Sat Oct 7 23:40:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0050352 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050352/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0050352 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-928 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: 66074808 63500996 2573812 1737676 0 56876712 -/+ buffers/cache: 6624284 59450524 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: ntraut Machine: tars-928 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: ntraut Machine: tars-928 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-6.0.0/0050352 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050352/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050352/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050352/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-6.0.0/0050352/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 23:40:23 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 23:40:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-928 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 23:40:32 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.775 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.775/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.775/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.775/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 23:40:34 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.775/nu0.mnc ./tmp.mri_nu_correct.mni.775/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.775/0/ -iterations 1000 -distance 50 [ntraut@tars-928:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/] [2017-10-07 23:40:34] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.775/0/ ./tmp.mri_nu_correct.mni.775/nu0.mnc ./tmp.mri_nu_correct.mni.775/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 38 CV of field change: 0.00098934 mri_convert ./tmp.mri_nu_correct.mni.775/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.775/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.775/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sat Oct 7 23:41:50 CEST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Oct 7 23:41:50 CEST 2017 Ended at Sat Oct 7 23:42:58 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 23:43:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6900, 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-6.0.0/0050352/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/talairach_avi.log TalAviQA: 0.97893 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 23:43:00 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-6.0.0/0050352/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-928 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 23:43:00 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.1549 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1549/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1549/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.1549/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 23:43:02 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.1549/nu0.mnc ./tmp.mri_nu_correct.mni.1549/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1549/0/ [ntraut@tars-928:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/] [2017-10-07 23:43:02] 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.1549/0/ ./tmp.mri_nu_correct.mni.1549/nu0.mnc ./tmp.mri_nu_correct.mni.1549/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 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[ntraut@tars-928:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/] [2017-10-07 23:43:55] 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.1549/1/ ./tmp.mri_nu_correct.mni.1549/nu1.mnc ./tmp.mri_nu_correct.mni.1549/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 Number of iterations: 13 CV of field change: 0.000984039 mri_binarize --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1549/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-6.0.0/0050352/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1549/ones.mgz sysname Linux hostname tars-928 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.1549/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.1549/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.1549/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/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.1549/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/input.mean.dat sysname Linux hostname tars-928 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1549/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.1549/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1549/ones.mgz --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/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.1549/ones.mgz --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/output.mean.dat sysname Linux hostname tars-928 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1549/ones.mgz Loading ./tmp.mri_nu_correct.mni.1549/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.1549/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.1549/nu2.mnc ./tmp.mri_nu_correct.mni.1549/nu2.mnc mul 1.02105105068371572756 Saving result to './tmp.mri_nu_correct.mni.1549/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.1549/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.1549/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.1549/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 8 seconds. mapping (10, 116) to ( 3, 110) Sat Oct 7 23:45:18 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 23:45:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 1.00814 -0.09572 -0.06711 -112.88490; 0.08598 1.00471 0.13264 -170.62601; 0.05585 -0.04674 1.10461 -74.57378; 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 = 14 Starting OpenSpline(): npoints = 14 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 76 (76), valley at 42 (42) csf peak at 38, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 72 (72), valley at 18 (18) csf peak at 37, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 1 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 23:47:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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=8.0 skull bounding box = (40, 55, 31) --> (216, 198, 230) using (99, 103, 131) as brain centroid... mean wm in atlas = 108, using box (77,85,106) --> (120, 120,155) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 102 +- 7.2 after smoothing, mri peak at 102, scaling input intensities by 1.059 scaling channel 0 by 1.05882 initial log_p = -4.484 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.515277 @ (-9.091, -9.091, -27.273) max log p = -4.385285 @ (4.545, 4.545, 4.545) max log p = -4.283016 @ (6.818, -2.273, 2.273) max log p = -4.283016 @ (0.000, 0.000, 0.000) max log p = -4.283016 @ (0.000, 0.000, 0.000) max log p = -4.283016 @ (0.000, 0.000, 0.000) Found translation: (2.3, -6.8, -20.5): log p = -4.283 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.208, old_max_log_p =-4.283 (thresh=-4.3) 1.05669 -0.15727 0.11961 -4.45861; 0.13912 1.05429 0.15727 -52.62578; -0.13053 -0.12941 0.98296 17.06762; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.194, old_max_log_p =-4.208 (thresh=-4.2) 1.05669 -0.15727 0.11961 -4.45861; 0.14955 1.13337 0.16907 -67.23579; -0.13053 -0.12941 0.98296 17.06762; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.186, old_max_log_p =-4.194 (thresh=-4.2) 1.06717 -0.00799 0.14065 -30.68564; 0.01112 1.23001 0.16341 -55.36808; -0.13053 -0.12941 0.98296 17.06762; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.186, old_max_log_p =-4.186 (thresh=-4.2) 1.06717 -0.00799 0.14065 -30.68564; 0.01112 1.23001 0.16341 -55.36808; -0.13053 -0.12941 0.98296 17.06762; 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=-4.091, old_max_log_p =-4.186 (thresh=-4.2) 1.01124 -0.00386 0.10478 -17.39266; 0.01133 1.25308 0.16648 -59.07198; -0.09649 -0.13446 1.02424 9.70394; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.091, old_max_log_p =-4.091 (thresh=-4.1) 1.01124 -0.00386 0.10478 -17.39266; 0.01133 1.25308 0.16648 -59.07198; -0.09649 -0.13446 1.02424 9.70394; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.073, old_max_log_p =-4.091 (thresh=-4.1) 1.01005 -0.00385 0.10466 -16.28694; 0.00976 1.25217 0.18343 -61.40710; -0.09655 -0.15476 1.02018 12.18664; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.070, old_max_log_p =-4.073 (thresh=-4.1) 1.01199 -0.00251 0.09643 -16.12133; 0.00897 1.25086 0.19177 -61.73931; -0.08846 -0.16522 1.02066 12.58875; 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 1.01199 -0.00251 0.09643 -16.12133; 0.00897 1.25086 0.19177 -61.73931; -0.08846 -0.16522 1.02066 12.58875; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.01199 -0.00251 0.09643 -16.12133; 0.00897 1.25086 0.19177 -61.73931; -0.08846 -0.16522 1.02066 12.58875; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01199 -0.00251 0.09643 -16.12133; 0.00897 1.25086 0.19177 -61.73931; -0.08846 -0.16522 1.02066 12.58875; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.070 (old=-4.484) transform before final EM align: 1.01199 -0.00251 0.09643 -16.12133; 0.00897 1.25086 0.19177 -61.73931; -0.08846 -0.16522 1.02066 12.58875; 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 1.01199 -0.00251 0.09643 -16.12133; 0.00897 1.25086 0.19177 -61.73931; -0.08846 -0.16522 1.02066 12.58875; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.01199 -0.00251 0.09643 -16.12133; 0.00897 1.25086 0.19177 -61.73931; -0.08846 -0.16522 1.02066 12.58875; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.5 tol 0.000000 final transform: 1.01199 -0.00251 0.09643 -16.12133; 0.00897 1.25086 0.19177 -61.73931; -0.08846 -0.16522 1.02066 12.58875; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1546.076960 mri_em_register stimesec 1.354794 mri_em_register ru_maxrss 611716 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157535 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 246 mri_em_register ru_nivcsw 21665 registration took 13 minutes and 25 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=121 z=127 r=70 first estimation of the main basin volume: 1457595 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=109, y=109, z=93, 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=9237295665 voxels, voxel volume =1.000 = 9237295665 mmm3 = 9237296.128 cm3 done. PostAnalyze...Basin Prior 8 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=126, z=123, r=9764 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 44432 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1097445714 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1123489156 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1124157906 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1072194438 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1076085098 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 6, 35, 64 after analyzing : 4, 25, 35, 34 RIGHT_CER before analyzing : 4, 4, 24, 76 after analyzing : 4, 18, 25, 32 LEFT_CER before analyzing : 4, 5, 34, 73 after analyzing : 4, 24, 34, 36 RIGHT_BRAIN before analyzing : 5, 8, 37, 64 after analyzing : 5, 27, 37, 36 LEFT_BRAIN before analyzing : 4, 5, 32, 64 after analyzing : 4, 23, 32, 33 OTHER before analyzing : 4, 4, 12, 91 after analyzing : 4, 18, 25, 36 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...60 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.008 curvature mean = 74.943, std = 7.408 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.59, sigma = 5.15 after rotation: sse = 3.59, sigma = 5.15 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.87, its var is 4.93 before Erosion-Dilatation 0.74% 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...28 iterations mri_strip_skull: done peeling brain Brain Size = 1813268 voxels, voxel volume = 1.000 mm3 = 1813268 mmm3 = 1813.268 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 27.649796 mri_watershed stimesec 0.458930 mri_watershed ru_maxrss 821328 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212670 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2848 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 2251 mri_watershed ru_nivcsw 119 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sun Oct 8 00:01:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach.log reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=25.0 skull bounding box = (57, 65, 43) --> (201, 181, 215) using (105, 104, 129) as brain centroid... mean wm in atlas = 107, using box (87,90,108) --> (122, 118,150) to find MRI wm before smoothing, mri peak at 101 robust fit to distribution - 102 +- 5.9 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 initial log_p = -4.285 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.116086 @ (-9.091, -9.091, -9.091) max log p = -3.932616 @ (4.545, 4.545, -13.636) max log p = -3.848806 @ (2.273, -2.273, 2.273) max log p = -3.810682 @ (1.136, 1.136, 1.136) max log p = -3.810517 @ (0.568, 0.568, 0.568) max log p = -3.800771 @ (0.284, -0.284, 0.284) Found translation: (-0.3, -5.4, -18.5): log p = -3.801 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.790, old_max_log_p =-3.801 (thresh=-3.8) 0.91709 0.00000 0.12074 -4.71285; 0.00000 1.07500 0.00000 -14.74931; -0.13053 0.00000 0.99144 -0.82625; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.790, old_max_log_p =-3.790 (thresh=-3.8) 0.91709 0.00000 0.12074 -4.71285; 0.00000 1.07500 0.00000 -14.74931; -0.13053 0.00000 0.99144 -0.82625; 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=-3.674, old_max_log_p =-3.790 (thresh=-3.8) 0.95367 -0.07410 0.08683 4.08018; 0.05916 1.09140 0.03647 -28.82669; -0.10077 -0.03716 0.97485 3.95822; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.674, old_max_log_p =-3.674 (thresh=-3.7) 0.95367 -0.07410 0.08683 4.08018; 0.05916 1.09140 0.03647 -28.82669; -0.10077 -0.03716 0.97485 3.95822; 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=-3.637, old_max_log_p =-3.674 (thresh=-3.7) 0.95525 -0.06528 0.08710 2.73941; 0.05277 1.08859 0.01973 -26.09005; -0.09990 -0.01932 0.97646 0.95923; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.629, old_max_log_p =-3.637 (thresh=-3.6) 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.629, old_max_log_p =-3.629 (thresh=-3.6) 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 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 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.629 (old=-4.285) transform before final EM align: 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 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 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1393.353178 mri_em_register stimesec 1.640750 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 163581 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 464 mri_em_register ru_nivcsw 19873 registration took 11 minutes and 57 seconds. #-------------------------------------- #@# CA Normalize Sun Oct 8 00:13:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=25.0 skull bounding box = (57, 65, 43) --> (201, 181, 215) using (105, 104, 129) as brain centroid... mean wm in atlas = 107, using box (87,90,108) --> (122, 118,150) to find MRI wm before smoothing, mri peak at 101 robust fit to distribution - 102 +- 5.9 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 using 246344 sample points... INFO: compute sample coordinates transform 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 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 (123, 63, 43) --> (198, 171, 214) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 1 of 910 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (59, 64, 40) --> (129, 175, 212) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 1 of 1455 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 143, 66) --> (184, 180, 122) Left_Cerebellum_White_Matter: limiting intensities to 112.0 --> 132.0 3 of 10 (30.