7 distance 74 vertices at 8 distance 40 vertices at 9 distance 16 vertices at 10 distance 20 vertices at 11 distance 18 vertices at 12 distance 15 vertices at 13 distance 9 vertices at 14 distance 4 vertices at 15 distance 6 vertices at 16 distance 8 vertices at 17 distance 1 vertices at 18 distance 1 vertices at 19 distance 0 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.thickness positioning took 15.3 minutes PIDs (20700 20703) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sat Oct 7 23:56:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.cortex.label Total face volume 217672 Total vertex volume 214840 (mask=0) #@# 0051362 lh 214840 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sat Oct 7 23:56:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.cortex.label Total face volume 223356 Total vertex volume 220256 (mask=0) #@# 0051362 rh 220256 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sat Oct 7 23:56:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 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 = 115 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/ribbon.mgz mris_volmask took 16.48 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 00:12:38 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 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 0051362 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 00:12:38 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 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 0051362 rh pial Waiting for PID 22425 of (22425 22428 22431 22434) to complete... Waiting for PID 22428 of (22425 22428 22431 22434) to complete... Waiting for PID 22431 of (22425 22428 22431 22434) to complete... Waiting for PID 22434 of (22425 22428 22431 22434) 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 0051362 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 217672 Total vertex volume 214840 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 1329 909 1932 2.260 0.341 0.112 0.024 9 1.4 bankssts 845 552 1385 2.190 0.709 0.138 0.030 13 0.9 caudalanteriorcingulate 3441 2299 5801 2.331 0.413 0.124 0.033 34 4.5 caudalmiddlefrontal 3049 1853 3327 1.720 0.396 0.141 0.042 42 5.3 cuneus 609 418 1722 2.991 1.000 0.127 0.032 5 0.9 entorhinal 4121 2721 9034 2.747 0.604 0.133 0.046 65 7.2 fusiform 6010 3919 9580 2.276 0.418 0.130 0.034 80 8.0 inferiorparietal 5024 3324 10421 2.598 0.638 0.143 0.050 90 10.2 inferiortemporal 1560 989 2536 2.315 0.807 0.142 0.045 31 2.4 isthmuscingulate 7455 4645 10315 2.055 0.517 0.139 0.040 106 11.3 lateraloccipital 3782 2457 6707 2.517 0.565 0.134 0.046 54 7.1 lateralorbitofrontal 5548 3606 7261 1.961 0.625 0.147 0.048 89 10.4 lingual 2980 1989 4783 2.235 0.661 0.130 0.037 51 4.3 medialorbitofrontal 4603 3113 10047 2.725 0.568 0.128 0.034 61 6.5 middletemporal 946 638 2103 2.792 0.646 0.106 0.025 7 0.9 parahippocampal 2131 1282 3007 2.264 0.462 0.103 0.030 16 2.5 paracentral 2383 1548 4046 2.367 0.391 0.119 0.031 29 2.7 parsopercularis 1153 725 2239 2.418 0.472 0.154 0.044 23 1.8 parsorbitalis 2106 1351 3277 2.198 0.410 0.128 0.031 30 2.6 parstriangularis 2429 1639 2527 1.759 0.473 0.139 0.044 28 4.4 pericalcarine 7172 4461 9543 1.954 0.501 0.119 0.034 87 9.6 postcentral 1731 1127 2803 2.240 0.730 0.139 0.037 30 2.7 posteriorcingulate 7505 4555 11238 2.311 0.417 0.114 0.045 90 12.2 precentral 5924 3885 9405 2.279 0.507 0.132 0.037 81 8.9 precuneus 1065 663 1909 2.783 0.625 0.122 0.032 16 1.2 rostralanteriorcingulate 9757 6459 15940 2.228 0.422 0.143 0.038 153 15.0 rostralmiddlefrontal 10002 6650 18998 2.513 0.469 0.130 0.037 117 13.8 superiorfrontal 8142 5192 11965 2.131 0.384 0.129 0.032 114 10.3 superiorparietal 5856 3836 11907 2.691 0.563 0.113 0.031 60 6.9 superiortemporal 5253 3453 9104 2.381 0.468 0.138 0.039 76 8.0 supramarginal 393 261 901 2.550 0.325 0.146 0.042 7 0.5 frontalpole 695 456 2120 3.424 0.696 0.165 0.068 14 2.1 temporalpole 740 404 900 2.130 0.356 0.116 0.044 10 1.0 transversetemporal 3535 2293 6058 2.604 0.718 0.138 0.060 91 9.7 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0051362 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 217672 Total vertex volume 214840 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 1329 837 1932 2.260 0.341 0.124 0.034 20 1.9 bankssts 845 688 1385 2.190 0.709 0.154 0.038 18 1.3 caudalanteriorcingulate 3441 2640 5801 2.331 0.413 0.126 0.029 40 4.3 caudalmiddlefrontal 3049 2116 3327 1.720 0.396 0.129 0.034 47 4.7 cuneus 609 669 1722 2.991 1.000 0.180 0.048 8 1.4 entorhinal 4121 3711 9034 2.747 0.604 0.169 0.048 89 8.9 fusiform 6010 4464 9580 2.276 0.418 0.139 0.033 94 9.0 inferiorparietal 5024 4447 10421 2.598 0.638 0.169 0.045 101 10.1 inferiortemporal 1560 1221 2536 2.315 0.807 0.156 0.049 36 2.7 isthmuscingulate 7455 5456 10315 2.055 0.517 0.131 0.035 124 11.3 lateraloccipital 3782 2754 6707 2.517 0.565 0.147 0.044 67 7.1 lateralorbitofrontal 5548 4029 7261 1.961 0.625 0.138 0.041 97 9.9 lingual 2980 2300 4783 2.235 0.661 0.142 0.036 44 4.7 medialorbitofrontal 4603 4083 10047 2.725 0.568 0.146 0.033 54 7.0 middletemporal 946 903 2103 2.792 0.646 0.150 0.034 8 1.7 parahippocampal 2131 1408 3007 2.264 0.462 0.115 0.028 20 2.6 paracentral 2383 1878 4046 2.367 0.391 0.148 0.032 30 3.5 parsopercularis 1153 1074 2239 2.418 0.472 0.167 0.040 15 2.0 parsorbitalis 2106 1586 3277 2.198 0.410 0.149 0.035 31 3.1 parstriangularis 2429 1302 2527 1.759 0.473 0.101 0.029 32 2.5 pericalcarine 7172 5282 9543 1.954 0.501 0.125 0.026 71 8.1 postcentral 1731 1292 2803 2.240 0.730 0.144 0.043 30 2.9 posteriorcingulate 7505 5081 11238 2.311 0.417 0.108 0.027 82 8.3 precentral 5924 4240 9405 2.279 0.507 0.136 0.056 94 18.1 precuneus 1065 824 1909 2.783 0.625 0.154 0.048 25 2.2 rostralanteriorcingulate 9757 7684 15940 2.228 0.422 0.159 0.041 156 17.7 rostralmiddlefrontal 10002 8119 18998 2.513 0.469 0.144 0.037 127 15.6 superiorfrontal 8142 5937 11965 2.131 0.384 0.134 0.030 110 10.6 superiorparietal 5856 4745 11907 2.691 0.563 0.139 0.035 90 9.4 superiortemporal 5253 4127 9104 2.381 0.468 0.154 0.040 89 9.3 supramarginal 393 437 901 2.550 0.325 0.189 0.035 5 0.7 frontalpole 695 787 2120 3.424 0.696 0.192 0.048 11 1.7 temporalpole 740 462 900 2.130 0.356 0.104 0.023 8 0.7 transversetemporal 3535 2297 6058 2.604 0.718 0.145 0.049 72 7.7 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051362 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 223356 Total vertex volume 220256 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 1343 891 2226 2.584 0.303 0.119 0.025 11 1.4 bankssts 818 545 1143 1.989 0.596 0.145 0.024 15 0.7 caudalanteriorcingulate 3132 2064 5414 2.430 0.380 0.120 0.029 33 3.7 caudalmiddlefrontal 2700 1547 3426 1.979 0.542 0.135 0.039 42 4.2 cuneus 563 369 1685 3.282 0.765 0.152 0.058 10 1.3 entorhinal 4392 2866 8859 2.769 0.582 0.137 0.044 66 7.7 fusiform 8540 5562 14602 2.450 0.414 0.126 0.029 104 9.4 inferiorparietal 4913 3166 9642 2.677 0.604 0.132 0.041 73 7.9 inferiortemporal 1469 898 2363 2.355 0.711 0.124 0.041 20 1.8 isthmuscingulate 7185 4411 9107 1.982 0.474 0.134 0.036 94 9.8 lateraloccipital 3580 2348 6316 2.511 0.681 0.131 0.044 58 6.0 