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 143, 61) --> (133, 182, 120) Right_Cerebellum_White_Matter: limiting intensities to 117.0 --> 132.0 11 of 15 (73.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 135, 101) --> (148, 199, 133) Brain_Stem: limiting intensities to 106.0 --> 132.0 0 of 12 (0.0%) samples deleted using 2402 total control points for intensity normalization... bias field = 0.954 +- 0.051 15 of 2386 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 63, 43) --> (198, 171, 214) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 1400 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (59, 64, 40) --> (129, 175, 212) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 2035 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 143, 66) --> (184, 180, 122) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 72 (20.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 143, 61) --> (133, 182, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 11 of 75 (14.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 135, 101) --> (148, 199, 133) Brain_Stem: limiting intensities to 88.0 --> 132.0 16 of 90 (17.8%) samples deleted using 3672 total control points for intensity normalization... bias field = 1.039 +- 0.062 11 of 3595 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 63, 43) --> (198, 171, 214) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 1492 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (59, 64, 40) --> (129, 175, 212) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 2098 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 143, 66) --> (184, 180, 122) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 71 of 133 (53.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 143, 61) --> (133, 182, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 14 of 63 (22.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 135, 101) --> (148, 199, 133) Brain_Stem: limiting intensities to 88.0 --> 132.0 65 of 186 (34.9%) samples deleted using 3972 total control points for intensity normalization... bias field = 1.040 +- 0.058 14 of 3738 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 43 seconds. #-------------------------------------- #@# CA Reg Sun Oct 8 00:14:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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) = 1.03 (predicted orig area = 7.8) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.823, neg=0, invalid=762 0001: dt=296.742586, rms=0.760 (7.589%), neg=0, invalid=762 0002: dt=161.210811, rms=0.751 (1.242%), neg=0, invalid=762 0003: dt=517.888000, rms=0.741 (1.339%), neg=0, invalid=762 0004: dt=131.605634, rms=0.738 (0.357%), neg=0, invalid=762 0005: dt=1775.616000, rms=0.728 (1.452%), neg=0, invalid=762 0006: dt=129.472000, rms=0.725 (0.370%), neg=0, invalid=762 0007: dt=517.888000, rms=0.722 (0.459%), neg=0, invalid=762 0008: dt=221.952000, rms=0.720 (0.187%), neg=0, invalid=762 0009: dt=221.952000, rms=0.719 (0.134%), neg=0, invalid=762 0010: dt=221.952000, rms=0.718 (0.163%), neg=0, invalid=762 0011: dt=221.952000, rms=0.716 (0.233%), neg=0, invalid=762 0012: dt=221.952000, rms=0.714 (0.337%), neg=0, invalid=762 0013: dt=221.952000, rms=0.712 (0.294%), neg=0, invalid=762 0014: dt=221.952000, rms=0.710 (0.251%), neg=0, invalid=762 0015: dt=221.952000, rms=0.709 (0.213%), neg=0, invalid=762 0016: dt=221.952000, rms=0.707 (0.255%), neg=0, invalid=762 0017: dt=221.952000, rms=0.705 (0.211%), neg=0, invalid=762 0018: dt=221.952000, rms=0.704 (0.133%), neg=0, invalid=762 0019: dt=221.952000, rms=0.703 (0.127%), neg=0, invalid=762 0020: dt=221.952000, rms=0.702 (0.197%), neg=0, invalid=762 0021: dt=221.952000, rms=0.701 (0.173%), neg=0, invalid=762 0022: dt=221.952000, rms=0.700 (0.142%), neg=0, invalid=762 0023: dt=221.952000, rms=0.699 (0.142%), neg=0, invalid=762 0024: dt=221.952000, rms=0.697 (0.214%), neg=0, invalid=762 0025: dt=221.952000, rms=0.696 (0.172%), neg=0, invalid=762 0026: dt=221.952000, rms=0.695 (0.124%), neg=0, invalid=762 0027: dt=221.952000, rms=0.695 (0.116%), neg=0, invalid=762 0028: dt=517.888000, rms=0.694 (0.098%), neg=0, invalid=762 0029: dt=517.888000, rms=0.694 (-0.436%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.694, neg=0, invalid=762 0030: dt=129.472000, rms=0.693 (0.165%), neg=0, invalid=762 0031: dt=443.904000, rms=0.692 (0.105%), neg=0, invalid=762 0032: dt=443.904000, rms=0.692 (0.113%), neg=0, invalid=762 0033: dt=443.904000, rms=0.691 (0.120%), neg=0, invalid=762 0034: dt=443.904000, rms=0.690 (0.106%), neg=0, invalid=762 0035: dt=443.904000, rms=0.689 (0.146%), neg=0, invalid=762 0036: dt=443.904000, rms=0.688 (0.132%), neg=0, invalid=762 0037: dt=443.904000, rms=0.688 (0.037%), neg=0, invalid=762 0038: dt=443.904000, rms=0.687 (0.077%), neg=0, invalid=762 0039: dt=443.904000, rms=0.687 (0.098%), neg=0, invalid=762 0040: dt=443.904000, rms=0.686 (0.031%), neg=0, invalid=762 0041: dt=129.472000, rms=0.686 (0.063%), neg=0, invalid=762 0042: dt=887.808000, rms=0.686 (0.032%), neg=0, invalid=762 0043: dt=887.808000, rms=0.686 (-0.138%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.693, neg=0, invalid=762 0044: dt=81.190083, rms=0.689 (0.507%), neg=0, invalid=762 0045: dt=248.832000, rms=0.680 (1.327%), neg=0, invalid=762 0046: dt=36.288000, rms=0.678 (0.350%), neg=0, invalid=762 0047: dt=145.152000, rms=0.675 (0.412%), neg=0, invalid=762 0048: dt=103.680000, rms=0.671 (0.581%), neg=0, invalid=762 0049: dt=36.288000, rms=0.670 (0.157%), neg=0, invalid=762 0050: dt=36.288000, rms=0.669 (0.097%), neg=0, invalid=762 0051: dt=36.288000, rms=0.668 (0.182%), neg=0, invalid=762 0052: dt=36.288000, rms=0.666 (0.271%), neg=0, invalid=762 0053: dt=36.288000, rms=0.664 (0.339%), neg=0, invalid=762 0054: dt=36.288000, rms=0.661 (0.362%), neg=0, invalid=762 0055: dt=36.288000, rms=0.659 (0.359%), neg=0, invalid=762 0056: dt=36.288000, rms=0.657 (0.350%), neg=0, invalid=762 0057: dt=36.288000, rms=0.654 (0.342%), neg=0, invalid=762 0058: dt=36.288000, rms=0.652 (0.327%), neg=0, invalid=762 0059: dt=36.288000, rms=0.650 (0.307%), neg=0, invalid=762 0060: dt=36.288000, rms=0.649 (0.279%), neg=0, invalid=762 0061: dt=36.288000, rms=0.647 (0.237%), neg=0, invalid=762 0062: dt=36.288000, rms=0.646 (0.207%), neg=0, invalid=762 0063: dt=36.288000, rms=0.644 (0.195%), neg=0, invalid=762 0064: dt=36.288000, rms=0.643 (0.192%), neg=0, invalid=762 0065: dt=36.288000, rms=0.642 (0.176%), neg=0, invalid=762 0066: dt=36.288000, rms=0.641 (0.161%), neg=0, invalid=762 0067: dt=36.288000, rms=0.640 (0.145%), neg=0, invalid=762 0068: dt=36.288000, rms=0.639 (0.144%), neg=0, invalid=762 0069: dt=36.288000, rms=0.638 (0.138%), neg=0, invalid=762 0070: dt=36.288000, rms=0.637 (0.120%), neg=0, invalid=762 0071: dt=36.288000, rms=0.637 (0.100%), neg=0, invalid=762 0072: dt=145.152000, rms=0.637 (0.028%), neg=0, invalid=762 0073: dt=145.152000, rms=0.637 (0.018%), neg=0, invalid=762 0074: dt=145.152000, rms=0.637 (-0.236%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.637, neg=0, invalid=762 0075: dt=67.706564, rms=0.635 (0.292%), neg=0, invalid=762 0076: dt=124.416000, rms=0.635 (0.122%), neg=0, invalid=762 0077: dt=124.416000, rms=0.635 (-0.085%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0078: dt=11.200000, rms=0.662 (0.331%), neg=0, invalid=762 0079: dt=9.600000, rms=0.662 (0.058%), neg=0, invalid=762 0080: dt=9.600000, rms=0.662 (0.025%), neg=0, invalid=762 0081: dt=9.600000, rms=0.662 (-0.081%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.662, neg=0, invalid=762 0082: dt=0.037500, rms=0.662 (0.075%), neg=0, invalid=762 0083: dt=0.007812, rms=0.662 (0.000%), neg=0, invalid=762 0084: dt=0.007812, rms=0.662 (-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=0.725, neg=0, invalid=762 0085: dt=5.990338, rms=0.710 (2.032%), neg=0, invalid=762 0086: dt=5.333333, rms=0.708 (0.257%), neg=0, invalid=762 0087: dt=4.000000, rms=0.708 (0.033%), neg=0, invalid=762 0088: dt=4.000000, rms=0.708 (0.004%), neg=0, invalid=762 0089: dt=4.000000, rms=0.708 (-0.083%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.708, neg=0, invalid=762 0090: dt=0.000000, rms=0.708 (0.060%), neg=0, invalid=762 0091: dt=0.000000, rms=0.708 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.756, neg=0, invalid=762 0092: dt=0.000000, rms=0.756 (0.053%), neg=0, invalid=762 0093: dt=0.000000, rms=0.756 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.756, neg=0, invalid=762 0094: dt=0.000000, rms=0.756 (0.053%), neg=0, invalid=762 0095: dt=0.000000, rms=0.756 (0.000%), 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=0.675, neg=0, invalid=762 0096: dt=0.764925, rms=0.659 (2.380%), neg=0, invalid=762 0097: dt=0.064000, rms=0.658 (0.093%), neg=0, invalid=762 0098: dt=0.064000, rms=0.658 (-0.056%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.659, neg=0, invalid=762 0099: dt=0.028000, rms=0.658 (0.087%), neg=0, invalid=762 0100: dt=0.005000, rms=0.658 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.06617 (27) Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2270 voxels, overlap=0.772) Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2270 voxels, peak = 26), gca=26.5 gca peak = 0.15565 (16) mri peak = 0.07752 (28) Right_Lateral_Ventricle (43): linear fit = 1.83 x + 0.0 (1912 voxels, overlap=0.177) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1912 voxels, peak = 29), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.09275 (96) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1215 voxels, overlap=0.744) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1215 voxels, peak = 92), gca=91.7 gca peak = 0.20183 (93) mri peak = 0.08561 (92) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (1110 voxels, overlap=1.005) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (1110 voxels, peak = 89), gca=88.8 gca peak = 0.21683 (55) mri peak = 0.05678 (65) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1373 voxels, overlap=0.364) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1373 voxels, peak = 62), gca=62.4 gca peak = 0.30730 (58) mri peak = 0.06620 (59) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1283 voxels, overlap=0.972) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1283 voxels, peak = 64), gca=63.5 gca peak = 0.11430 (101) mri peak = 0.07921 (103) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (85912 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (85912 voxels, peak = 104), gca=103.5 gca peak = 0.12076 (102) mri peak = 0.07317 (103) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (84816 voxels, overlap=0.828) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (84816 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.03216 (71) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (34054 voxels, overlap=0.285) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (34054 voxels, peak = 68), gca=67.6 gca peak = 0.15082 (58) mri peak = 0.03328 (72) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (34337 voxels, overlap=0.050) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (34337 voxels, peak = 71), gca=71.1 gca peak = 0.14161 (67) mri peak = 0.06435 (72) Right_Caudate (50): linear fit = 1.07 x + 0.0 (1320 voxels, overlap=0.881) Right_Caudate (50): linear fit = 1.07 x + 0.0 (1320 voxels, peak = 71), gca=71.4 gca peak = 0.15243 (71) mri peak = 0.06299 (83) Left_Caudate (11): linear fit = 1.08 x + 0.0 (1342 voxels, overlap=0.951) Left_Caudate (11): linear fit = 1.08 x + 0.0 (1342 voxels, peak = 76), gca=76.3 gca peak = 0.13336 (57) mri peak = 0.04329 (64) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (32035 voxels, overlap=0.745) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (32035 voxels, peak = 64), gca=63.6 gca peak = 0.13252 (56) mri peak = 0.04187 (67) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (35082 voxels, overlap=0.310) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (35082 voxels, peak = 67), gca=67.5 gca peak = 0.18181 (84) mri peak = 0.06090 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (12496 voxels, overlap=0.929) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (12496 voxels, peak = 86), gca=86.1 gca peak = 0.20573 (83) mri peak = 0.05121 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (10895 voxels, overlap=0.923) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (10895 voxels, peak = 86), gca=85.9 gca peak = 0.21969 (57) mri peak = 0.05783 (78) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (513 voxels, overlap=0.052) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (513 voxels, peak = 76), gca=75.5 gca peak = 0.39313 (56) mri peak = 0.09059 (70) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (707 voxels, overlap=0.028) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (707 voxels, peak = 69), gca=68.6 gca peak = 0.14181 (85) mri peak = 0.06436 (88) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6351 voxels, overlap=0.967) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6351 voxels, peak = 86), gca=86.3 gca peak = 0.11978 (83) mri peak = 0.06183 (84) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (5494 voxels, overlap=0.895) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (5494 voxels, peak = 86), gca=85.9 gca peak = 0.13399 (79) mri peak = 0.06316 (84) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2998 voxels, overlap=0.986) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2998 voxels, peak = 83), gca=82.6 gca peak = 0.14159 (79) mri peak = 0.06607 (82) Right_Putamen (51): linear fit = 1.04 x + 0.0 (3136 voxels, overlap=0.900) Right_Putamen (51): linear fit = 1.04 x + 0.0 (3136 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.07802 (85) Brain_Stem (16): linear fit = 1.10 x + 0.0 (14832 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (14832 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07388 (87) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (2074 voxels, overlap=0.724) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (2074 voxels, peak = 89), gca=89.0 gca peak = 0.12801 (89) mri peak = 0.06712 (86) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (2122 voxels, overlap=0.796) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (2122 voxels, peak = 92), gca=92.1 gca peak = 0.20494 (23) mri peak = 0.10321 (18) gca peak = 0.15061 (21) mri peak = 0.07988 (13) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (416 voxels, overlap=0.685) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (416 voxels, peak = 17), gca=17.