lateralorbitofrontal 5781 3625 8394 2.079 0.662 0.142 0.049 91 10.7 lingual 2904 1942 5014 2.263 0.552 0.130 0.036 54 3.9 medialorbitofrontal 5759 3776 12612 2.912 0.524 0.122 0.032 75 7.2 middletemporal 905 610 2062 2.866 0.759 0.113 0.029 8 1.0 parahippocampal 2628 1531 3529 2.255 0.415 0.111 0.030 20 3.3 paracentral 2099 1349 3726 2.602 0.382 0.113 0.029 20 2.4 parsopercularis 1349 860 2774 2.508 0.534 0.152 0.049 25 2.7 parsorbitalis 2944 1935 5122 2.357 0.386 0.133 0.036 38 4.3 parstriangularis 2744 1780 2962 1.857 0.510 0.134 0.042 32 5.0 pericalcarine 6237 3618 8188 2.067 0.526 0.112 0.030 63 7.7 postcentral 1910 1243 3303 2.277 0.647 0.144 0.041 35 2.8 posteriorcingulate 7754 4444 11626 2.502 0.436 0.106 0.032 75 10.7 precentral 5678 3664 8865 2.293 0.460 0.125 0.033 70 7.3 precuneus 660 393 998 2.429 0.542 0.137 0.039 13 0.9 rostralanteriorcingulate 9454 6249 15610 2.240 0.468 0.135 0.040 142 14.9 rostralmiddlefrontal 9588 6340 17916 2.430 0.494 0.130 0.036 122 13.9 superiorfrontal 8443 5285 12218 2.146 0.353 0.127 0.030 108 9.7 superiorparietal 6054 3731 11140 2.727 0.526 0.104 0.027 55 6.2 superiortemporal 5226 3250 8743 2.459 0.425 0.120 0.029 59 5.7 supramarginal 499 283 971 2.437 0.481 0.146 0.044 13 0.8 frontalpole 758 478 2225 3.290 0.797 0.161 0.060 15 2.0 temporalpole 677 295 864 2.432 0.376 0.084 0.027 5 0.7 transversetemporal 3808 2404 6566 2.638 0.970 0.130 0.049 70 7.6 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 0051362 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 223356 Total vertex volume 220256 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 1343 826 2226 2.584 0.303 0.124 0.037 21 2.4 bankssts 818 622 1143 1.989 0.596 0.181 0.052 75 2.0 caudalanteriorcingulate 3132 2374 5414 2.430 0.380 0.123 0.025 34 3.3 caudalmiddlefrontal 2700 1967 3426 1.979 0.542 0.125 0.033 37 4.0 cuneus 563 595 1685 3.282 0.765 0.173 0.054 9 1.2 entorhinal 4392 3574 8859 2.769 0.582 0.153 0.044 83 9.1 fusiform 8540 6235 14602 2.450 0.414 0.130 0.029 105 10.7 inferiorparietal 4913 3949 9642 2.677 0.604 0.147 0.039 90 8.3 inferiortemporal 1469 1036 2363 2.355 0.711 0.148 0.046 45 2.8 isthmuscingulate 7185 4880 9107 1.982 0.474 0.126 0.032 140 9.8 lateraloccipital 3580 2630 6316 2.511 0.681 0.145 0.052 62 6.3 lateralorbitofrontal 5781 4393 8394 2.079 0.662 0.142 0.039 90 10.4 lingual 2904 2501 5014 2.263 0.552 0.157 0.043 43 5.2 medialorbitofrontal 5759 4917 12612 2.912 0.524 0.136 0.032 58 8.1 middletemporal 905 809 2062 2.866 0.759 0.149 0.037 10 1.5 parahippocampal 2628 1628 3529 2.255 0.415 0.109 0.026 31 3.0 paracentral 2099 1560 3726 2.602 0.382 0.129 0.034 26 3.1 parsopercularis 1349 1336 2774 2.508 0.534 0.178 0.039 16 2.5 parsorbitalis 2944 2395 5122 2.357 0.386 0.150 0.035 39 4.5 parstriangularis 2744 1465 2962 1.857 0.510 0.102 0.029 36 3.1 pericalcarine 6237 4338 8188 2.067 0.526 0.112 0.023 53 6.1 postcentral 1910 1540 3303 2.277 0.647 0.160 0.044 35 3.7 posteriorcingulate 7754 4834 11626 2.502 0.436 0.094 0.030 194 6.6 precentral 5678 4049 8865 2.293 0.460 0.131 0.033 72 8.0 precuneus 660 465 998 2.429 0.542 0.158 0.046 12 1.3 rostralanteriorcingulate 9454 7475 15610 2.240 0.468 0.154 0.037 150 14.9 rostralmiddlefrontal 9588 8084 17916 2.430 0.494 0.150 0.037 120 15.2 superiorfrontal 8443 6110 12218 2.146 0.353 0.131 0.029 118 10.2 superiorparietal 6054 4416 11140 2.727 0.526 0.116 0.026 66 6.7 superiortemporal 5226 3743 8743 2.459 0.425 0.130 0.032 63 7.0 supramarginal 499 483 971 2.437 0.481 0.172 0.034 6 0.7 frontalpole 758 821 2225 3.290 0.797 0.180 0.046 12 1.7 temporalpole 677 404 864 2.432 0.376 0.086 0.018 3 0.5 transversetemporal 3808 2291 6566 2.638 0.970 0.133 0.062 100 12.2 insula PIDs (22425 22428 22431 22434) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 00:14:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 00:14:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 22522 of (22522 22525) to complete... Waiting for PID 22525 of (22522 22525) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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... 52 labels changed using aseg relabeling using gibbs priors... 000: 8888 changed, 137434 examined... 001: 2108 changed, 34819 examined... 002: 573 changed, 11187 examined... 003: 237 changed, 3285 examined... 004: 108 changed, 1365 examined... 005: 43 changed, 629 examined... 006: 25 changed, 247 examined... 007: 18 changed, 154 examined... 008: 9 changed, 106 examined... 009: 1 changed, 57 examined... 010: 1 changed, 5 examined... 011: 2 changed, 9 examined... 012: 2 changed, 9 examined... 013: 0 changed, 6 examined... 16 labels changed using aseg 000: 244 total segments, 161 labels (2458 vertices) changed 001: 96 total segments, 13 labels (43 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 17 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1024 vertices marked for relabeling... 1024 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 0051362 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... 38 labels changed using aseg relabeling using gibbs priors... 000: 9060 changed, 140379 examined... 001: 2066 changed, 35768 examined... 002: 614 changed, 10811 examined... 003: 236 changed, 3404 examined... 004: 113 changed, 1317 examined... 005: 65 changed, 679 examined... 006: 32 changed, 346 examined... 007: 19 changed, 189 examined... 008: 10 changed, 108 examined... 009: 5 changed, 58 examined... 010: 2 changed, 32 examined... 011: 0 changed, 11 examined... 12 labels changed using aseg 000: 267 total segments, 174 labels (2107 vertices) changed 001: 98 total segments, 8 labels (46 vertices) changed 002: 90 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1223 vertices marked for relabeling... 1223 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 20 seconds. PIDs (22522 22525) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 00:14:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 00:14:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 rh white Waiting for PID 22579 of (22579 22582) to complete... Waiting for PID 22582 of (22579 22582) 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 0051362 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 217672 Total vertex volume 214840 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 1593 1048 2725 2.328 0.427 0.153 0.042 28 2.8 G&S_frontomargin 1655 1060 2781 2.316 0.559 0.150 0.042 25 2.8 G&S_occipital_inf 1709 981 2410 2.113 0.448 0.125 0.047 23 3.2 G&S_paracentral 1481 948 2785 2.491 0.460 0.135 0.041 23 2.2 G&S_subcentral 710 468 1448 2.407 0.411 0.146 0.036 11 1.0 G&S_transv_frontopol 1874 1247 3436 2.655 0.519 0.120 0.030 21 2.1 G&S_cingul-Ant 1120 774 1843 2.296 0.439 0.113 0.023 8 1.0 G&S_cingul-Mid-Ant 1271 853 2146 2.437 0.395 0.118 0.028 12 1.4 G&S_cingul-Mid-Post 664 412 1550 2.901 0.431 0.153 0.047 12 1.1 G_cingul-Post-dorsal 344 192 714 2.750 0.732 0.137 0.039 6 0.4 G_cingul-Post-ventral 2598 1619 2940 1.655 0.413 0.148 0.046 40 4.9 G_cuneus 1322 815 2613 2.426 0.410 0.133 0.041 24 1.9 G_front_inf-Opercular 438 259 943 2.566 0.426 0.137 0.041 10 0.6 G_front_inf-Orbital 1192 748 2289 2.365 0.394 0.142 0.040 23 1.8 G_front_inf-Triangul 5345 3485 10471 2.377 0.422 0.142 0.040 98 8.4 G_front_middle 7358 4741 15222 2.617 0.475 0.139 0.042 108 11.6 G_front_sup 722 485 1296 2.523 0.728 0.153 0.058 13 1.6 G_Ins_lg&S_cent_ins 948 535 2128 2.911 0.985 0.153 0.104 62 5.1 G_insular_short 2168 1327 4252 2.428 0.467 0.147 0.043 42 3.4 G_occipital_middle 1873 1061 2410 1.928 0.524 0.131 0.038 36 2.9 G_occipital_sup 1719 1084 4038 2.805 0.597 0.140 0.054 31 3.4 G_oc-temp_lat-fusifor 3950 2460 5146 1.850 0.646 0.160 0.056 77 8.8 G_oc-temp_med-Lingual 1229 801 3182 2.957 0.836 0.112 0.028 9 1.3 G_oc-temp_med-Parahip 2378 1475 4889 2.534 0.598 0.138 0.053 44 4.7 G_orbital 2165 1390 4413 2.432 0.445 0.148 0.043 44 3.7 G_pariet_inf-Angular 2525 1644 5129 2.543 0.486 0.149 0.045 44 4.2 G_pariet_inf-Supramar 3153 2029 5375 2.204 0.392 0.137 0.036 51 4.4 G_parietal_sup 2815 1623 3875 1.971 0.450 0.123 0.041 45 4.3 G_postcentral 2708 1513 4828 2.492 0.372 0.119 0.051 46 5.9 G_precentral 2864 1881 5589 2.380 0.514 0.143 0.042 51 4.5 G_precuneus 903 580 1746 2.297 0.555 0.144 0.049 23 1.7 G_rectus 681 429 805 1.977 0.965 0.097 0.050 8 1.0 G_subcallosal 495 262 698 2.124 0.376 0.114 0.050 7 0.7 G_temp_sup-G_T_transv 2105 1325 5588 2.965 0.579 0.132 0.042 32 3.1 G_temp_sup-Lateral 574 379 1487 3.312 0.626 0.104 0.030 4 0.8 G_temp_sup-Plan_polar 938 606 1893 2.617 0.423 0.130 0.042 14 1.4 G_temp_sup-Plan_tempo 2809 1771 6845 2.738 0.692 0.158 0.072 80 8.2 G_temporal_inf 2229 1468 5832 2.857 0.598 0.135 0.039 38 3.3 G_temporal_middle 274 185 314 1.875 0.310 0.104 0.019 2 0.2 Lat_Fis-ant-Horizont 394 275 491 2.086 0.295 0.115 0.021 3 0.3 Lat_Fis-ant-Vertical 921 607 1110 2.332 0.320 0.119 0.034 7 1.2 Lat_Fis-post 2039 1233 2367 1.809 0.505 0.142 0.043 34 3.2 Pole_occipital 1721 1151 5196 3.150 0.744 0.152 0.055 31 4.0 Pole_temporal 3236 2185 3608 1.900 0.522 0.128 0.041 36 5.6 S_calcarine 3559 2306 3920 1.916 0.481 0.110 0.042 27 4.4 S_central 1008 685 1367 2.133 0.368 0.106 0.020 6 0.9 S_cingul-Marginalis 388 264 586 2.702 0.495 0.118 0.033 2 0.6 S_circular_insula_ant 1405 985 1979 2.416 0.451 0.100 0.024 7 1.7 S_circular_insula_inf 1717 1146 2213 2.334 0.353 0.107 0.024 9 1.8 S_circular_insula_sup 817 557 1361 2.393 0.547 0.120 0.030 7 0.9 S_collat_transv_ant 533 347 542 2.139 0.414 0.157 0.048 7 1.0 S_collat_transv_post 2635 1788 3670 2.124 0.365 0.132 0.030 27 3.4 S_front_inf 1484 992 1863 2.132 0.389 0.139 0.035 17 2.1 S_front_middle 3047 2049 4364 2.175 0.356 0.119 0.030 29 3.6 S_front_sup 253 167 338 2.217 0.332 0.123 0.025 2 0.3 S_interm_prim-Jensen 2470 1623 3161 2.129 0.362 0.119 0.028 24 2.8 S_intrapariet&P_trans 1061 698 1175 2.040 0.340 0.137 0.038 10 1.7 S_oc_middle&Lunatus 1431 945 1811 2.143 0.306 0.127 0.027 13 1.6 S_oc_sup&transversal 744 510 1070 2.179 0.302 0.096 0.019 4 0.6 S_occipital_ant 754 534 1344 2.617 0.435 0.129 0.028 7 1.0 S_oc-temp_lat 1990 1415 3021 2.457 0.407 0.121 0.028 15 2.1 S_oc-temp_med&Lingual 505 349 643 2.016 0.409 0.125 0.028 3 0.6 S_orbital_lateral 679 480 924 2.233 0.549 0.120 0.030 5 0.9 S_orbital_med-olfact 1556 1066 2637 2.459 0.476 0.140 0.037 19 2.5 S_orbital-H_Shaped 2484 1596 3065 2.118 0.445 0.116 0.028 19 2.8 S_parieto_occipital 1182 716 771 1.486 0.690 0.156 0.052 36 2.2 S_pericallosal 3675 2404 4338 1.992 0.365 0.112 0.024 31 3.5 S_postcentral 1699 1123 2327 2.298 0.370 0.106 0.023 10 1.6 S_precentral-inf-part 1262 837 1554 2.122 0.355 0.105 0.027 7 1.3 S_precentral-sup-part 631 454 871 2.245 0.578 0.132 0.022 5 0.6 S_suborbital 1037 708 1362 2.272 0.377 0.133 0.030 9 1.4 S_subparietal 1765 1250 2535 2.358 0.420 0.122 0.026 12 2.1 S_temporal_inf 5932 4012 8739 2.347 0.431 0.112 0.025 47 6.4 S_temporal_sup 347 242 440 2.147 0.293 0.125 0.033 3 0.4 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0051362 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 223356 Total vertex volume 220256 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 970 624 1572 2.189 0.494 0.131 0.040 15 1.5 G&S_frontomargin 1363 865 2035 2.091 0.494 0.133 0.031 17 1.6 G&S_occipital_inf 1656 867 2210 2.141 0.524 0.107 0.035 16 2.3 G&S_paracentral 1369 879 2474 2.487 0.450 0.139 0.043 19 2.0 G&S_subcentral 1248 794 2515 2.569 0.490 0.162 0.050 33 2.6 G&S_transv_frontopol 3069 2041 5009 2.276 0.535 0.140 0.037 47 4.4 G&S_cingul-Ant 1306 891 2203 2.302 0.540 0.136 0.030 16 1.6 G&S_cingul-Mid-Ant 1443 943 2484 2.399 0.465 0.119 0.032 14 1.6 G&S_cingul-Mid-Post 679 423 1429 2.693 0.418 0.161 0.052 16 1.1 G_cingul-Post-dorsal 388 221 879 2.755 0.609 0.127 0.045 5 0.6 G_cingul-Post-ventral 2543 1439 3397 1.990 0.581 0.140 0.044 46 4.6 G_cuneus 1507 932 3102 2.613 0.396 0.124 0.035 21 2.0 G_front_inf-Opercular 485 290 1130 2.648 0.358 0.144 0.043 10 0.8 G_front_inf-Orbital 1322 854 2711 2.445 0.363 0.148 0.048 25 2.3 G_front_inf-Triangul 4406 2812 9175 2.457 0.417 0.147 0.049 95 8.1 G_front_middle 6282 3960 12592 2.523 0.476 0.137 0.042 100 10.4 G_front_sup 673 426 1229 2.730 0.710 0.149 0.070 17 2.1 G_Ins_lg&S_cent_ins 1231 745 2385 2.515 1.455 0.154 0.071 42 3.5 G_insular_short 2373 1447 4616 2.398 0.428 0.130 0.033 37 2.9 G_occipital_middle 1815 991 2245 1.965 0.383 0.128 0.037 26 2.4 G_occipital_sup 1932 1203 4390 2.794 0.651 0.153 0.060 44 4.6 G_oc-temp_lat-fusifor 3872 2299 5903 2.101 0.724 0.146 0.055 69 7.8 G_oc-temp_med-Lingual 1187 738 3330 3.262 0.743 0.136 0.049 17 2.2 G_oc-temp_med-Parahip 2657 1677 5866 2.602 0.669 0.144 0.057 61 5.9 G_orbital 3228 2015 6789 2.611 0.435 0.139 0.035 55 4.4 G_pariet_inf-Angular 2584 1518 5068 2.652 0.445 0.126 0.032 38 3.0 G_pariet_inf-Supramar 2174 1381 4018 2.303 0.332 0.135 0.033 33 2.7 G_parietal_sup 2497 1186 3398 2.212 0.513 0.105 0.032 27 3.2 G_postcentral 3142 1453 5268 2.698 0.388 0.097 0.039 42 5.4 G_precentral 2694 1667 4822 2.362 0.459 0.140 0.043 53 4.2 G_precuneus 818 554 1711 2.257 0.512 0.128 0.040 20 1.0 G_rectus 341 188 589 2.800 0.664 0.086 0.028 2 0.3 G_subcallosal 565 262 801 2.411 0.359 0.081 0.027 4 0.5 G_temp_sup-G_T_transv 2157 1211 4625 2.835 0.511 0.113 0.036 29 2.8 G_temp_sup-Lateral 873 547 1646 2.817 0.668 0.105 0.033 7 1.2 G_temp_sup-Plan_polar 992 574 1536 2.513 0.383 0.103 0.027 8 1.0 G_temp_sup-Plan_tempo 2668 1636 5754 2.708 0.651 0.138 0.050 52 5.1 G_temporal_inf 3402 2106 8398 3.000 0.517 0.125 0.034 54 4.3 G_temporal_middle 559 382 705 2.190 0.306 0.128 0.030 4 0.8 Lat_Fis-ant-Horizont 357 233 569 2.564 0.345 0.130 0.033 4 0.4 Lat_Fis-ant-Vertical 1422 891 1816 2.421 0.386 0.112 0.025 9 1.5 Lat_Fis-post 3407 2000 3601 1.698 0.442 0.135 0.044 50 5.8 Pole_occipital 1799 1182 5250 3.291 0.672 0.155 0.053 32 4.0 Pole_temporal 2848 1938 3261 1.993 0.500 0.133 0.036 28 4.5 S_calcarine 3133 2147 3614 1.980 0.483 0.112 0.024 19 3.6 S_central 1394 946 1906 2.200 0.362 0.111 0.025 10 1.4 S_cingul-Marginalis 545 360 843 2.716 0.553 0.111 0.029 3 0.6 S_circular_insula_ant 1180 811 1692 2.444 0.485 0.087 0.018 5 0.9 S_circular_insula_inf 1355 912 1918 2.482 0.429 0.113 0.027 8 1.6 S_circular_insula_sup 916 655 1525 2.643 0.436 0.112 0.027 6 0.9 S_collat_transv_ant 531 351 613 2.062 0.481 0.168 0.049 8 1.1 S_collat_transv_post 2253 1500 2960 2.190 0.379 0.114 0.027 15 2.4 S_front_inf 2322 1612 3231 