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.19 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.21 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=0.646, neg=0, invalid=762 0101: dt=99.618625, rms=0.636 (1.496%), neg=0, invalid=762 0102: dt=295.936000, rms=0.633 (0.508%), neg=0, invalid=762 0103: dt=295.936000, rms=0.631 (0.327%), neg=0, invalid=762 0104: dt=110.976000, rms=0.630 (0.119%), neg=0, invalid=762 0105: dt=517.888000, rms=0.629 (0.220%), neg=0, invalid=762 0106: dt=92.480000, rms=0.628 (0.130%), neg=0, invalid=762 0107: dt=1479.680000, rms=0.626 (0.357%), neg=0, invalid=762 0108: dt=129.472000, rms=0.625 (0.139%), neg=0, invalid=762 0109: dt=295.936000, rms=0.624 (0.067%), neg=0, invalid=762 0110: dt=92.480000, rms=0.624 (0.036%), neg=0, invalid=762 0111: dt=92.480000, rms=0.624 (0.018%), neg=0, invalid=762 0112: dt=92.480000, rms=0.624 (0.032%), neg=0, invalid=762 0113: dt=92.480000, rms=0.623 (0.042%), neg=0, invalid=762 0114: dt=92.480000, rms=0.623 (0.055%), neg=0, invalid=762 0115: dt=92.480000, rms=0.623 (0.060%), neg=0, invalid=762 0116: dt=92.480000, rms=0.622 (0.063%), neg=0, invalid=762 0117: dt=92.480000, rms=0.622 (0.067%), neg=0, invalid=762 0118: dt=92.480000, rms=0.622 (0.068%), neg=0, invalid=762 0119: dt=92.480000, rms=0.621 (0.062%), neg=0, invalid=762 0120: dt=92.480000, rms=0.621 (0.056%), neg=0, invalid=762 0121: dt=92.480000, rms=0.620 (0.053%), neg=0, invalid=762 0122: dt=92.480000, rms=0.620 (0.053%), neg=0, invalid=762 0123: dt=92.480000, rms=0.620 (0.054%), neg=0, invalid=762 0124: dt=92.480000, rms=0.619 (0.054%), neg=0, invalid=762 0125: dt=92.480000, rms=0.619 (0.051%), neg=0, invalid=762 0126: dt=92.480000, rms=0.619 (0.046%), neg=0, invalid=762 0127: dt=92.480000, rms=0.619 (0.044%), neg=0, invalid=762 0128: dt=92.480000, rms=0.618 (0.043%), neg=0, invalid=762 0129: dt=92.480000, rms=0.618 (0.042%), neg=0, invalid=762 0130: dt=92.480000, rms=0.618 (0.042%), neg=0, invalid=762 0131: dt=92.480000, rms=0.618 (0.041%), neg=0, invalid=762 0132: dt=92.480000, rms=0.617 (0.038%), neg=0, invalid=762 0133: dt=92.480000, rms=0.617 (0.039%), neg=0, invalid=762 0134: dt=92.480000, rms=0.617 (0.036%), neg=0, invalid=762 0135: dt=92.480000, rms=0.617 (0.035%), neg=0, invalid=762 0136: dt=92.480000, rms=0.616 (0.032%), neg=0, invalid=762 0137: dt=92.480000, rms=0.616 (0.032%), neg=0, invalid=762 0138: dt=92.480000, rms=0.616 (0.030%), neg=0, invalid=762 0139: dt=92.480000, rms=0.616 (0.031%), neg=0, invalid=762 0140: dt=92.480000, rms=0.616 (0.028%), neg=0, invalid=762 0141: dt=92.480000, rms=0.616 (0.031%), neg=0, invalid=762 0142: dt=92.480000, rms=0.615 (0.025%), neg=0, invalid=762 0143: dt=92.480000, rms=0.615 (0.024%), neg=0, invalid=762 0144: dt=92.480000, rms=0.615 (0.023%), neg=0, invalid=762 0145: dt=5918.720000, rms=0.614 (0.117%), neg=0, invalid=762 0146: dt=92.480000, rms=0.614 (0.034%), neg=0, invalid=762 0147: dt=92.480000, rms=0.614 (0.003%), neg=0, invalid=762 0148: dt=92.480000, rms=0.614 (0.000%), neg=0, invalid=762 0149: dt=92.480000, rms=0.614 (0.002%), neg=0, invalid=762 0150: dt=92.480000, rms=0.614 (0.014%), neg=0, invalid=762 0151: dt=92.480000, rms=0.614 (0.018%), neg=0, invalid=762 0152: dt=92.480000, rms=0.614 (0.016%), neg=0, invalid=762 0153: dt=0.000000, rms=0.614 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.614, neg=0, invalid=762 0154: dt=295.936000, rms=0.613 (0.186%), neg=0, invalid=762 0155: dt=129.472000, rms=0.613 (0.048%), neg=0, invalid=762 0156: dt=129.472000, rms=0.613 (0.016%), neg=0, invalid=762 0157: dt=129.472000, rms=0.612 (0.035%), neg=0, invalid=762 0158: dt=129.472000, rms=0.612 (0.042%), neg=0, invalid=762 0159: dt=129.472000, rms=0.612 (0.037%), neg=0, invalid=762 0160: dt=129.472000, rms=0.612 (0.032%), neg=0, invalid=762 0161: dt=129.472000, rms=0.612 (0.030%), neg=0, invalid=762 0162: dt=129.472000, rms=0.611 (0.025%), neg=0, invalid=762 0163: dt=129.472000, rms=0.611 (0.028%), neg=0, invalid=762 0164: dt=129.472000, rms=0.611 (0.025%), neg=0, invalid=762 0165: dt=129.472000, rms=0.611 (0.023%), neg=0, invalid=762 0166: dt=129.472000, rms=0.611 (0.023%), neg=0, invalid=762 0167: dt=1479.680000, rms=0.611 (0.036%), neg=0, invalid=762 0168: dt=110.976000, rms=0.610 (0.011%), neg=0, invalid=762 0169: dt=110.976000, rms=0.610 (0.006%), neg=0, invalid=762 0170: dt=110.976000, rms=0.610 (0.002%), neg=0, invalid=762 0171: dt=110.976000, rms=0.610 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.611, neg=0, invalid=762 0172: dt=161.635036, rms=0.608 (0.601%), neg=0, invalid=762 0173: dt=181.612565, rms=0.602 (0.954%), neg=0, invalid=762 0174: dt=36.288000, rms=0.600 (0.385%), neg=0, invalid=762 0175: dt=103.680000, rms=0.598 (0.181%), neg=0, invalid=762 0176: dt=145.152000, rms=0.596 (0.435%), neg=0, invalid=762 0177: dt=36.288000, rms=0.595 (0.184%), neg=0, invalid=762 0178: dt=248.832000, rms=0.593 (0.360%), neg=0, invalid=762 0179: dt=63.806647, rms=0.591 (0.270%), neg=0, invalid=762 0180: dt=103.680000, rms=0.590 (0.188%), neg=0, invalid=762 0181: dt=36.288000, rms=0.589 (0.102%), neg=0, invalid=762 0182: dt=580.608000, rms=0.585 (0.772%), neg=0, invalid=762 0183: dt=2.268000, rms=0.585 (0.010%), neg=0, invalid=762 0184: dt=0.567000, rms=0.585 (0.002%), neg=0, invalid=762 0185: dt=0.141750, rms=0.585 (0.001%), neg=0, invalid=762 0186: dt=0.070875, rms=0.585 (0.000%), neg=0, invalid=762 0187: dt=0.035437, rms=0.585 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.585, neg=0, invalid=762 0188: dt=0.035437, rms=0.585 (0.083%), neg=0, invalid=762 0189: dt=0.000000, rms=0.585 (0.000%), neg=0, invalid=762 0190: dt=0.000879, rms=0.585 (0.000%), neg=0, invalid=762 0191: dt=0.000110, rms=0.585 (0.000%), neg=0, invalid=762 0192: dt=0.000055, rms=0.585 (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=0.589, neg=0, invalid=762 0193: dt=44.800000, rms=0.574 (2.528%), neg=0, invalid=762 0194: dt=44.800000, rms=0.565 (1.462%), neg=0, invalid=762 0195: dt=53.828571, rms=0.560 (0.989%), neg=0, invalid=762 0196: dt=24.251710, rms=0.556 (0.734%), neg=0, invalid=762 0197: dt=67.840000, rms=0.552 (0.652%), neg=0, invalid=762 0198: dt=21.136364, rms=0.549 (0.617%), neg=0, invalid=762 0199: dt=44.800000, rms=0.546 (0.427%), neg=0, invalid=762 0200: dt=44.800000, rms=0.545 (0.252%), neg=0, invalid=762 0201: dt=31.627907, rms=0.543 (0.315%), neg=0, invalid=762 0202: dt=11.200000, rms=0.543 (0.108%), neg=0, invalid=762 0203: dt=2.800000, rms=0.543 (0.029%), neg=0, invalid=762 0204: dt=1.400000, rms=0.542 (0.011%), neg=0, invalid=762 0205: dt=0.021875, rms=0.542 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.543, neg=0, invalid=762 0206: dt=91.954023, rms=0.538 (0.867%), neg=0, invalid=762 0207: dt=29.151335, rms=0.536 (0.360%), neg=0, invalid=762 0208: dt=44.800000, rms=0.535 (0.162%), neg=0, invalid=762 0209: dt=9.600000, rms=0.535 (0.094%), neg=0, invalid=762 0210: dt=0.700000, rms=0.535 (0.012%), neg=0, invalid=762 0211: dt=0.350000, rms=0.535 (0.001%), neg=0, invalid=762 0212: dt=0.175000, rms=0.535 (0.001%), neg=0, invalid=762 0213: dt=0.087500, rms=0.535 (0.001%), neg=0, invalid=762 0214: dt=0.010937, rms=0.535 (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=0.550, neg=0, invalid=762 0215: dt=6.333333, rms=0.548 (0.265%), neg=0, invalid=762 0216: dt=4.032000, rms=0.548 (0.068%), neg=0, invalid=762 0217: dt=0.864000, rms=0.548 (0.019%), neg=0, invalid=762 0218: dt=0.006750, rms=0.548 (0.001%), neg=0, invalid=762 0219: dt=0.003375, rms=0.548 (0.000%), neg=0, invalid=762 0220: dt=0.000422, rms=0.548 (0.000%), neg=0, invalid=762 0221: dt=0.000211, rms=0.548 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.548, neg=0, invalid=762 0222: dt=7.724138, rms=0.547 (0.197%), neg=0, invalid=762 0223: dt=11.200000, rms=0.547 (0.087%), neg=0, invalid=762 0224: dt=16.128000, rms=0.546 (0.178%), neg=0, invalid=762 0225: dt=4.032000, rms=0.545 (0.058%), neg=0, invalid=762 0226: dt=3.456000, rms=0.545 (0.049%), neg=0, invalid=762 0227: dt=0.108000, rms=0.545 (0.002%), neg=0, invalid=762 0228: dt=0.054000, rms=0.545 (0.001%), neg=0, invalid=762 0229: dt=0.027000, rms=0.545 (0.000%), neg=0, invalid=762 0230: dt=0.002813, rms=0.545 (0.000%), neg=0, invalid=762 0231: dt=0.000000, rms=0.545 (-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=0.561, neg=0, invalid=762 0232: dt=0.000000, rms=0.561 (0.078%), neg=0, invalid=762 0233: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=762 0234: dt=0.100000, rms=0.561 (-0.049%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.561, neg=0, invalid=762 0235: dt=0.000000, rms=0.561 (0.078%), neg=0, invalid=762 0236: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=762 0237: dt=0.100000, rms=0.561 (-0.034%), 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=0.535, neg=0, invalid=762 0238: dt=0.384000, rms=0.523 (2.160%), neg=0, invalid=762 0239: dt=0.384000, rms=0.520 (0.692%), neg=0, invalid=762 0240: dt=0.384000, rms=0.518 (0.335%), neg=0, invalid=762 0241: dt=0.384000, rms=0.517 (0.208%), neg=0, invalid=762 0242: dt=0.384000, rms=0.516 (0.143%), neg=0, invalid=762 0243: dt=0.384000, rms=0.515 (0.112%), neg=0, invalid=762 0244: dt=0.384000, rms=0.515 (0.085%), neg=0, invalid=762 0245: dt=0.384000, rms=0.515 (0.070%), neg=0, invalid=762 0246: dt=0.384000, rms=0.514 (0.058%), neg=0, invalid=762 0247: dt=0.384000, rms=0.514 (0.045%), neg=0, invalid=762 0248: dt=0.384000, rms=0.514 (0.043%), neg=0, invalid=762 0249: dt=0.384000, rms=0.514 (0.071%), neg=0, invalid=762 0250: dt=0.192000, rms=0.513 (0.017%), neg=0, invalid=762 0251: dt=0.192000, rms=0.513 (0.028%), neg=0, invalid=762 0252: dt=0.192000, rms=0.513 (0.011%), neg=0, invalid=762 0253: dt=0.192000, rms=0.513 (0.021%), neg=0, invalid=762 0254: dt=0.192000, rms=0.513 (0.027%), neg=0, invalid=762 0255: dt=0.192000, rms=0.513 (0.032%), neg=0, invalid=762 0256: dt=0.192000, rms=0.513 (0.035%), neg=0, invalid=762 0257: dt=0.192000, rms=0.512 (0.034%), neg=0, invalid=762 0258: dt=0.192000, rms=0.512 (0.002%), neg=0, invalid=762 0259: dt=0.192000, rms=0.512 (0.008%), neg=0, invalid=762 0260: dt=0.192000, rms=0.512 (0.008%), neg=0, invalid=762 0261: dt=0.192000, rms=0.512 (0.006%), neg=0, invalid=762 0262: dt=0.320000, rms=0.512 (0.003%), neg=0, invalid=762 0263: dt=0.320000, rms=0.512 (0.005%), neg=0, invalid=762 0264: dt=0.320000, rms=0.512 (0.005%), neg=0, invalid=762 0265: dt=0.160000, rms=0.512 (0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.513, neg=0, invalid=762 0266: dt=0.320000, rms=0.509 (0.781%), neg=0, invalid=762 0267: dt=0.448000, rms=0.507 (0.352%), neg=0, invalid=762 0268: dt=0.448000, rms=0.507 (0.043%), neg=0, invalid=762 0269: dt=0.448000, rms=0.507 (0.006%), neg=0, invalid=762 0270: dt=0.448000, rms=0.507 (0.004%), neg=0, invalid=762 0271: dt=0.224000, rms=0.507 (-0.003%), 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=0.505, neg=0, invalid=762 0272: dt=0.000000, rms=0.504 (0.105%), neg=0, invalid=762 0273: dt=0.000000, rms=0.504 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.505, neg=0, invalid=762 0274: dt=32.368000, rms=0.504 (0.108%), neg=0, invalid=762 0275: dt=73.984000, rms=0.504 (0.001%), neg=0, invalid=762 0276: dt=73.984000, rms=0.504 (0.007%), neg=0, invalid=762 0277: dt=73.984000, rms=0.504 (0.009%), neg=0, invalid=762 0278: dt=73.984000, rms=0.504 (0.011%), neg=0, invalid=762 0279: dt=73.984000, rms=0.504 (0.017%), neg=0, invalid=762 0280: dt=73.984000, rms=0.504 (0.015%), neg=0, invalid=762 0281: dt=73.984000, rms=0.504 (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=0.505, neg=0, invalid=762 0282: dt=25.920000, rms=0.504 (0.131%), neg=0, invalid=762 0283: dt=25.920000, rms=0.504 (0.010%), neg=0, invalid=762 0284: dt=25.920000, rms=0.504 (0.009%), neg=0, invalid=762 0285: dt=25.920000, rms=0.504 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.504, neg=0, invalid=762 0286: dt=103.680000, rms=0.502 (0.388%), neg=0, invalid=762 0287: dt=36.288000, rms=0.502 (0.087%), neg=0, invalid=762 0288: dt=36.288000, rms=0.502 (0.044%), neg=0, invalid=762 0289: dt=36.288000, rms=0.501 (0.075%), neg=0, invalid=762 0290: dt=36.288000, rms=0.501 (0.090%), neg=0, invalid=762 0291: dt=36.288000, rms=0.500 (0.107%), neg=0, invalid=762 0292: dt=36.288000, rms=0.500 (0.112%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 8 iterations, nbhd size=1, neg = 0 0293: dt=36.288000, rms=0.499 (0.097%), neg=0, invalid=762 0294: dt=36.288000, rms=0.499 (0.095%), neg=0, invalid=762 0295: dt=103.680000, rms=0.499 (0.018%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.500, neg=0, invalid=762 iter 0, gcam->neg = 5 after 10 iterations, nbhd size=1, neg = 0 0296: dt=32.000000, rms=0.497 (0.471%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 11 iterations, nbhd size=1, neg = 0 0297: dt=73.513514, rms=0.495 (0.487%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0298: dt=32.000000, rms=0.494 (0.247%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0299: dt=32.000000, rms=0.492 (0.285%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0300: dt=32.000000, rms=0.491 (0.246%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 0301: dt=32.000000, rms=0.490 (0.197%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 10 iterations, nbhd size=1, neg = 0 0302: dt=32.000000, rms=0.489 (0.194%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 12 iterations, nbhd size=1, neg = 0 0303: dt=32.000000, rms=0.488 (0.164%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 12 iterations, nbhd size=1, neg = 0 0304: dt=32.000000, rms=0.488 (0.109%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 13 iterations, nbhd size=1, neg = 0 0305: dt=32.000000, rms=0.487 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 12 iterations, nbhd size=1, neg = 0 0306: dt=32.000000, rms=0.486 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0307: dt=32.000000, rms=0.486 (0.143%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 12 iterations, nbhd size=1, neg = 0 0308: dt=32.000000, rms=0.485 (0.120%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 10 iterations, nbhd size=1, neg = 0 0309: dt=32.000000, rms=0.485 (0.131%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 4 iterations, nbhd size=0, neg = 0 0310: dt=32.000000, rms=0.484 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 7 iterations, nbhd size=0, neg = 0 0311: dt=32.000000, rms=0.484 (0.088%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0312: dt=38.400000, rms=0.483 (0.060%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0313: dt=38.400000, rms=0.483 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.484, neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0314: dt=53.937107, rms=0.480 (0.786%), neg=0, invalid=762 0315: dt=25.600000, rms=0.479 (0.262%), neg=0, invalid=762 0316: dt=44.800000, rms=0.478 (0.195%), neg=0, invalid=762 0317: dt=44.800000, rms=0.478 (0.011%), neg=0, invalid=762 0318: dt=44.800000, rms=0.476 (0.312%), neg=0, invalid=762 0319: dt=44.800000, rms=0.476 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0320: dt=44.800000, rms=0.476 (0.183%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0321: dt=44.800000, rms=0.475 (-0.086%), neg=0, invalid=762 0322: dt=19.200000, rms=0.475 (0.081%), neg=0, invalid=762 0323: dt=44.800000, rms=0.475 (0.068%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.482, neg=0, invalid=762 0324: dt=2.880000, rms=0.482 (0.126%), neg=0, invalid=762 0325: dt=0.720000, rms=0.482 (0.005%), neg=0, invalid=762 0326: dt=0.720000, rms=0.482 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.482, neg=0, invalid=762 0327: dt=6.000000, rms=0.481 (0.189%), neg=0, invalid=762 0328: dt=4.032000, rms=0.481 (0.026%), neg=0, invalid=762 0329: dt=4.032000, rms=0.481 (0.012%), neg=0, invalid=762 0330: dt=4.032000, rms=0.481 (-0.022%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 0331: dt=0.000000, rms=0.489 (0.104%), neg=0, invalid=762 0332: dt=0.000000, rms=0.489 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 0333: dt=1.280000, rms=0.488 (0.235%), neg=0, invalid=762 0334: dt=0.768000, rms=0.488 (0.029%), neg=0, invalid=762 0335: dt=0.768000, rms=0.488 (0.006%), neg=0, invalid=762 0336: dt=0.768000, rms=0.488 (-0.047%), 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=0.480, neg=0, invalid=762 iter 0, gcam->neg = 664 after 14 iterations, nbhd size=1, neg = 0 0337: dt=2.087838, rms=0.453 (5.751%), neg=0, invalid=762 0338: dt=0.064000, rms=0.453 (0.037%), neg=0, invalid=762 0339: dt=0.064000, rms=0.453 (-0.038%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.453, neg=0, invalid=762 0340: dt=0.080000, rms=0.452 (0.182%), neg=0, invalid=762 0341: dt=0.004000, rms=0.452 (0.000%), neg=0, invalid=762 0342: dt=0.004000, rms=0.452 (-0.000%), 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=0.438, neg=0, invalid=762 0343: dt=0.000000, rms=0.438 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 0344: dt=6.936000, rms=0.438 (0.000%), neg=0, invalid=762 0345: dt=1.445000, rms=0.438 (0.000%), neg=0, invalid=762 0346: dt=1.445000, rms=0.438 (-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=0.439, neg=0, invalid=762 0347: dt=0.000000, rms=0.439 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.439, neg=0, invalid=762 0348: dt=36.288000, rms=0.439 (0.024%), neg=0, invalid=762 0349: dt=103.680000, rms=0.438 (0.026%), neg=0, invalid=762 0350: dt=248.832000, rms=0.438 (0.099%), neg=0, invalid=762 0351: dt=20.736000, rms=0.438 (0.008%), neg=0, invalid=762 0352: dt=20.736000, rms=0.438 (0.001%), neg=0, invalid=762 0353: dt=20.736000, rms=0.438 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.439, neg=0, invalid=762 0354: dt=11.200000, rms=0.438 (0.075%), neg=0, invalid=762 0355: dt=9.600000, rms=0.438 (0.020%), neg=0, invalid=762 0356: dt=9.600000, rms=0.438 (0.005%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0357: dt=9.600000, rms=0.438 (-0.048%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 0358: dt=61.440000, rms=0.436 (0.547%), neg=0, invalid=762 0359: dt=25.600000, rms=0.435 (0.235%), neg=0, invalid=762 0360: dt=25.600000, rms=0.434 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0361: dt=25.600000, rms=0.434 (0.143%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0362: dt=25.600000, rms=0.433 (0.192%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0363: dt=25.600000, rms=0.432 (0.179%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0364: dt=25.600000, rms=0.431 (0.174%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0365: dt=25.600000, rms=0.431 (0.153%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0366: dt=25.600000, rms=0.430 (0.130%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0367: dt=25.600000, rms=0.430 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0368: dt=25.600000, rms=0.429 (0.068%), neg=0, invalid=762 0369: dt=38.400000, rms=0.429 (0.021%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0370: dt=38.400000, rms=0.429 (0.010%), neg=0, invalid=762 0371: dt=38.400000, rms=0.429 (0.021%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0372: dt=38.400000, rms=0.429 (0.012%), neg=0, invalid=762 0373: dt=38.400000, rms=0.429 (0.025%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0374: dt=38.400000, rms=0.429 (0.013%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.433, neg=0, invalid=762 0375: dt=0.000422, rms=0.433 (0.000%), neg=0, invalid=762 0376: dt=0.000000, rms=0.433 (0.000%), neg=0, invalid=762 0377: dt=0.150000, rms=0.433 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.433, neg=0, invalid=762 0378: dt=4.800000, rms=0.433 (0.027%), neg=0, invalid=762 0379: dt=4.032000, rms=0.433 (0.011%), neg=0, invalid=762 0380: dt=4.032000, rms=0.433 (0.007%), neg=0, invalid=762 0381: dt=4.032000, rms=0.433 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.440, neg=0, invalid=762 0382: dt=0.000000, rms=0.440 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.440, neg=0, invalid=762 0383: dt=0.000000, rms=0.440 (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=0.428, neg=0, invalid=762 iter 0, gcam->neg = 480 after 16 iterations, nbhd size=1, neg = 0 0384: dt=1.280000, rms=0.419 (2.022%), neg=0, invalid=762 0385: dt=0.000023, rms=0.419 (0.000%), neg=0, invalid=762 0386: dt=0.000023, rms=0.419 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0387: dt=0.112000, rms=0.419 (0.082%), neg=0, invalid=762 0388: dt=0.112000, rms=0.419 (0.033%), neg=0, invalid=762 0389: dt=0.112000, rms=0.419 (0.023%), neg=0, invalid=762 0390: dt=0.112000, rms=0.419 (-0.021%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 28 minutes and 56 seconds. mri_ca_register utimesec 10050.217134 mri_ca_register stimesec 9.829505 mri_ca_register ru_maxrss 1333540 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4480819 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63336 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 3340 mri_ca_register ru_nivcsw 43366 FSRUNTIME@ mri_ca_register 2.4823 hours 2 threads #-------------------------------------- #@# SubCort Seg Sun Oct 8 02:43:47 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-928 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-6.0.0/0050352/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 2 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.80 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 = 0.06742 (29) Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2482 voxels, overlap=0.935) Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2482 voxels, peak = 26), gca=26.5 gca peak = 0.17677 (13) mri peak = 0.08856 (28) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (2048 voxels, overlap=0.177) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2048 voxels, peak = 27), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.14358 (96) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, overlap=0.823) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, peak = 95), gca=94.5 gca peak = 0.16930 (96) mri peak = 0.12101 (93) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (593 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (593 voxels, peak = 94), gca=93.6 gca peak = 0.24553 (55) mri peak = 0.07667 (65) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1352 voxels, overlap=0.367) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1352 voxels, peak = 62), gca=62.4 gca peak = 0.30264 (59) mri peak = 0.06650 (64) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1207 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1207 voxels, peak = 62), gca=61.7 gca peak = 0.07580 (103) mri peak = 0.08078 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, overlap=0.784) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, peak = 104), gca=103.5 gca peak = 0.07714 (104) mri peak = 0.07366 (103) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (61498 voxels, overlap=0.750) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (61498 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.03610 (66) Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (39627 voxels, overlap=0.641) Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (39627 voxels, peak = 66), gca=65.8 gca peak = 0.11620 (58) mri peak = 0.04075 (68) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (40904 voxels, overlap=0.321) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (40904 voxels, peak = 69), gca=69.3 gca peak = 0.30970 (66) mri peak = 0.08816 (76) Right_Caudate (50): linear fit = 1.10 x + 0.0 (1185 voxels, overlap=0.379) Right_Caudate (50): linear fit = 1.10 x + 0.0 (1185 voxels, peak = 72), gca=72.3 gca peak = 0.15280 (69) mri peak = 0.07814 (76) Left_Caudate (11): linear fit = 1.07 x + 0.0 (1200 voxels, overlap=0.853) Left_Caudate (11): linear fit = 1.07 x + 0.0 (1200 voxels, peak = 73), gca=73.5 gca peak = 0.13902 (56) mri peak = 0.04564 (65) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (31494 voxels, overlap=0.797) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (31494 voxels, peak = 64), gca=63.6 gca peak = 0.14777 (55) mri peak = 0.05111 (64) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (32655 voxels, overlap=0.439) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (32655 voxels, peak = 66), gca=65.7 gca peak = 0.16765 (84) mri peak = 0.09173 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7206 voxels, overlap=0.937) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7206 voxels, peak = 85), gca=85.3 gca peak = 0.18739 (84) mri peak = 0.08231 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6204 voxels, overlap=0.911) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6204 voxels, peak = 87), gca=86.9 gca peak = 0.29869 (57) mri peak = 0.06845 (78) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (683 voxels, overlap=0.077) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (683 voxels, peak = 74), gca=73.8 gca peak = 0.33601 (57) mri peak = 0.07428 (74) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (728 voxels, overlap=0.064) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (728 voxels, peak = 74), gca=74.4 gca peak = 0.11131 (90) mri peak = 0.07421 (88) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, overlap=1.000) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, peak = 90), gca=89.6 gca peak = 0.11793 (83) mri peak = 0.07008 (86) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4931 voxels, overlap=0.949) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4931 voxels, peak = 85), gca=85.1 gca peak = 0.08324 (81) mri peak = 0.07627 (84) Left_Putamen (12): linear fit = 1.02 x + 0.0 (2240 voxels, overlap=0.838) Left_Putamen (12): linear fit = 1.02 x + 0.0 (2240 voxels, peak = 83), gca=83.0 gca peak = 0.10360 (77) mri peak = 0.08326 (83) Right_Putamen (51): linear fit = 1.03 x + 0.0 (2306 voxels, overlap=0.916) Right_Putamen (51): linear fit = 1.03 x + 0.0 (2306 voxels, peak = 80), gca=79.7 gca peak = 0.08424 (78) mri peak = 0.06986 (87) Brain_Stem (16): linear fit = 1.11 x + 0.0 (14679 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.11 x + 0.0 (14679 voxels, peak = 86), gca=86.2 gca peak = 0.12631 (89) mri peak = 0.07740 (90) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1862 voxels, overlap=0.823) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1862 voxels, peak = 92), gca=92.1 gca peak = 0.14500 (87) mri peak = 0.07510 (93) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1883 voxels, overlap=0.893) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1883 voxels, peak = 89), gca=89.2 gca peak = 0.14975 (24) mri peak = 0.11509 (18) gca peak = 0.19357 (14) mri peak = 0.09064 (13) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (314 voxels, overlap=0.848) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (314 voxels, peak = 14), gca=14.