2.069 0.398 0.117 0.025 16 2.7 S_front_middle 2467 1679 3365 2.173 0.350 0.107 0.024 15 2.4 S_front_sup 262 181 382 2.120 0.290 0.071 0.010 0 0.1 S_interm_prim-Jensen 3668 2433 4852 2.183 0.351 0.119 0.024 34 3.4 S_intrapariet&P_trans 826 554 848 1.935 0.405 0.147 0.035 11 1.1 S_oc_middle&Lunatus 1813 1182 2196 2.077 0.337 0.125 0.027 18 1.9 S_oc_sup&transversal 879 588 1211 2.346 0.313 0.106 0.019 6 0.7 S_occipital_ant 1121 749 1865 2.626 0.430 0.109 0.025 9 1.1 S_oc-temp_lat 1930 1389 3050 2.501 0.451 0.116 0.024 12 1.9 S_oc-temp_med&Lingual 613 424 687 1.866 0.384 0.125 0.028 5 0.7 S_orbital_lateral 912 631 1198 2.147 0.685 0.103 0.019 5 0.7 S_orbital_med-olfact 1272 859 2143 2.484 0.560 0.129 0.034 14 1.8 S_orbital-H_Shaped 2124 1377 2551 2.061 0.394 0.114 0.025 16 2.2 S_parieto_occipital 1272 786 973 1.649 0.602 0.142 0.039 26 1.5 S_pericallosal 2545 1658 3121 2.118 0.331 0.116 0.027 23 2.7 S_postcentral 1727 1145 2379 2.490 0.344 0.103 0.020 10 1.5 S_precentral-inf-part 1200 805 1638 2.390 0.375 0.096 0.018 5 1.0 S_precentral-sup-part 312 213 478 2.310 0.320 0.143 0.029 3 0.4 S_suborbital 1237 827 1821 2.343 0.413 0.126 0.027 12 1.5 S_subparietal 1255 878 1945 2.658 0.554 0.122 0.027 9 1.6 S_temporal_inf 6907 4670 10508 2.562 0.406 0.111 0.023 50 6.4 S_temporal_sup 212 147 240 2.054 0.309 0.139 0.032 2 0.3 S_temporal_transverse PIDs (22579 22582) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 00:15:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 00:15:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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 22648 of (22648 22651) to complete... Waiting for PID 22651 of (22648 22651) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051362 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... 1380 labels changed using aseg relabeling using gibbs priors... 000: 2007 changed, 137434 examined... 001: 500 changed, 9351 examined... 002: 144 changed, 2779 examined... 003: 64 changed, 855 examined... 004: 24 changed, 368 examined... 005: 11 changed, 147 examined... 006: 6 changed, 68 examined... 007: 5 changed, 34 examined... 008: 8 changed, 22 examined... 009: 3 changed, 35 examined... 010: 1 changed, 20 examined... 011: 0 changed, 6 examined... 211 labels changed using aseg 000: 60 total segments, 27 labels (172 vertices) changed 001: 33 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... 530 vertices marked for relabeling... 530 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 0051362 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... 1292 labels changed using aseg relabeling using gibbs priors... 000: 1934 changed, 140379 examined... 001: 445 changed, 9245 examined... 002: 111 changed, 2507 examined... 003: 43 changed, 665 examined... 004: 19 changed, 256 examined... 005: 18 changed, 111 examined... 006: 14 changed, 98 examined... 007: 10 changed, 61 examined... 008: 7 changed, 50 examined... 009: 10 changed, 39 examined... 010: 7 changed, 40 examined... 011: 4 changed, 27 examined... 012: 3 changed, 18 examined... 013: 4 changed, 20 examined... 014: 3 changed, 20 examined... 015: 0 changed, 15 examined... 244 labels changed using aseg 000: 54 total segments, 21 labels (213 vertices) changed 001: 34 total segments, 1 labels (3 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 8 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 896 vertices marked for relabeling... 896 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. PIDs (22648 22651) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 00:15:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 00:15:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 rh white Waiting for PID 22701 of (22701 22704) to complete... Waiting for PID 22704 of (22701 22704) 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 0051362 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 217672 Total vertex volume 214840 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 1556 1023 2624 2.331 0.652 0.132 0.030 21 1.7 caudalanteriorcingulate 3703 2478 6167 2.323 0.407 0.124 0.034 36 4.9 caudalmiddlefrontal 3857 2381 4406 1.764 0.399 0.133 0.038 47 6.1 cuneus 575 387 1589 3.023 1.007 0.125 0.031 5 0.8 entorhinal 3732 2479 7433 2.660 0.550 0.132 0.043 49 6.0 fusiform 5946 3896 9649 2.284 0.422 0.133 0.035 83 8.1 inferiorparietal 5067 3348 11409 2.677 0.686 0.145 0.054 102 11.3 inferiortemporal 1531 965 2505 2.351 0.789 0.142 0.045 30 2.4 isthmuscingulate 7668 4715 10682 2.063 0.528 0.138 0.039 117 11.5 lateraloccipital 4456 2880 8108 2.495 0.575 0.141 0.052 74 9.3 lateralorbitofrontal 5606 3645 7290 1.953 0.618 0.147 0.048 90 10.5 lingual 2460 1634 4181 2.220 0.668 0.127 0.039 44 3.7 medialorbitofrontal 6090 4116 12262 2.623 0.568 0.125 0.033 76 8.3 middletemporal 996 670 2232 2.798 0.656 0.105 0.026 8 1.0 parahippocampal 2466 1481 3583 2.285 0.456 0.103 0.030 19 2.9 paracentral 2336 1500 3938 2.382 0.387 0.121 0.032 30 2.7 parsopercularis 988 646 1608 2.293 0.474 0.135 0.036 15 1.4 parsorbitalis 2457 1595 3853 2.216 0.393 0.128 0.031 33 3.0 parstriangularis 2433 1645 2534 1.765 0.466 0.137 0.043 27 4.4 pericalcarine 7964 4999 10583 1.967 0.488 0.120 0.034 95 10.6 postcentral 1864 1209 2935 2.251 0.719 0.137 0.038 30 2.8 posteriorcingulate 7444 4504 11161 2.321 0.416 0.114 0.045 90 12.0 precentral 5713 3760 9249 2.298 0.501 0.137 0.039 82 8.9 precuneus 1487 950 2573 2.742 0.599 0.126 0.031 20 1.7 rostralanteriorcingulate 7182 4726 11925 2.213 0.433 0.144 0.038 117 11.1 rostralmiddlefrontal 11171 7449 20797 2.458 0.468 0.134 0.037 145 15.9 superiorfrontal 6431 4122 9517 2.143 0.377 0.129 0.032 87 8.0 superiorparietal 7507 4956 15552 2.705 0.618 0.119 0.034 82 10.0 superiortemporal 4858 3182 8355 2.384 0.472 0.136 0.038 69 7.1 supramarginal 737 401 896 2.125 0.354 0.115 0.044 10 1.0 transversetemporal 2979 1919 5244 2.675 0.718 0.136 0.058 79 8.0 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 0051362 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 223356 Total vertex volume 220256 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 1065 708 1668 2.117 0.647 0.148 0.028 19 1.2 caudalanteriorcingulate 3289 2159 5622 2.424 0.383 0.120 0.030 35 3.9 caudalmiddlefrontal 3166 1815 4019 1.970 0.511 0.131 0.037 46 4.8 cuneus 514 337 1541 3.270 0.786 0.150 0.055 8 1.1 entorhinal 4024 2643 7826 2.718 0.550 0.136 0.045 60 7.1 fusiform 8443 5493 14279 2.443 0.415 0.128 0.029 106 9.6 inferiorparietal 5296 3408 10727 2.712 0.633 0.133 0.041 78 8.5 inferiortemporal 1442 891 2290 2.356 0.690 0.124 0.041 19 1.7 isthmuscingulate 7236 4434 9116 1.966 0.470 0.134 0.036 95 9.9 lateraloccipital 4162 2739 7529 2.481 0.686 0.133 0.044 67 7.1 lateralorbitofrontal 5688 3546 8246 2.080 0.657 0.141 0.049 88 10.5 lingual 2400 1527 3889 2.093 0.827 0.121 0.039 57 3.7 medialorbitofrontal 6884 4509 14449 2.860 0.515 0.120 0.031 84 8.4 middletemporal 956 651 2225 2.901 0.753 0.118 0.029 10 1.1 parahippocampal 2729 1588 3667 2.249 0.419 0.112 0.031 21 3.5 paracentral 2679 1710 4651 2.562 0.383 0.117 0.032 28 3.3 parsopercularis 1217 767 2397 2.492 0.514 0.147 0.051 23 2.4 parsorbitalis 2710 1793 4521 2.309 0.408 0.135 0.038 36 