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.19 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.29 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14196 (24) mri peak = 0.06742 (29) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (2482 voxels, overlap=0.860) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (2482 voxels, peak = 23), gca=23.4 gca peak = 0.14095 (19) mri peak = 0.08856 (28) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (2048 voxels, overlap=0.422) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (2048 voxels, peak = 27), gca=26.7 gca peak = 0.28191 (93) mri peak = 0.14358 (96) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, overlap=0.825) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, peak = 93), gca=92.5 gca peak = 0.18416 (94) mri peak = 0.12101 (93) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (593 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (593 voxels, peak = 95), gca=95.4 gca peak = 0.26749 (63) mri peak = 0.07667 (65) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1352 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1352 voxels, peak = 64), gca=63.9 gca peak = 0.27972 (59) mri peak = 0.06650 (64) Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (1207 voxels, overlap=1.002) Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (1207 voxels, peak = 61), gca=61.1 gca peak = 0.07875 (103) mri peak = 0.08078 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, overlap=0.802) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, peak = 103), gca=103.0 gca peak = 0.07720 (107) mri peak = 0.07366 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (61498 voxels, overlap=0.847) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (61498 voxels, peak = 106), gca=106.5 gca peak = 0.08624 (66) mri peak = 0.03610 (66) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (39627 voxels, overlap=0.971) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (39627 voxels, peak = 66), gca=66.0 gca peak = 0.09981 (69) mri peak = 0.04075 (68) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (40904 voxels, overlap=0.963) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (40904 voxels, peak = 68), gca=68.0 gca peak = 0.25613 (73) mri peak = 0.08816 (76) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1185 voxels, overlap=1.007) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1185 voxels, peak = 73), gca=73.0 gca peak = 0.12839 (73) mri peak = 0.07814 (76) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1200 voxels, overlap=1.003) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1200 voxels, peak = 73), gca=73.0 gca peak = 0.12384 (63) mri peak = 0.04564 (65) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (31494 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (31494 voxels, peak = 63), gca=63.0 gca peak = 0.12172 (66) mri peak = 0.05111 (64) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32655 voxels, overlap=0.993) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32655 voxels, peak = 65), gca=65.0 gca peak = 0.16169 (86) mri peak = 0.09173 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7206 voxels, overlap=0.963) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7206 voxels, peak = 86), gca=85.6 gca peak = 0.18134 (87) mri peak = 0.08231 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6204 voxels, overlap=0.979) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6204 voxels, peak = 87), gca=86.6 gca peak = 0.27803 (75) mri peak = 0.06845 (78) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (683 voxels, overlap=0.997) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (683 voxels, peak = 74), gca=73.9 gca peak = 0.31967 (74) mri peak = 0.07428 (74) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (728 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (728 voxels, peak = 77), gca=76.6 gca peak = 0.10636 (89) mri peak = 0.07421 (88) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, overlap=0.998) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, peak = 89), gca=88.6 gca peak = 0.11628 (85) mri peak = 0.07008 (86) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4931 voxels, overlap=0.976) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4931 voxels, peak = 85), gca=84.6 gca peak = 0.09217 (77) mri peak = 0.07627 (84) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2240 voxels, overlap=0.880) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2240 voxels, peak = 78), gca=78.2 gca peak = 0.10883 (78) mri peak = 0.08326 (83) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2306 voxels, overlap=0.906) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2306 voxels, peak = 78), gca=78.0 gca peak = 0.07147 (86) mri peak = 0.06986 (87) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14679 voxels, overlap=0.809) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14679 voxels, peak = 86), gca=85.6 gca peak = 0.12083 (87) mri peak = 0.07740 (90) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1862 voxels, overlap=0.868) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1862 voxels, peak = 87), gca=86.6 gca peak = 0.14063 (89) mri peak = 0.07510 (93) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1883 voxels, overlap=0.933) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1883 voxels, peak = 88), gca=87.7 gca peak = 0.12335 (33) mri peak = 0.11509 (18) gca peak = 0.18343 (17) mri peak = 0.09064 (13) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (314 voxels, overlap=0.843) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (314 voxels, peak = 14), gca=13.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16503 (28) gca peak Left_Thalamus = 0.64095 (104) gca peak Third_Ventricle = 0.12335 (33) gca peak CSF = 0.20554 (47) gca peak Left_Accumbens_area = 0.64163 (66) gca peak Left_undetermined = 0.95280 (30) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.21972 (26) gca peak Right_Accumbens_area = 0.34807 (71) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14509 (37) gca peak Fifth_Ventricle = 0.75707 (40) gca peak WM_hypointensities = 0.07483 (78) gca peak non_WM_hypointensities = 0.09744 (44) gca peak Optic_Chiasm = 0.71121 (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 1.06 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 89664 voxels changed in iteration 0 of unlikely voxel relabeling 444 voxels changed in iteration 1 of unlikely voxel relabeling 19 voxels changed in iteration 2 of unlikely voxel relabeling 11 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 76959 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 497 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 87748 changed. image ll: -2.152, PF=0.500 pass 2: 24203 changed. image ll: -2.150, PF=0.500 pass 3: 7330 changed. pass 4: 2452 changed. 69360 voxels changed in iteration 0 of unlikely voxel relabeling 482 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 9213 voxels changed in iteration 0 of unlikely voxel relabeling 203 voxels changed in iteration 1 of unlikely voxel relabeling 16 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6597 voxels changed in iteration 0 of unlikely voxel relabeling 105 voxels changed in iteration 1 of unlikely voxel relabeling 8 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6776 voxels changed in iteration 0 of unlikely voxel relabeling 49 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 4206.011589 mri_ca_label stimesec 1.858717 mri_ca_label ru_maxrss 2108192 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 640551 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 63328 mri_ca_label ru_oublock 504 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 352 mri_ca_label ru_nivcsw 6784 auto-labeling took 69 minutes and 22 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/cc_up.lta 0050352 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-6.0.0/0050352/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/norm.mgz 80449 voxels in left wm, 111265 in right wm, xrange [116, 134] searching rotation angles z=[-5 9], y=[-2 12] searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.8 global minimum found at slice 126.0, rotations (4.70, 2.06) final transformation (x=126.0, yr=4.704, zr=2.060): 0.99599 -0.03595 0.08195 -3.95324; 0.03583 0.99935 0.00295 20.18620; -0.08200 -0.00000 0.99663 14.75014; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 132] in xformed coordinates best xformed slice 129 cc center is found at 129 103 124 eigenvectors: 0.00183 0.00166 1.00000; 0.01257 -0.99992 0.00164; 0.99992 0.01257 -0.00185; error in mid anterior detected - correcting... writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aseg.auto.mgz... corpus callosum segmentation took 2.1 minutes #-------------------------------------- #@# Merge ASeg Sun Oct 8 03:55:18 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sun Oct 8 03:55:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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... 1755 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 70 (70), valley at 36 (36) csf peak at 36, setting threshold to 58 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 69 (69), valley at 35 (35) csf peak at 35, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 6 seconds. #-------------------------------------------- #@# Mask BFS Sun Oct 8 03:58:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1774278 voxels in mask (pct= 10.58) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sun Oct 8 03:58:27 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 (102.0): 102.3 +- 7.0 [79.0 --> 125.0] GM (72.0) : 70.3 +- 9.3 [30.0 --> 95.0] setting bottom of white matter range to 79.6 setting top of gray matter range to 88.8 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... 6346 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3553 filled 1511 bright non-wm voxels segmented. 3366 diagonally connected voxels added... white matter segmentation took 1.8 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 0.54 minutes reading wm segmentation from wm.seg.mgz... 232 voxels added to wm to prevent paths from MTL structures to cortex 3164 additional wm voxels added 0 additional wm voxels added SEG EDIT: 50721 voxels turned on, 45036 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 26 found - 26 modified | TOTAL: 26 pass 2 (xy+): 0 found - 26 modified | TOTAL: 26 pass 1 (xy-): 24 found - 24 modified | TOTAL: 50 pass 2 (xy-): 0 found - 24 modified | TOTAL: 50 pass 1 (yz+): 24 found - 24 modified | TOTAL: 74 pass 2 (yz+): 0 found - 24 modified | TOTAL: 74 pass 1 (yz-): 27 found - 27 modified | TOTAL: 101 pass 2 (yz-): 0 found - 27 modified | TOTAL: 101 pass 1 (xz+): 19 found - 19 modified | TOTAL: 120 pass 2 (xz+): 0 found - 19 modified | TOTAL: 120 pass 1 (xz-): 27 found - 27 modified | TOTAL: 147 pass 2 (xz-): 0 found - 27 modified | TOTAL: 147 Iteration Number : 1 pass 1 (+++): 61 found - 61 modified | TOTAL: 61 pass 2 (+++): 0 found - 61 modified | TOTAL: 61 pass 1 (+++): 37 found - 37 modified | TOTAL: 98 pass 2 (+++): 0 found - 37 modified | TOTAL: 98 pass 1 (+++): 45 found - 45 modified | TOTAL: 143 pass 2 (+++): 0 found - 45 modified | TOTAL: 143 pass 1 (+++): 33 found - 33 modified | TOTAL: 176 pass 2 (+++): 0 found - 33 modified | TOTAL: 176 Iteration Number : 1 pass 1 (++): 110 found - 110 modified | TOTAL: 110 pass 2 (++): 0 found - 110 modified | TOTAL: 110 pass 1 (+-): 67 found - 67 modified | TOTAL: 177 pass 2 (+-): 0 found - 67 modified | TOTAL: 177 pass 1 (--): 63 found - 63 modified | TOTAL: 240 pass 2 (--): 0 found - 63 modified | TOTAL: 240 pass 1 (-+): 79 found - 79 modified | TOTAL: 319 pass 2 (-+): 0 found - 79 modified | TOTAL: 319 Iteration Number : 2 pass 1 (xy+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 8 found - 8 modified | TOTAL: 18 pass 2 (xy-): 0 found - 8 modified | TOTAL: 18 pass 1 (yz+): 9 found - 9 modified | TOTAL: 27 pass 2 (yz+): 0 found - 9 modified | TOTAL: 27 pass 1 (yz-): 4 found - 4 modified | TOTAL: 31 pass 2 (yz-): 0 found - 4 modified | TOTAL: 31 pass 1 (xz+): 10 found - 10 modified | TOTAL: 41 pass 2 (xz+): 0 found - 10 modified | TOTAL: 41 pass 1 (xz-): 18 found - 18 modified | TOTAL: 59 pass 2 (xz-): 0 found - 18 modified | TOTAL: 59 Iteration Number : 2 pass 1 (+++): 5 found - 5 modified | TOTAL: 5 pass 2 (+++): 0 found - 5 modified | TOTAL: 5 pass 1 (+++): 4 found - 4 modified | TOTAL: 9 pass 2 (+++): 0 found - 4 modified | TOTAL: 9 pass 1 (+++): 2 found - 2 modified | TOTAL: 11 pass 2 (+++): 0 found - 2 modified | TOTAL: 11 pass 1 (+++): 0 found - 0 modified | TOTAL: 11 Iteration Number : 2 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 5 found - 5 modified | TOTAL: 11 pass 2 (+-): 0 found - 5 modified | TOTAL: 11 pass 1 (--): 5 found - 5 modified | TOTAL: 16 pass 2 (--): 0 found - 5 modified | TOTAL: 16 pass 1 (-+): 9 found - 9 modified | TOTAL: 25 pass 2 (-+): 0 found - 9 modified | TOTAL: 25 Iteration Number : 3 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-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 Iteration Number : 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 = 744 (out of 694527: 0.107123) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sun Oct 8 04:00:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.95413 -0.06520 0.08700 2.88472; 0.05271 1.08731 0.01970 -25.91927; -0.09979 -0.01929 0.97531 1.08168; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1320 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75) no need to search using seed (127, 121, 91), TAL = (1.0, -37.0, 7.0) talairach voxel to voxel transform 1.03496 0.06040 -0.09354 -1.31879; -0.05207 0.91633 -0.01387 23.91576; 0.10486 0.02431 1.01547 -0.77087; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 121, 91) --> (1.0, -37.0, 7.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (1.00, -37.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, -37.00, 7.00) SRC: (110.29, 127.85, 106.01) search lh wm seed point around talairach space (-17.00, -37.00, 7.00), SRC: (147.55, 125.98, 109.78) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sun Oct 8 04:01:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 4 found - 4 modified | TOTAL: 9 pass 2 (xy-): 0 found - 4 modified | TOTAL: 9 pass 1 (yz+): 5 found - 5 modified | TOTAL: 14 pass 2 (yz+): 0 found - 5 modified | TOTAL: 14 pass 1 (yz-): 3 found - 3 modified | TOTAL: 17 pass 2 (yz-): 0 found - 3 modified | TOTAL: 17 pass 1 (xz+): 3 found - 3 modified | TOTAL: 20 pass 2 (xz+): 0 found - 3 modified | TOTAL: 20 pass 1 (xz-): 4 found - 4 modified | TOTAL: 24 pass 2 (xz-): 0 found - 4 modified | TOTAL: 24 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 2 found - 2 modified | TOTAL: 4 pass 2 (--): 0 found - 2 modified | TOTAL: 4 pass 1 (-+): 2 found - 2 modified | TOTAL: 6 pass 2 (-+): 0 found - 2 modified | TOTAL: 6 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 = 30 (out of 327785: 0.009152) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 908 vertices, 1007 faces slice 60: 6411 vertices, 6668 faces slice 70: 15533 vertices, 15901 faces slice 80: 25661 vertices, 26084 faces slice 90: 37638 vertices, 38060 faces slice 100: 49324 vertices, 49776 faces slice 110: 61767 vertices, 62287 faces slice 120: 75034 vertices, 75611 faces slice 130: 88695 vertices, 89288 faces slice 140: 102788 vertices, 103442 faces slice 150: 117164 vertices, 117866 faces slice 160: 131053 vertices, 131690 faces slice 170: 141710 vertices, 142296 faces slice 180: 151516 vertices, 152084 faces slice 190: 159921 vertices, 160464 faces slice 200: 166966 vertices, 167489 faces slice 210: 171723 vertices, 172108 faces slice 220: 172174 vertices, 172468 faces slice 230: 172174 vertices, 172468 faces slice 240: 172174 vertices, 172468 faces slice 250: 172174 vertices, 172468 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... 172174 voxel in cpt #1: X=-294 [v=172174,e=517404,f=344936] located at (-28.166349, -1.312951, 9.485765) For the whole surface: X=-294 [v=172174,e=517404,f=344936] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sun Oct 8 04:01:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 2 found - 2 modified | TOTAL: 11 pass 2 (xy-): 0 found - 2 modified | TOTAL: 11 pass 1 (yz+): 2 found - 2 modified | TOTAL: 13 pass 2 (yz+): 0 found - 2 modified | TOTAL: 13 pass 1 (yz-): 2 found - 2 modified | TOTAL: 15 pass 2 (yz-): 0 found - 2 modified | TOTAL: 15 pass 1 (xz+): 2 found - 2 modified | TOTAL: 17 pass 2 (xz+): 0 found - 2 modified | TOTAL: 17 pass 1 (xz-): 7 found - 7 modified | TOTAL: 24 pass 2 (xz-): 0 found - 7 modified | TOTAL: 24 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 2 found - 2 modified | TOTAL: 5 pass 2 (--): 0 found - 2 modified | TOTAL: 5 pass 1 (-+): 5 found - 5 modified | TOTAL: 10 pass 2 (-+): 0 found - 5 modified | TOTAL: 10 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 = 36 (out of 342713: 0.010504) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 1463 vertices, 1596 faces slice 60: 8749 vertices, 9066 faces slice 70: 19184 vertices, 19639 faces slice 80: 32377 vertices, 32963 faces slice 90: 47305 vertices, 47862 faces slice 100: 60944 vertices, 61505 faces slice 110: 75515 vertices, 76169 faces slice 120: 90167 vertices, 90778 faces slice 130: 104430 vertices, 105108 faces slice 140: 119587 vertices, 120369 faces slice 150: 133510 vertices, 134196 faces slice 160: 146115 vertices, 146852 faces slice 170: 156195 vertices, 156838 faces slice 180: 165046 vertices, 165653 faces slice 190: 172950 vertices, 173534 faces slice 200: 179473 vertices, 180009 faces slice 210: 183407 vertices, 183819 faces slice 220: 183780 vertices, 184134 faces slice 230: 183780 vertices, 184134 faces slice 240: 183780 vertices, 184134 faces slice 250: 183780 vertices, 184134 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... 183780 voxel in cpt #1: X=-354 [v=183780,e=552402,f=368268] located at (30.536516, -6.303988, 8.369474) For the whole surface: X=-354 [v=183780,e=552402,f=368268] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sun Oct 8 04:01:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sun Oct 8 04:01:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 16188 of (16188 16191) to complete... Waiting for PID 16191 of (16188 16191) 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 (16188 16191) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sun Oct 8 04:01:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sun Oct 8 04:01:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 16253 of (16253 16256) to complete... Waiting for PID 16256 of (16253 16256) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 49.1 mm, total surface area = 88904 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes step 000: RMS=0.173 (target=0.015) step 005: RMS=0.136 (target=0.015) step 010: RMS=0.111 (target=0.015) step 015: RMS=0.099 (target=0.015) step 020: RMS=0.092 (target=0.015) step 025: RMS=0.085 (target=0.015) step 030: RMS=0.080 (target=0.015) step 035: RMS=0.077 (target=0.015) step 040: RMS=0.074 (target=0.015) step 045: RMS=0.072 (target=0.015) step 050: RMS=0.071 (target=0.015) step 055: RMS=0.070 (target=0.015) step 060: RMS=0.070 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 53.210910 mris_inflate stimesec 0.133979 mris_inflate ru_maxrss 252252 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 36435 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 12144 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2043 mris_inflate ru_nivcsw 5301 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 49.6 mm, total surface area = 94197 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.9 minutes step 000: RMS=0.177 (target=0.015) step 005: RMS=0.139 (target=0.015) step 010: RMS=0.113 (target=0.015) step 015: RMS=0.103 (target=0.015) step 020: RMS=0.094 (target=0.015) step 025: RMS=0.088 (target=0.015) step 030: RMS=0.085 (target=0.015) step 035: RMS=0.081 (target=0.015) step 040: RMS=0.079 (target=0.015) step 045: RMS=0.077 (target=0.015) step 050: RMS=0.075 (target=0.015) step 055: RMS=0.075 (target=0.015) step 060: RMS=0.074 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 55.976490 mris_inflate stimesec 0.143978 mris_inflate ru_maxrss 269028 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 38579 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 12944 mris_inflate ru_oublock 12960 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 4920 mris_inflate ru_nivcsw 4102 PIDs (16253 16256) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sun Oct 8 04:02:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sun Oct 8 04:02:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 16310 of (16310 16314) to complete... Waiting for PID 16314 of (16310 16314) 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 0.89 +- 0.55 (0.00-->6.93) (max @ vno 57444 --> 57445) face area 0.02 +- 0.03 (-0.21-->0.70) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.292... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.350, avgs=0 005/300: dt: 0.9000, rms radial error=176.091, avgs=0 010/300: dt: 0.9000, rms radial error=175.535, avgs=0 015/300: dt: 0.9000, rms radial error=174.806, avgs=0 020/300: dt: 0.9000, rms radial error=173.977, avgs=0 025/300: dt: 0.9000, rms radial error=173.090, avgs=0 030/300: dt: 0.9000, rms radial error=172.171, avgs=0 035/300: dt: 0.9000, rms radial error=171.235, avgs=0 040/300: dt: 0.9000, rms radial error=170.292, avgs=0 045/300: dt: 0.9000, rms radial error=169.345, avgs=0 050/300: dt: 0.9000, rms radial error=168.399, avgs=0 055/300: dt: 0.9000, rms radial error=167.455, avgs=0 060/300: dt: 0.9000, rms radial error=166.515, avgs=0 065/300: dt: 0.9000, rms radial error=165.580, avgs=0 070/300: dt: 0.9000, rms radial error=164.649, avgs=0 075/300: dt: 0.9000, rms radial error=163.723, avgs=0 080/300: dt: 0.9000, rms radial error=162.802, avgs=0 085/300: dt: 0.9000, rms radial error=161.886, avgs=0 090/300: dt: 0.9000, rms radial error=160.975, avgs=0 095/300: dt: 0.9000, rms radial error=160.069, avgs=0 100/300: dt: 0.9000, rms radial error=159.168, avgs=0 105/300: dt: 0.9000, rms radial error=158.271, avgs=0 110/300: dt: 0.9000, rms radial error=157.380, avgs=0 115/300: dt: 0.9000, rms radial error=156.493, avgs=0 120/300: dt: 0.9000, rms radial error=155.612, avgs=0 125/300: dt: 0.9000, rms radial error=154.735, avgs=0 130/300: dt: 0.9000, rms radial error=153.863, avgs=0 135/300: dt: 0.9000, rms radial error=152.995, avgs=0 140/300: dt: 0.9000, rms radial error=152.133, avgs=0 145/300: dt: 0.9000, rms radial error=151.275, avgs=0 150/300: dt: 0.9000, rms radial error=150.422, avgs=0 155/300: dt: 0.9000, rms radial error=149.574, avgs=0 160/300: dt: 0.9000, rms radial error=148.730, avgs=0 165/300: dt: 0.9000, rms radial error=147.891, avgs=0 170/300: dt: 0.9000, rms radial error=147.057, avgs=0 175/300: dt: 0.9000, rms radial error=146.227, avgs=0 180/300: dt: 0.9000, rms radial error=145.402, avgs=0 185/300: dt: 0.9000, rms radial error=144.582, avgs=0 190/300: dt: 0.9000, rms radial error=143.766, avgs=0 195/300: dt: 0.9000, rms radial error=142.955, avgs=0 200/300: dt: 0.9000, rms radial error=142.148, avgs=0 205/300: dt: 0.9000, rms radial error=141.346, avgs=0 210/300: dt: 0.9000, rms radial error=140.548, avgs=0 215/300: dt: 0.9000, rms radial error=139.755, avgs=0 220/300: dt: 0.9000, rms radial error=138.966, avgs=0 225/300: dt: 0.9000, rms radial error=138.181, avgs=0 230/300: dt: 0.9000, rms radial error=137.401, avgs=0 235/300: dt: 0.9000, rms radial error=136.625, avgs=0 240/300: dt: 0.9000, rms radial error=135.853, avgs=0 245/300: dt: 0.9000, rms radial error=135.085, avgs=0 250/300: dt: 0.9000, rms radial error=134.322, avgs=0 255/300: dt: 0.9000, rms radial error=133.563, avgs=0 260/300: dt: 0.9000, rms radial error=132.809, avgs=0 265/300: dt: 0.9000, rms radial error=132.059, avgs=0 270/300: dt: 0.9000, rms radial error=131.312, avgs=0 275/300: dt: 0.9000, rms radial error=130.571, avgs=0 280/300: dt: 0.9000, rms radial error=129.833, avgs=0 285/300: dt: 0.9000, rms radial error=129.100, avgs=0 290/300: dt: 0.9000, rms radial error=128.371, avgs=0 295/300: dt: 0.9000, rms radial error=127.646, avgs=0 300/300: dt: 0.9000, rms radial error=126.925, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20645.08 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 3646.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 3 (K=160.0), pass 1, starting sse = 452.69 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00421 epoch 4 (K=640.0), pass 1, starting sse = 54.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/12 = 0.00671 final distance error %26.88 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.09 hours mris_sphere utimesec 307.246291 mris_sphere stimesec 0.179972 mris_sphere ru_maxrss 252452 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 36475 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 12128 mris_sphere ru_oublock 12168 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8235 mris_sphere ru_nivcsw 23619 FSRUNTIME@ mris_sphere 0.0855 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 0.87 +- 0.55 (0.00-->7.78) (max @ vno 70471 --> 70472) face area 0.02 +- 0.03 (-0.20-->0.56) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.287... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.280, avgs=0 005/300: dt: 0.9000, rms radial error=176.020, avgs=0 010/300: dt: 0.9000, rms radial error=175.463, avgs=0 015/300: dt: 0.9000, rms radial error=174.731, avgs=0 020/300: dt: 0.9000, rms radial error=173.899, avgs=0 025/300: dt: 0.9000, rms radial error=173.009, avgs=0 030/300: dt: 0.9000, rms radial error=172.087, avgs=0 035/300: dt: 0.9000, rms radial error=171.149, avgs=0 040/300: dt: 0.9000, rms radial error=170.203, avgs=0 045/300: dt: 0.9000, rms radial error=169.256, avgs=0 050/300: dt: 0.9000, rms radial error=168.310, avgs=0 055/300: dt: 0.9000, rms radial error=167.368, avgs=0 060/300: dt: 0.9000, rms radial error=166.429, avgs=0 065/300: dt: 0.9000, rms radial error=165.495, avgs=0 070/300: dt: 0.9000, rms radial error=164.566, avgs=0 075/300: dt: 0.9000, rms radial error=163.642, avgs=0 080/300: dt: 0.9000, rms radial error=162.723, avgs=0 085/300: dt: 0.9000, rms radial error=161.808, avgs=0 090/300: dt: 0.9000, rms radial error=160.899, avgs=0 095/300: dt: 0.9000, rms radial error=159.994, avgs=0 100/300: dt: 0.9000, rms radial error=159.094, avgs=0 105/300: dt: 0.9000, rms radial error=158.199, avgs=0 110/300: dt: 0.9000, rms radial error=157.309, avgs=0 115/300: dt: 0.9000, rms radial error=156.423, avgs=0 120/300: dt: 0.9000, rms radial error=155.542, avgs=0 125/300: dt: 0.9000, rms radial error=154.667, avgs=0 130/300: dt: 0.9000, rms radial error=153.795, avgs=0 135/300: dt: 0.9000, rms radial error=152.929, avgs=0 140/300: dt: 0.9000, rms radial error=152.067, avgs=0 145/300: dt: 0.9000, rms radial error=151.211, avgs=0 150/300: dt: 0.9000, rms radial error=150.359, avgs=0 155/300: dt: 0.9000, rms radial error=149.512, avgs=0 160/300: dt: 0.9000, rms radial error=148.669, avgs=0 165/300: dt: 0.9000, rms radial error=147.831, avgs=0 170/300: dt: 0.9000, rms radial error=146.998, avgs=0 175/300: dt: 0.9000, rms radial error=146.170, avgs=0 180/300: dt: 0.9000, rms radial error=145.346, avgs=0 185/300: dt: 0.9000, rms radial error=144.527, avgs=0 190/300: dt: 0.9000, rms radial error=143.713, avgs=0 195/300: dt: 0.9000, rms radial error=142.903, avgs=0 200/300: dt: 0.9000, rms radial error=142.098, avgs=0 205/300: dt: 0.9000, rms radial error=141.297, avgs=0 210/300: dt: 0.9000, rms radial error=140.501, avgs=0 215/300: dt: 0.9000, rms radial error=139.709, avgs=0 220/300: dt: 0.9000, rms radial error=138.921, avgs=0 225/300: dt: 0.9000, rms radial error=138.138, avgs=0 230/300: dt: 0.9000, rms radial error=137.359, avgs=0 235/300: dt: 0.9000, rms radial error=136.585, avgs=0 240/300: dt: 0.9000, rms radial error=135.815, avgs=0 245/300: dt: 0.9000, rms radial error=135.049, avgs=0 250/300: dt: 0.9000, rms radial error=134.288, avgs=0 255/300: dt: 0.9000, rms radial error=133.531, avgs=0 260/300: dt: 0.9000, rms radial error=132.778, avgs=0 265/300: dt: 0.9000, rms radial error=132.030, avgs=0 270/300: dt: 0.9000, rms radial error=131.285, avgs=0 275/300: dt: 0.9000, rms radial error=130.545, avgs=0 280/300: dt: 0.9000, rms radial error=129.810, avgs=0 285/300: dt: 0.9000, rms radial error=129.078, avgs=0 290/300: dt: 0.9000, rms radial error=128.350, avgs=0 295/300: dt: 0.9000, rms radial error=127.626, avgs=0 300/300: dt: 0.9000, rms radial error=126.907, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 22174.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 4004.38 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 522.09 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00198 epoch 4 (K=640.0), pass 1, starting sse = 72.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00478 final distance error %26.73 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.09 hours mris_sphere utimesec 313.009415 mris_sphere stimesec 0.192970 mris_sphere ru_maxrss 269252 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 38634 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 12984 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 10345 mris_sphere ru_nivcsw 22229 FSRUNTIME@ mris_sphere 0.0865 hours 1 threads PIDs (16310 16314) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sun Oct 8 04:08:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sun Oct 8 04:08:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sun Oct 8 04:08:04 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 lh #@# Fix Topology rh Sun Oct 8 04:08:04 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 rh Waiting for PID 16546 of (16546 16549) to complete... Waiting for PID 16549 of (16546 16549) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 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=-294 (nv=172174, nf=344936, ne=517404, g=148) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 27566 ambiguous faces found in tessellation segmenting defects... 