4.0 parstriangularis 2687 1740 2888 1.855 0.512 0.133 0.042 31 4.8 pericalcarine 6889 4036 9150 2.087 0.517 0.114 0.031 72 8.3 postcentral 1971 1284 3372 2.278 0.643 0.143 0.041 35 2.8 posteriorcingulate 7487 4278 11344 2.511 0.435 0.105 0.032 72 10.4 precentral 5816 3773 9134 2.292 0.464 0.127 0.033 74 7.5 precuneus 854 520 1257 2.463 0.516 0.138 0.037 15 1.2 rostralanteriorcingulate 6933 4598 11622 2.218 0.454 0.136 0.040 107 11.2 rostralmiddlefrontal 12494 8201 22495 2.393 0.499 0.132 0.037 174 18.4 superiorfrontal 7068 4436 10377 2.161 0.353 0.127 0.030 92 8.1 superiorparietal 7752 4833 14945 2.771 0.573 0.112 0.032 80 9.9 superiortemporal 5015 3105 8443 2.467 0.439 0.117 0.028 55 5.2 supramarginal 648 280 841 2.458 0.371 0.083 0.027 5 0.6 transversetemporal 2972 1949 5728 2.864 0.744 0.129 0.042 42 4.9 insula PIDs (22701 22704) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 00:16:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts pctsurfcon --s 0051362 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 00:16:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts pctsurfcon --s 0051362 --rh-only Waiting for PID 22766 of (22766 22776) to complete... Waiting for PID 22776 of (22766 22776) to complete... pctsurfcon --s 0051362 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts/pctsurfcon.log Sun Oct 8 00:16:05 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-6.0.0/0051362/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-382 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-6.0.0/0051362/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.wm.mgh --regheader 0051362 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 72496 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.wm.mgh Dim: 137434 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.gm.mgh --projfrac 0.3 --regheader 0051362 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 89117 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.gm.mgh Dim: 137434 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22766/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.w-g.pct.mgh --annot 0051362 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/lh.w-g.pct.mgh --annot 0051362 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-382 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/lh.w-g.pct.mgh Vertex Area is 0.647128 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 0051362 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/scripts/pctsurfcon.log Sun Oct 8 00:16:05 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-6.0.0/0051362/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-382 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-6.0.0/0051362/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.wm.mgh --regheader 0051362 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 72873 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.wm.mgh Dim: 140379 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.gm.mgh --projfrac 0.3 --regheader 0051362 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 89908 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.gm.mgh Dim: 140379 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/tmp.pctsurfcon.22776/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.w-g.pct.mgh --annot 0051362 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.w-g.pct.mgh --annot 0051362 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-382 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.w-g.pct.mgh Vertex Area is 0.633852 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 (22766 22776) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 00:16:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1434 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1397 voxels changed to hypointensity... 2826 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 00:16:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362 mri_aparc2aseg --s 0051362 --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 00:16:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362 mri_aparc2aseg --s 0051362 --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 00:16:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362 mri_aparc2aseg --s 0051362 --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 22994 of (22994 22997 23000) to complete... Waiting for PID 22997 of (22994 22997 23000) to complete... Waiting for PID 23000 of (22994 22997 23000) to complete... mri_aparc2aseg --s 0051362 --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 0051362 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.21 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 63 rescaling Left_Lateral_Ventricle from 13 --> 16 rescaling Left_Inf_Lat_Vent from 34 --> 36 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 61 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 29 rescaling Fourth_Ventricle from 22 --> 20 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 64 rescaling Left_Amygdala from 56 --> 65 rescaling CSF from 32 --> 42 rescaling Left_Accumbens_area from 62 --> 65 rescaling Left_VentralDC from 87 --> 94 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 16 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 66 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 75 rescaling Right_Putamen from 80 --> 81 rescaling Right_Pallidum from 97 --> 97 rescaling Right_Hippocampus from 53 --> 62 rescaling Right_Amygdala from 55 --> 64 rescaling Right_Accumbens_area from 65 --> 73 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 36 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 77 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 = 430878 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 114 changed. pass 2: 1 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aparc+aseg.mgz mri_aparc2aseg --s 0051362 --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 0051362 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.21 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 63 rescaling Left_Lateral_Ventricle from 13 --> 16 rescaling Left_Inf_Lat_Vent from 34 --> 36 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 61 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 29 rescaling Fourth_Ventricle from 22 --> 20 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 64 rescaling Left_Amygdala from 56 --> 65 rescaling CSF from 32 --> 42 rescaling Left_Accumbens_area from 62 --> 65 rescaling Left_VentralDC from 87 --> 94 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 16 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 66 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 75 rescaling Right_Putamen from 80 --> 81 rescaling Right_Pallidum from 97 --> 97 rescaling Right_Hippocampus from 53 --> 62 rescaling Right_Amygdala from 55 --> 64 rescaling Right_Accumbens_area from 65 --> 73 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 36 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 77 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 = 430873 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 114 changed. pass 2: 1 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0051362 --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 0051362 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/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-6.0.0/0051362/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.21 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 63 rescaling Left_Lateral_Ventricle from 13 --> 16 rescaling Left_Inf_Lat_Vent from 34 --> 36 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 61 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 29 rescaling Fourth_Ventricle from 22 --> 20 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 64 rescaling Left_Amygdala from 56 --> 65 rescaling CSF from 32 --> 42 rescaling Left_Accumbens_area from 62 --> 65 rescaling Left_VentralDC from 87 --> 94 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 16 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 66 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 75 rescaling Right_Putamen from 80 --> 81 rescaling Right_Pallidum from 97 --> 97 rescaling Right_Hippocampus from 53 --> 62 rescaling Right_Amygdala from 55 --> 64 rescaling Right_Accumbens_area from 65 --> 73 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 36 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 77 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 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#----------------------------------------- #@# APas-to-ASeg Sun Oct 8 00:24:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 00:24:40 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-382 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-6.0.0/0051362/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-382 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 00:24:40 CEST 2017 Ended at Sun Oct 8 00:24:47 CEST 2017 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 00:24:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362 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 0051362 $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 0051362 sysname Linux hostname tars-382 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1467537 mm^3 (det: 1.327466 ) Computing euler number orig.nofix lheno = -90, rheno = -96 orig.nofix lhholes = 46, rhholes = 49 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 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 00:26:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362 mri_aparc2aseg --s 0051362 --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 0051362 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-6.0.0/0051362/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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-6.0.0/0051362/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8160 vertices from left hemi Ripped 7885 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-6.0.0/0051362/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 = 868255 Used brute-force search on 224 voxels Fixing Parahip LH WM Found 6 clusters 0 k 1.000000 1 k 1451.000000 2 k 30.000000 3 k 2.000000 4 k 1.000000 5 k 1.000000 Fixing Parahip RH WM Found 9 clusters 0 k 2.000000 1 k 1.000000 2 k 1.000000 3 k 5.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 1339.000000 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 0051362 --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 0051362 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-382 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1467537 mm^3 (det: 1.327466 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 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-6.0.0/0051362/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 00:36:33 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 24489 of (24489 24495 24501 24506 24513) to complete... Waiting for PID 24495 of (24489 24495 24501 24506 24513) to complete... Waiting for PID 24501 of (24489 24495 24501 24506 24513) to complete... Waiting for PID 24506 of (24489 24495 24501 24506 24513) to complete... Waiting for PID 24513 of (24489 24495 24501 24506 24513) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 614 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4743 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 789 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8698 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 290 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4367 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 683 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6666 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 506 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6290 mri_label2label: Done PIDs (24489 24495 24501 24506 24513) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 24565 of (24565 24571 24577 24582) to complete... Waiting for PID 24571 of (24565 24571 24577 24582) to complete... Waiting for PID 24577 of (24565 24571 24577 24582) to complete... Waiting for PID 24582 of (24565 24571 24577 24582) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 419 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4489 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 944 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14533 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 332 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4513 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 842 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4264 mri_label2label: Done PIDs (24565 24571 24577 24582) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 24645 of (24645 24652 24658 24663 24670) to complete... Waiting for PID 24652 of (24645 24652 24658 24663 24670) to complete... Waiting for PID 24658 of (24645 24652 24658 24663 24670) to complete... Waiting for PID 24663 of (24645 24652 24658 24663 24670) to complete... Waiting for PID 24670 of (24645 24652 24658 24663 24670) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 2033 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6674 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 4236 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 12350 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 230 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2248 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1388 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1266 mri_label2label: Done PIDs (24645 24652 24658 24663 24670) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 24783 of (24783 24789 24795 24801 24807) to complete... Waiting for PID 24789 of (24783 24789 24795 24801 24807) to complete... Waiting for PID 24795 of (24783 24789 24795 24801 24807) to complete... Waiting for PID 24801 of (24783 24789 24795 24801 24807) to complete... Waiting for PID 24807 of (24783 24789 24795 24801 24807) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 156 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1170 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 232 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2324 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1577 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 