116 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 35 into 32 -merging segment 43 into 40 -merging segment 48 into 40 -merging segment 42 into 41 -merging segment 63 into 61 -merging segment 61 into 73 -merging segment 88 into 90 -merging segment 104 into 101 -merging segment 115 into 114 107 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2572 (-4.6286) -vertex loglikelihood: -6.0585 (-3.0292) -normal dot loglikelihood: -3.6004 (-3.6004) -quad curv loglikelihood: -6.5483 (-3.2742) Total Loglikelihood : -25.4644 CORRECTING DEFECT 0 (vertices=29, convex hull=53, v0=2) After retessellation of defect 0 (v0=2), euler #=-105 (156084,463153,306964) : difference with theory (-104) = 1 CORRECTING DEFECT 1 (vertices=48, convex hull=55, v0=23) After retessellation of defect 1 (v0=23), euler #=-104 (156089,463189,306996) : difference with theory (-103) = 1 CORRECTING DEFECT 2 (vertices=42, convex hull=81, v0=229) After retessellation of defect 2 (v0=229), euler #=-103 (156100,463254,307051) : difference with theory (-102) = 1 CORRECTING DEFECT 3 (vertices=766, convex hull=362, v0=378) After retessellation of defect 3 (v0=378), euler #=-103 (156287,464017,307627) : difference with theory (-101) = 2 CORRECTING DEFECT 4 (vertices=6, convex hull=25, v0=668) After retessellation of defect 4 (v0=668), euler #=-102 (156288,464026,307636) : difference with theory (-100) = 2 CORRECTING DEFECT 5 (vertices=118, convex hull=27, v0=848) After retessellation of defect 5 (v0=848), euler #=-101 (156292,464044,307651) : difference with theory (-99) = 2 CORRECTING DEFECT 6 (vertices=50, convex hull=57, v0=1702) After retessellation of defect 6 (v0=1702), euler #=-100 (156303,464100,307697) : difference with theory (-98) = 2 CORRECTING DEFECT 7 (vertices=10, convex hull=26, v0=1939) After retessellation of defect 7 (v0=1939), euler #=-99 (156304,464112,307709) : difference with theory (-97) = 2 CORRECTING DEFECT 8 (vertices=21, convex hull=37, v0=2126) After retessellation of defect 8 (v0=2126), euler #=-98 (156309,464142,307735) : difference with theory (-96) = 2 CORRECTING DEFECT 9 (vertices=530, convex hull=427, v0=2918) After retessellation of defect 9 (v0=2918), euler #=-98 (156481,464883,308304) : difference with theory (-95) = 3 CORRECTING DEFECT 10 (vertices=13, convex hull=20, v0=3106) After retessellation of defect 10 (v0=3106), euler #=-97 (156482,464893,308314) : difference with theory (-94) = 3 CORRECTING DEFECT 11 (vertices=33, convex hull=81, v0=3766) After retessellation of defect 11 (v0=3766), euler #=-96 (156499,464980,308385) : difference with theory (-93) = 3 CORRECTING DEFECT 12 (vertices=62, convex hull=68, v0=5713) After retessellation of defect 12 (v0=5713), euler #=-95 (156522,465076,308459) : difference with theory (-92) = 3 CORRECTING DEFECT 13 (vertices=20, convex hull=55, v0=6929) After retessellation of defect 13 (v0=6929), euler #=-94 (156534,465132,308504) : difference with theory (-91) = 3 CORRECTING DEFECT 14 (vertices=10, convex hull=28, v0=7172) After retessellation of defect 14 (v0=7172), euler #=-93 (156535,465144,308516) : difference with theory (-90) = 3 CORRECTING DEFECT 15 (vertices=30, convex hull=47, v0=8715) After retessellation of defect 15 (v0=8715), euler #=-92 (156540,465176,308544) : difference with theory (-89) = 3 CORRECTING DEFECT 16 (vertices=33, convex hull=79, v0=8844) After retessellation of defect 16 (v0=8844), euler #=-91 (156557,465254,308606) : difference with theory (-88) = 3 CORRECTING DEFECT 17 (vertices=51, convex hull=43, v0=9644) After retessellation of defect 17 (v0=9644), euler #=-90 (156566,465298,308642) : difference with theory (-87) = 3 CORRECTING DEFECT 18 (vertices=157, convex hull=56, v0=13009) After retessellation of defect 18 (v0=13009), euler #=-89 (156583,465374,308702) : difference with theory (-86) = 3 CORRECTING DEFECT 19 (vertices=50, convex hull=90, v0=13928) After retessellation of defect 19 (v0=13928), euler #=-88 (156608,465488,308792) : difference with theory (-85) = 3 CORRECTING DEFECT 20 (vertices=6, convex hull=29, v0=14464) After retessellation of defect 20 (v0=14464), euler #=-87 (156608,465496,308801) : difference with theory (-84) = 3 CORRECTING DEFECT 21 (vertices=35, convex hull=59, v0=20239) After retessellation of defect 21 (v0=20239), euler #=-86 (156625,465575,308864) : difference with theory (-83) = 3 CORRECTING DEFECT 22 (vertices=74, convex hull=133, v0=20596) After retessellation of defect 22 (v0=20596), euler #=-85 (156676,465789,309028) : difference with theory (-82) = 3 CORRECTING DEFECT 23 (vertices=40, convex hull=21, v0=20599) After retessellation of defect 23 (v0=20599), euler #=-84 (156678,465800,309038) : difference with theory (-81) = 3 CORRECTING DEFECT 24 (vertices=33, convex hull=74, v0=22662) After retessellation of defect 24 (v0=22662), euler #=-83 (156696,465884,309105) : difference with theory (-80) = 3 CORRECTING DEFECT 25 (vertices=50, convex hull=84, v0=26818) After retessellation of defect 25 (v0=26818), euler #=-82 (156729,466019,309208) : difference with theory (-79) = 3 CORRECTING DEFECT 26 (vertices=26, convex hull=58, v0=27815) After retessellation of defect 26 (v0=27815), euler #=-81 (156741,466079,309257) : difference with theory (-78) = 3 CORRECTING DEFECT 27 (vertices=6, convex hull=17, v0=29119) After retessellation of defect 27 (v0=29119), euler #=-80 (156742,466085,309263) : difference with theory (-77) = 3 CORRECTING DEFECT 28 (vertices=50, convex hull=102, v0=35491) After retessellation of defect 28 (v0=35491), euler #=-79 (156769,466210,309362) : difference with theory (-76) = 3 CORRECTING DEFECT 29 (vertices=85, convex hull=118, v0=36517) After retessellation of defect 29 (v0=36517), euler #=-78 (156818,466409,309513) : difference with theory (-75) = 3 CORRECTING DEFECT 30 (vertices=40, convex hull=83, v0=39096) After retessellation of defect 30 (v0=39096), euler #=-77 (156843,466515,309595) : difference with theory (-74) = 3 CORRECTING DEFECT 31 (vertices=137, convex hull=67, v0=40936) After retessellation of defect 31 (v0=40936), euler #=-76 (156868,466616,309672) : difference with theory (-73) = 3 CORRECTING DEFECT 32 (vertices=881, convex hull=309, v0=42366) After retessellation of defect 32 (v0=42366), euler #=-75 (156978,467093,310040) : difference with theory (-72) = 3 CORRECTING DEFECT 33 (vertices=32, convex hull=64, v0=44298) After retessellation of defect 33 (v0=44298), euler #=-74 (156993,467161,310094) : difference with theory (-71) = 3 CORRECTING DEFECT 34 (vertices=26, convex hull=66, v0=44592) After retessellation of defect 34 (v0=44592), euler #=-73 (157007,467231,310151) : difference with theory (-70) = 3 CORRECTING DEFECT 35 (vertices=66, convex hull=83, v0=48182) After retessellation of defect 35 (v0=48182), euler #=-72 (157035,467346,310239) : difference with theory (-69) = 3 CORRECTING DEFECT 36 (vertices=91, convex hull=90, v0=50023) After retessellation of defect 36 (v0=50023), euler #=-71 (157077,467509,310361) : difference with theory (-68) = 3 CORRECTING DEFECT 37 (vertices=91, convex hull=120, v0=51833) After retessellation of defect 37 (v0=51833), euler #=-70 (157127,467714,310517) : difference with theory (-67) = 3 CORRECTING DEFECT 38 (vertices=27, convex hull=57, v0=52332) After retessellation of defect 38 (v0=52332), euler #=-69 (157139,467772,310564) : difference with theory (-66) = 3 CORRECTING DEFECT 39 (vertices=530, convex hull=303, v0=52876) After retessellation of defect 39 (v0=52876), euler #=-66 (157304,468431,311061) : difference with theory (-65) = 1 CORRECTING DEFECT 40 (vertices=527, convex hull=246, v0=55061) After retessellation of defect 40 (v0=55061), euler #=-64 (157332,468638,311242) : difference with theory (-64) = 0 CORRECTING DEFECT 41 (vertices=74, convex hull=133, v0=63103) After retessellation of defect 41 (v0=63103), euler #=-63 (157365,468797,311369) : difference with theory (-63) = 0 CORRECTING DEFECT 42 (vertices=18, convex hull=25, v0=63370) After retessellation of defect 42 (v0=63370), euler #=-62 (157368,468814,311384) : difference with theory (-62) = 0 CORRECTING DEFECT 43 (vertices=26, convex hull=52, v0=64436) After retessellation of defect 43 (v0=64436), euler #=-61 (157378,468861,311422) : difference with theory (-61) = 0 CORRECTING DEFECT 44 (vertices=118, convex hull=124, v0=68002) After retessellation of defect 44 (v0=68002), euler #=-60 (157437,469097,311600) : difference with theory (-60) = 0 CORRECTING DEFECT 45 (vertices=72, convex hull=71, v0=69339) After retessellation of defect 45 (v0=69339), euler #=-59 (157471,469228,311698) : difference with theory (-59) = 0 CORRECTING DEFECT 46 (vertices=245, convex hull=237, v0=70700) After retessellation of defect 46 (v0=70700), euler #=-58 (157523,469504,311923) : difference with theory (-58) = 0 CORRECTING DEFECT 47 (vertices=76, convex hull=113, v0=70911) After retessellation of defect 47 (v0=70911), euler #=-57 (157565,469676,312054) : difference with theory (-57) = 0 CORRECTING DEFECT 48 (vertices=16, convex hull=26, v0=73542) After retessellation of defect 48 (v0=73542), euler #=-56 (157567,469690,312067) : difference with theory (-56) = 0 CORRECTING DEFECT 49 (vertices=41, convex hull=65, v0=74200) After retessellation of defect 49 (v0=74200), euler #=-55 (157590,469784,312139) : difference with theory (-55) = 0 CORRECTING DEFECT 50 (vertices=27, convex hull=78, v0=82043) After retessellation of defect 50 (v0=82043), euler #=-54 (157605,469860,312201) : difference with theory (-54) = 0 CORRECTING DEFECT 51 (vertices=21, convex hull=12, v0=84998) After retessellation of defect 51 (v0=84998), euler #=-53 (157606,469866,312207) : difference with theory (-53) = 0 CORRECTING DEFECT 52 (vertices=661, convex hull=249, v0=85827) After retessellation of defect 52 (v0=85827), euler #=-54 (157640,470101,312407) : difference with theory (-52) = 2 CORRECTING DEFECT 53 (vertices=28, convex hull=42, v0=86243) After retessellation of defect 53 (v0=86243), euler #=-53 (157652,470152,312447) : difference with theory (-51) = 2 CORRECTING DEFECT 54 (vertices=248, convex hull=218, v0=87211) After retessellation of defect 54 (v0=87211), euler #=-52 (157724,470473,312697) : difference with theory (-50) = 2 CORRECTING DEFECT 55 (vertices=71, convex hull=64, v0=89208) After retessellation of defect 55 (v0=89208), euler #=-51 (157743,470557,312763) : difference with theory (-49) = 2 CORRECTING DEFECT 56 (vertices=49, convex hull=30, v0=89444) After retessellation of defect 56 (v0=89444), euler #=-50 (157750,470586,312786) : difference with theory (-48) = 2 CORRECTING DEFECT 57 (vertices=56, convex hull=81, v0=92147) After retessellation of defect 57 (v0=92147), euler #=-49 (157766,470667,312852) : difference with theory (-47) = 2 CORRECTING DEFECT 58 (vertices=40, convex hull=75, v0=95424) After retessellation of defect 58 (v0=95424), euler #=-48 (157787,470760,312925) : difference with theory (-46) = 2 CORRECTING DEFECT 59 (vertices=306, convex hull=111, v0=96898) After retessellation of defect 59 (v0=96898), euler #=-48 (157823,470929,313058) : difference with theory (-45) = 3 CORRECTING DEFECT 60 (vertices=37, convex hull=68, v0=97736) After retessellation of defect 60 (v0=97736), euler #=-47 (157848,471030,313135) : difference with theory (-44) = 3 CORRECTING DEFECT 61 (vertices=48, convex hull=38, v0=98345) After retessellation of defect 61 (v0=98345), euler #=-46 (157856,471068,313166) : difference with theory (-43) = 3 CORRECTING DEFECT 62 (vertices=9, convex hull=16, v0=101032) After retessellation of defect 62 (v0=101032), euler #=-45 (157856,471071,313170) : difference with theory (-42) = 3 CORRECTING DEFECT 63 (vertices=1511, convex hull=649, v0=102420) XL defect detected... After retessellation of defect 63 (v0=102420), euler #=-44 (158282,472737,314411) : difference with theory (-41) = 3 CORRECTING DEFECT 64 (vertices=803, convex hull=286, v0=102689) After retessellation of defect 64 (v0=102689), euler #=-44 (158501,473547,315002) : difference with theory (-40) = 4 CORRECTING DEFECT 65 (vertices=132, convex hull=138, v0=102717) After retessellation of defect 65 (v0=102717), euler #=-43 (158542,473733,315148) : difference with theory (-39) = 4 CORRECTING DEFECT 66 (vertices=8, convex hull=13, v0=106833) After retessellation of defect 66 (v0=106833), euler #=-42 (158542,473736,315152) : difference with theory (-38) = 4 CORRECTING DEFECT 67 (vertices=237, convex hull=268, v0=107060) After retessellation of defect 67 (v0=107060), euler #=-39 (158656,474227,315532) : difference with theory (-37) = 2 CORRECTING DEFECT 68 (vertices=31, convex hull=73, v0=111625) After retessellation of defect 68 (v0=111625), euler #=-38 (158667,474286,315581) : difference with theory (-36) = 2 CORRECTING DEFECT 69 (vertices=504, convex hull=110, v0=114254) After retessellation of defect 69 (v0=114254), euler #=-37 (158683,474389,315669) : difference with theory (-35) = 2 CORRECTING DEFECT 70 (vertices=1970, convex hull=583, v0=115182) XL defect detected... After retessellation of defect 70 (v0=115182), euler #=-36 (159002,475659,316621) : difference with theory (-34) = 2 CORRECTING DEFECT 71 (vertices=48, convex hull=68, v0=115744) After retessellation of defect 71 (v0=115744), euler #=-35 (159029,475766,316702) : difference with theory (-33) = 2 CORRECTING DEFECT 72 (vertices=48, convex hull=71, v0=116475) After retessellation of defect 72 (v0=116475), euler #=-34 (159038,475821,316749) : difference with theory (-32) = 2 CORRECTING DEFECT 73 (vertices=135, convex hull=144, v0=121405) After retessellation of defect 73 (v0=121405), euler #=-33 (159112,476106,316961) : difference with theory (-31) = 2 CORRECTING DEFECT 74 (vertices=35, convex hull=55, v0=123879) After retessellation of defect 74 (v0=123879), euler #=-32 (159130,476188,317026) : difference with theory (-30) = 2 CORRECTING DEFECT 75 (vertices=38, convex hull=19, v0=123938) After retessellation of defect 75 (v0=123938), euler #=-31 (159134,476205,317040) : difference with theory (-29) = 2 CORRECTING DEFECT 76 (vertices=352, convex hull=240, v0=123992) After retessellation of defect 76 (v0=123992), euler #=-30 (159168,476420,317222) : difference with theory (-28) = 2 CORRECTING DEFECT 77 (vertices=54, convex hull=42, v0=124126) After retessellation of defect 77 (v0=124126), euler #=-29 (159177,476460,317254) : difference with theory (-27) = 2 CORRECTING DEFECT 78 (vertices=319, convex hull=116, v0=124391) After retessellation of defect 78 (v0=124391), euler #=-28 (159198,476574,317348) : difference with theory (-26) = 2 CORRECTING DEFECT 79 (vertices=40, convex hull=50, v0=124436) After retessellation of defect 79 (v0=124436), euler #=-27 (159210,476629,317392) : difference with theory (-25) = 2 CORRECTING DEFECT 80 (vertices=353, convex hull=178, v0=128349) After retessellation of defect 80 (v0=128349), euler #=-26 (159310,477011,317675) : difference with theory (-24) = 2 CORRECTING DEFECT 81 (vertices=192, convex hull=146, v0=129529) After retessellation of defect 81 (v0=129529), euler #=-25 (159385,477313,317903) : difference with theory (-23) = 2 CORRECTING DEFECT 82 (vertices=24, convex