349 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2345 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 269 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2588 mri_label2label: Done PIDs (24783 24789 24795 24801 24807) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 24854 of (24854 24860 24866 24871) to complete... Waiting for PID 24860 of (24854 24860 24866 24871) to complete... Waiting for PID 24866 of (24854 24860 24866 24871) to complete... Waiting for PID 24871 of (24854 24860 24866 24871) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 196 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1745 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 322 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7357 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 134 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2046 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 289 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1440 mri_label2label: Done PIDs (24854 24860 24866 24871) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 24918 of (24918 24924 24930 24936 24940) to complete... Waiting for PID 24924 of (24918 24924 24930 24936 24940) to complete... Waiting for PID 24930 of (24918 24924 24930 24936 24940) to complete... Waiting for PID 24936 of (24918 24924 24930 24936 24940) to complete... Waiting for PID 24940 of (24918 24924 24930 24936 24940) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 1457 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4862 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 1960 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 5294 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 571 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 506 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 137434 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 466 mri_label2label: Done PIDs (24918 24924 24930 24936 24940) completed and logs appended. mris_label2annot --s 0051362 --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-6.0.0/0051362/label cmdline mris_label2annot --s 0051362 --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-382 machine x86_64 user ntraut subject 0051362 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-6.0.0/0051362/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 93569 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/lh.BA_exvivo.annot mris_label2annot --s 0051362 --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-6.0.0/0051362/label cmdline mris_label2annot --s 0051362 --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-382 machine x86_64 user ntraut subject 0051362 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-6.0.0/0051362/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 111381 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 217672 Total vertex volume 214840 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 1325 754 1887 2.063 0.492 0.135 0.051 25 2.6 BA1_exvivo 4548 2930 5954 2.026 0.402 0.115 0.025 45 4.5 BA2_exvivo 1081 753 1034 1.756 0.379 0.132 0.040 13 1.5 BA3a_exvivo 2775 1709 3637 1.876 0.546 0.116 0.037 31 3.9 BA3b_exvivo 1767 976 2550 2.362 0.402 0.113 0.043 19 3.4 BA4a_exvivo 1505 852 1907 2.377 0.365 0.100 0.070 19 3.5 BA4p_exvivo 8379 5343 15087 2.423 0.448 0.123 0.039 95 11.6 BA6_exvivo 2279 1458 3928 2.404 0.386 0.118 0.031 27 2.7 BA44_exvivo 3261 2153 5259 2.197 0.394 0.138 0.035 49 4.5 BA45_exvivo 4153 2732 4693 1.778 0.479 0.136 0.044 51 7.6 V1_exvivo 9886 6077 11461 1.809 0.524 0.150 0.049 174 18.9 V2_exvivo 1716 1137 3309 2.490 0.464 0.128 0.032 21 2.1 MT_exvivo 615 393 1940 3.317 0.829 0.131 0.043 7 1.3 perirhinal_exvivo 575 424 1106 2.563 0.723 0.126 0.031 4 0.8 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0051362 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 217672 Total vertex volume 214840 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 903 496 1213 2.009 0.477 0.141 0.057 19 1.9 BA1_exvivo 1848 1163 2447 1.984 0.400 0.108 0.022 18 1.6 BA2_exvivo 905 628 819 1.731 0.356 0.136 0.042 11 1.4 BA3a_exvivo 1851 1152 2086 1.684 0.429 0.109 0.034 18 2.4 BA3b_exvivo 1755 976 2496 2.383 0.389 0.109 0.040 16 3.3 BA4a_exvivo 1245 711 1516 2.307 0.380 0.101 0.078 18 3.0 BA4p_exvivo 4422 2751 7801 2.415 0.439 0.124 0.041 52 6.4 BA6_exvivo 1443 918 2421 2.352 0.377 0.124 0.034 20 1.9 BA44_exvivo 1251 818 2318 2.312 0.420 0.130 0.034 18 1.8 BA45_exvivo 4362 2856 5023 1.799 0.484 0.133 0.043 52 7.7 V1_exvivo 4990 3123 5165 1.619 0.464 0.155 0.050 91 10.0 V2_exvivo 467 324 883 2.531 0.414 0.124 0.025 5 0.5 MT_exvivo 304 193 994 3.284 0.763 0.107 0.023 2 0.3 perirhinal_exvivo 307 222 542 2.351 0.477 0.109 0.022 1 0.3 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 00:39:41 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 25117 of (25117 25123 25129 25134 25139) to complete... Waiting for PID 25123 of (25117 25123 25129 25134 25139) to complete... Waiting for PID 25129 of (25117 25123 25129 25134 25139) to complete... Waiting for PID 25134 of (25117 25123 25129 25134 25139) to complete... Waiting for PID 25139 of (25117 25123 25129 25134 25139) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 343 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4305 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 414 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7101 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4142 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 290 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4812 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 636 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6383 mri_label2label: Done PIDs (25117 25123 25129 25134 25139) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 25206 of (25206 25212 25218 25223) to complete... Waiting for PID 25212 of (25206 25212 25218 25223) to complete... Waiting for PID 25218 of (25206 25212 25218 25223) to complete... Waiting for PID 25223 of (25206 25212 25218 25223) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 374 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4847 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 1059 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13315 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 1190 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8102 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 1560 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6915 mri_label2label: Done PIDs (25206 25212 25218 25223) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 25272 of (25272 25278 25284 25289 25295) to complete... Waiting for PID 25278 of (25272 25278 25284 25289 25295) to complete... Waiting for PID 25284 of (25272 25278 25284 25289 25295) to complete... Waiting for PID 25289 of (25272 25278 25284 25289 25295) to complete... Waiting for PID 25295 of (25272 25278 25284 25289 25295) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 2239 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6966 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 3440 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11456 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 601 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2533 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1151 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 833 mri_label2label: Done PIDs (25272 25278 25284 25289 25295) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 25352 of (25352 25358 25364 25369 25376) to complete... Waiting for PID 25358 of (25352 25358 25364 25369 25376) to complete... Waiting for PID 25364 of (25352 25358 25364 25369 25376) to complete... Waiting for PID 25369 of (25352 25358 25364 25369 25376) to complete... Waiting for PID 25376 of (25352 25358 25364 25369 25376) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 119 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 995 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2826 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1754 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2316 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 170 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1558 mri_label2label: Done PIDs (25352 25358 25364 25369 25376) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 25424 of (25424 25430 25436 25442) to complete... Waiting for PID 25430 of (25424 25430 25436 25442) to complete... Waiting for PID 25436 of (25424 25430 25436 25442) to complete... Waiting for PID 25442 of (25424 25430 25436 25442) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1617 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 559 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7518 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 142 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1154 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 415 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1593 mri_label2label: Done PIDs (25424 25430 25436 25442) 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 0051362 --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 0051362 --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 0051362 --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 0051362 --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 0051362 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 25489 of (25489 25495 25501 25506 25511) to complete... Waiting for PID 25495 of (25489 25495 25501 25506 25511) to complete... Waiting for PID 25501 of (25489 25495 25501 25506 25511) to complete... Waiting for PID 25506 of (25489 25495 25501 25506 25511) to complete... Waiting for PID 25511 of (25489 25495 25501 25506 25511) 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 1544 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4776 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 1776 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5213 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 381 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 762 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 0051362 --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 = 0051362 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-6.0.0/0051362/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 140379 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 333 mri_label2label: Done PIDs (25489 25495 25501 25506 25511) completed and logs appended. mris_label2annot --s 0051362 --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-6.0.0/0051362/label cmdline mris_label2annot --s 0051362 --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-382 machine x86_64 user ntraut subject 0051362 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-6.0.0/0051362/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 96718 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/label/rh.BA_exvivo.annot mris_label2annot --s 0051362 --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-6.0.0/0051362/label cmdline mris_label2annot --s 0051362 --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-382 machine x86_64 user ntraut subject 0051362 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-6.0.0/0051362/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 115481 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/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 0051362 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 223356 Total vertex volume 220256 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 1048 442 1395 2.226 0.480 0.107 0.035 14 1.3 BA1_exvivo 3160 1905 4198 2.202 0.408 0.112 0.029 29 3.6 BA2_exvivo 1099 786 1108 1.804 0.373 0.141 0.033 10 1.6 BA3a_exvivo 1991 1225 2381 1.786 0.494 0.107 0.026 16 2.4 BA3b_exvivo 1780 908 2574 2.493 0.429 0.103 0.037 17 3.1 BA4a_exvivo 1382 832 1929 2.417 0.436 0.097 0.025 8 1.5 BA4p_exvivo 7618 4554 12980 2.501 0.427 0.111 0.034 80 10.4 BA6_exvivo 3778 2404 6305 2.542 0.384 0.110 0.028 32 4.1 BA44_exvivo 5188 3382 8915 2.342 0.449 0.138 0.041 75 8.4 BA45_exvivo 4605 2869 5541 1.886 0.519 0.130 0.041 58 8.2 V1_exvivo 8740 5230 10763 1.921 0.571 0.144 0.047 140 15.1 V2_exvivo 2331 1492 3572 2.330 0.357 0.114 0.026 21 2.2 MT_exvivo 555 363 1833 3.408 0.768 0.123 0.039 7 0.9 perirhinal_exvivo 386 246 815 3.042 0.605 0.154 0.049 6 0.9 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 0051362 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051362/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 223356 Total vertex volume 220256 (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) = 1467537 mm^3 (det: 1.327466 ) lhCtxGM: 214036.958 213091.000 diff= 946.0 pctdiff= 0.442 rhCtxGM: 218949.061 217938.000 diff= 1011.1 pctdiff= 0.462 lhCtxWM: 219192.958 219856.000 diff= -663.0 pctdiff=-0.302 rhCtxWM: 219057.185 220134.000 diff=-1076.8 pctdiff=-0.492 SubCortGMVol 57435.000 SupraTentVol 948745.161 (946066.000) diff=2679.161 pctdiff=0.282 SupraTentVolNotVent 931192.161 (928513.000) diff=2679.161 pctdiff=0.288 BrainSegVol 1070254.000 (1067055.000) diff=3199.000 pctdiff=0.299 BrainSegVolNotVent 1048570.000 (1048596.161) diff=-26.161 pctdiff=-0.002 BrainSegVolNotVent 1048570.000 CerebellumVol 119866.000 VentChorVol 17553.000 3rd4th5thCSF 4131.000 CSFVol 932.000, OptChiasmVol 191.000 MaskVol 1473252.000 742 284 917 2.186 0.499 0.097 0.038 9 0.9 BA1_exvivo 1868 1086 2586 2.217 0.436 0.101 0.024 14 1.9 BA2_exvivo 979 713 923 1.772 0.332 0.142 0.031 9 1.4 BA3a_exvivo 1575 998 1662 1.690 0.393 0.102 0.023 9 1.7 BA3b_exvivo 1069 551 1538 2.468 0.445 0.109 0.046 13 2.4 BA4a_exvivo 1146 714 1674 2.507 0.403 0.093 0.021 5 1.2 BA4p_exvivo 4918 2842 8396 2.533 0.429 0.109 0.034 54 6.7 BA6_exvivo 925 609 1862 2.680 0.331 0.116 0.032 10 1.2 BA44_exvivo 1469 955 2919 2.504 0.388 0.145 0.043 25 2.4 BA45_exvivo 4421 2768 5210 1.878 0.517 0.130 0.042 55 8.1 V1_exvivo 4838 2849 5735 1.829 0.550 0.148 0.052 83 9.3 V2_exvivo 359 209 635 2.391 0.350 0.138 0.038 6 0.6 MT_exvivo 326 205 1104 3.505 0.662 0.113 0.032 3 0.3 perirhinal_exvivo 263 177 547 3.012 0.691 0.152 0.043 3 0.6 entorhinal_exvivo Started at Sat Oct 7 16:52:34 CEST 2017 Ended at Sun Oct 8 00:42:52 CEST 2017 #@#%# recon-all-run-time-hours 7.838 recon-all -s 0051362 finished without error at Sun Oct 8 00:42:52 CEST 2017