hull=70, v0=133422) After retessellation of defect 82 (v0=133422), euler #=-24 (159401,477387,317962) : difference with theory (-22) = 2 CORRECTING DEFECT 83 (vertices=121, convex hull=140, v0=134413) After retessellation of defect 83 (v0=134413), euler #=-22 (159451,477601,318128) : difference with theory (-21) = 1 CORRECTING DEFECT 84 (vertices=189, convex hull=124, v0=137416) After retessellation of defect 84 (v0=137416), euler #=-21 (159469,477712,318222) : difference with theory (-20) = 1 CORRECTING DEFECT 85 (vertices=59, convex hull=54, v0=140396) After retessellation of defect 85 (v0=140396), euler #=-20 (159484,477778,318274) : difference with theory (-19) = 1 CORRECTING DEFECT 86 (vertices=412, convex hull=179, v0=143337) After retessellation of defect 86 (v0=143337), euler #=-19 (159581,478150,318550) : difference with theory (-18) = 1 CORRECTING DEFECT 87 (vertices=81, convex hull=101, v0=149604) After retessellation of defect 87 (v0=149604), euler #=-18 (159611,478279,318650) : difference with theory (-17) = 1 CORRECTING DEFECT 88 (vertices=72, convex hull=29, v0=152300) After retessellation of defect 88 (v0=152300), euler #=-17 (159613,478296,318666) : difference with theory (-16) = 1 CORRECTING DEFECT 89 (vertices=89, convex hull=127, v0=153501) After retessellation of defect 89 (v0=153501), euler #=-16 (159653,478474,318805) : difference with theory (-15) = 1 CORRECTING DEFECT 90 (vertices=49, convex hull=43, v0=154167) After retessellation of defect 90 (v0=154167), euler #=-15 (159661,478514,318838) : difference with theory (-14) = 1 CORRECTING DEFECT 91 (vertices=58, convex hull=96, v0=158119) After retessellation of defect 91 (v0=158119), euler #=-15 (159684,478628,318929) : difference with theory (-13) = 2 CORRECTING DEFECT 92 (vertices=40, convex hull=24, v0=158640) After retessellation of defect 92 (v0=158640), euler #=-14 (159687,478644,318943) : difference with theory (-12) = 2 CORRECTING DEFECT 93 (vertices=47, convex hull=81, v0=158691) After retessellation of defect 93 (v0=158691), euler #=-13 (159711,478754,319030) : difference with theory (-11) = 2 CORRECTING DEFECT 94 (vertices=31, convex hull=52, v0=159895) After retessellation of defect 94 (v0=159895), euler #=-11 (159712,478785,319062) : difference with theory (-10) = 1 CORRECTING DEFECT 95 (vertices=54, convex hull=76, v0=160084) After retessellation of defect 95 (v0=160084), euler #=-10 (159730,478873,319133) : difference with theory (-9) = 1 CORRECTING DEFECT 96 (vertices=48, convex hull=47, v0=161185) After retessellation of defect 96 (v0=161185), euler #=-9 (159736,478914,319169) : difference with theory (-8) = 1 CORRECTING DEFECT 97 (vertices=233, convex hull=147, v0=162026) After retessellation of defect 97 (v0=162026), euler #=-8 (159799,479173,319366) : difference with theory (-7) = 1 CORRECTING DEFECT 98 (vertices=69, convex hull=95, v0=165824) After retessellation of defect 98 (v0=165824), euler #=-7 (159834,479321,319480) : difference with theory (-6) = 1 CORRECTING DEFECT 99 (vertices=39, convex hull=62, v0=165959) After retessellation of defect 99 (v0=165959), euler #=-6 (159854,479403,319543) : difference with theory (-5) = 1 CORRECTING DEFECT 100 (vertices=52, convex hull=32, v0=166977) After retessellation of defect 100 (v0=166977), euler #=-5 (159856,479418,319557) : difference with theory (-4) = 1 CORRECTING DEFECT 101 (vertices=30, convex hull=37, v0=168434) After retessellation of defect 101 (v0=168434), euler #=-4 (159857,479435,319574) : difference with theory (-3) = 1 CORRECTING DEFECT 102 (vertices=36, convex hull=70, v0=168683) After retessellation of defect 102 (v0=168683), euler #=-3 (159868,479495,319624) : difference with theory (-2) = 1 CORRECTING DEFECT 103 (vertices=58, convex hull=80, v0=169808) After retessellation of defect 103 (v0=169808), euler #=-2 (159889,479589,319698) : difference with theory (-1) = 1 CORRECTING DEFECT 104 (vertices=14, convex hull=30, v0=169900) After retessellation of defect 104 (v0=169900), euler #=-1 (159890,479602,319711) : difference with theory (0) = 1 CORRECTING DEFECT 105 (vertices=59, convex hull=65, v0=169953) After retessellation of defect 105 (v0=169953), euler #=0 (159909,479688,319779) : difference with theory (1) = 1 CORRECTING DEFECT 106 (vertices=92, convex hull=77, v0=171367) After retessellation of defect 106 (v0=171367), euler #=2 (159921,479757,319838) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.29 (0.03-->16.29) (max @ vno 105861 --> 122187) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.29 (0.03-->16.29) (max @ vno 105861 --> 122187) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 290 mutations (32.2%), 611 crossovers (67.8%), 816 vertices were eliminated building final representation... 12253 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=159921, nf=319838, ne=479757, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 86.6 minutes 0 defective edges removing intersecting faces 000: 1135 intersecting 001: 27 intersecting mris_fix_topology utimesec 5196.526007 mris_fix_topology stimesec 0.649901 mris_fix_topology ru_maxrss 550368 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 65897 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 12128 mris_fix_topology ru_oublock 15896 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 612 mris_fix_topology ru_nivcsw 14443 FSRUNTIME@ mris_fix_topology lh 1.4436 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 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=-354 (nv=183780, nf=368268, ne=552402, g=178) 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... 41797 ambiguous faces found in tessellation segmenting defects... 106 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 39 into 18 -merging segment 27 into 26 -merging segment 38 into 37 -merging segment 44 into 37 102 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1383 (-4.5692) -vertex loglikelihood: -5.8863 (-2.9432) -normal dot loglikelihood: -3.5515 (-3.5515) -quad curv loglikelihood: -6.0103 (-3.0052) Total Loglikelihood : -24.5865 CORRECTING DEFECT 0 (vertices=37, convex hull=52, v0=0) After retessellation of defect 0 (v0=0), euler #=-90 (160015,473730,313625) : difference with theory (-99) = -9 CORRECTING DEFECT 1 (vertices=39, convex hull=27, v0=49) After retessellation of defect 1 (v0=49), euler #=-89 (160018,473747,313640) : difference with theory (-98) = -9 CORRECTING DEFECT 2 (vertices=126, convex hull=78, v0=54) After retessellation of defect 2 (v0=54), euler #=-88 (160030,473818,313700) : difference with theory (-97) = -9 CORRECTING DEFECT 3 (vertices=72, convex hull=99, v0=312) After retessellation of defect 3 (v0=312), euler #=-87 (160063,473960,313810) : difference with theory (-96) = -9 CORRECTING DEFECT 4 (vertices=203, convex hull=230, v0=504) After retessellation of defect 4 (v0=504), euler #=-86 (160144,474310,314080) : difference with theory (-95) = -9 CORRECTING DEFECT 5 (vertices=34, convex hull=89, v0=550) After retessellation of defect 5 (v0=550), euler #=-85 (160161,474395,314149) : difference with theory (-94) = -9 CORRECTING DEFECT 6 (vertices=124, convex hull=128, v0=658) After retessellation of defect 6 (v0=658), euler #=-84 (160208,474596,314304) : difference with theory (-93) = -9 CORRECTING DEFECT 7 (vertices=43, convex hull=74, v0=924) After retessellation of defect 7 (v0=924), euler #=-83 (160221,474665,314361) : difference with theory (-92) = -9 CORRECTING DEFECT 8 (vertices=723, convex hull=226, v0=1463) After retessellation of defect 8 (v0=1463), euler #=-82 (160329,475101,314690) : difference with theory (-91) = -9 CORRECTING DEFECT 9 (vertices=74, convex hull=88, v0=1785) After retessellation of defect 9 (v0=1785), euler #=-81 (160357,475225,314787) : difference with theory (-90) = -9 CORRECTING DEFECT 10 (vertices=25, convex hull=62, v0=2082) After retessellation of defect 10 (v0=2082), euler #=-80 (160369,475283,314834) : difference with theory (-89) = -9 CORRECTING DEFECT 11 (vertices=153, convex hull=143, v0=2328) After retessellation of defect 11 (v0=2328), euler #=-79 (160429,475529,315021) : difference with theory (-88) = -9 CORRECTING DEFECT 12 (vertices=274, convex hull=62, v0=2657) After retessellation of defect 12 (v0=2657), euler #=-78 (160445,475605,315082) : difference with theory (-87) = -9 CORRECTING DEFECT 13 (vertices=220, convex hull=177, v0=3059) After retessellation of defect 13 (v0=3059), euler #=-77 (160526,475921,315318) : difference with theory (-86) = -9 CORRECTING DEFECT 14 (vertices=58, convex hull=132, v0=3566) After retessellation of defect 14 (v0=3566), euler #=-76 (160558,476071,315437) : difference with theory (-85) = -9 CORRECTING DEFECT 15 (vertices=39, convex hull=75, v0=4530) After retessellation of defect 15 (v0=4530), euler #=-75 (160579,476167,315513) : difference with theory (-84) = -9 CORRECTING DEFECT 16 (vertices=14, convex hull=13, v0=6123) After retessellation of defect 16 (v0=6123), euler #=-74 (160579,476170,315517) : difference with theory (-83) = -9 CORRECTING DEFECT 17 (vertices=329, convex hull=50, v0=6143) After retessellation of defect 17 (v0=6143), euler #=-73 (160604,476265,315588) : difference with theory (-82) = -9 CORRECTING DEFECT 18 (vertices=5818, convex hull=1520, v0=6178) XL defect detected... After retessellation of defect 18 (v0=6178), euler #=-78 (161095,478550,317377) : difference with theory (-81) = -3 CORRECTING DEFECT 19 (vertices=75, convex hull=87, v0=6510) After retessellation of defect 19 (v0=6510), euler #=-77 (161111,478632,317444) : difference with theory (-80) = -3 CORRECTING DEFECT 20 (vertices=215, convex hull=222, v0=7492) After retessellation of defect 20 (v0=7492), euler #=-77 (161208,479032,317747) : difference with theory (-79) = -2 CORRECTING DEFECT 21 (vertices=35, convex hull=67, v0=10145) After retessellation of defect 21 (v0=10145), euler #=-76 (161217,479087,317794) : difference with theory (-78) = -2 CORRECTING DEFECT 22 (vertices=67, convex hull=80, v0=11171) After retessellation of defect 22 (v0=11171), euler #=-75 (161239,479184,317870) : difference with theory (-77) = -2 CORRECTING DEFECT 23 (vertices=47, convex hull=87, v0=13678) After retessellation of defect 23 (v0=13678), euler #=-74 (161259,479284,317951) : difference with theory (-76) = -2 CORRECTING DEFECT 24 (vertices=64, convex hull=33, v0=14984) After retessellation of defect 24 (v0=14984), euler #=-73 (161270,479327,317984) : difference with theory (-75) = -2 CORRECTING DEFECT 25 (vertices=43, convex hull=107, v0=18331) After retessellation of defect 25 (v0=18331), euler #=-72 (161297,479458,318089) : difference with theory (-74) = -2 CORRECTING DEFECT 26 (vertices=147, convex hull=232, v0=18468) After retessellation of defect 26 (v0=18468), euler #=-70 (161373,479799,318356) : difference with theory (-73) = -3 CORRECTING DEFECT 27 (vertices=232, convex hull=306, v0=25636) After retessellation of defect 27 (v0=25636), euler #=-69 (161481,480278,318728) : difference with theory (-72) = -3 CORRECTING DEFECT 28 (vertices=199, convex hull=163, v0=27626) After retessellation of defect 28 (v0=27626), euler #=-68 (161542,480537,318927) : difference with theory (-71) = -3 CORRECTING DEFECT 29 (vertices=85, convex hull=103, v0=30710) After retessellation of defect 29 (v0=30710), euler #=-67 (161587,480721,319067) : difference with theory (-70) = -3 CORRECTING DEFECT 30 (vertices=64, convex hull=76, v0=30737) After retessellation of defect 30 (v0=30737), euler #=-66 (161611,480827,319150) : difference with theory (-69) = -3 CORRECTING DEFECT 31 (vertices=34, convex hull=75, v0=37888) After retessellation of defect 31 (v0=37888), euler #=-65 (161629,480908,319214) : difference with theory (-68) = -3 CORRECTING DEFECT 32 (vertices=6, convex hull=22, v0=38071) After retessellation of defect 32 (v0=38071), euler #=-64 (161629,480913,319220) : difference with theory (-67) = -3 CORRECTING DEFECT 33 (vertices=6, convex hull=17, v0=38220) After retessellation of defect 33 (v0=38220), euler #=-63 (161630,480920,319227) : difference with theory (-66) = -3 CORRECTING DEFECT 34 (vertices=20, convex hull=22, v0=38369) After retessellation of defect 34 (v0=38369), euler #=-62 (161631,480931,319238) : difference with theory (-65) = -3 CORRECTING DEFECT 35 (vertices=12, convex hull=21, v0=41147) After retessellation of defect 35 (v0=41147), euler #=-61 (161634,480946,319251) : difference with theory (-64) = -3 CORRECTING DEFECT 36 (vertices=556, convex hull=392, v0=46035) After retessellation of defect 36 (v0=46035), euler #=-58 (161754,481512,319700) : difference with theory (-63) = -5 CORRECTING DEFECT 37 (vertices=774, convex hull=205, v0=66120) After retessellation of defect 37 (v0=66120), euler #=-57 (161798,481738,319883) : difference with theory (-62) = -5 CORRECTING DEFECT 38 (vertices=34, convex hull=50, v0=70793) After retessellation of defect 38 (v0=70793), euler #=-56 (161813,481801,319932) : difference with theory (-61) = -5 CORRECTING DEFECT 39 (vertices=165, convex hull=168, v0=70889) After retessellation of defect 39 (v0=70889), euler #=-55 (161907,482165,320203) : difference with theory (-60) = -5 CORRECTING DEFECT 40 (vertices=197, convex hull=199, v0=73834) After retessellation of defect 40 (v0=73834), euler #=-54 (161989,482506,320463) : difference with theory (-59) = -5 CORRECTING DEFECT 41 (vertices=31, convex hull=57, v0=74122) After retessellation of defect 41 (v0=74122), euler #=-53 (162002,482574,320519) : difference with theory (-58) = -5 CORRECTING DEFECT 42 (vertices=230, convex hull=309, v0=74758) After retessellation of defect 42 (v0=74758), euler #=-52 (162169,483227,321006) : difference with theory (-57) = -5 CORRECTING DEFECT 43 (vertices=76, convex hull=94, v0=80822) After retessellation of defect 43 (v0=80822), euler #=-51 (162187,483326,321088) : difference with theory (-56) = -5 CORRECTING DEFECT 44 (vertices=191, convex hull=233, v0=81364) After retessellation of defect 44 (v0=81364), euler #=-50 (162322,483840,321468) : difference with theory (-55) = -5 CORRECTING DEFECT 45 (vertices=45, convex hull=69, v0=83573) After retessellation of defect 45 (v0=83573), euler #=-49 (162347,483943,321547) : difference with theory (-54) = -5 CORRECTING DEFECT 46 (vertices=298, convex hull=332, v0=84908) After retessellation of defect 46 (v0=84908), euler #=-48 (162528,484636,322060) : difference with theory (-53) = -5 CORRECTING DEFECT 47 (vertices=65, convex hull=31, v0=86766) After retessellation of defect 47 (v0=86766), euler #=-47 (162533,484666,322086) : difference with theory (-52) = -5 CORRECTING DEFECT 48 (vertices=49, convex hull=71, v0=90673) After retessellation of defect 48 (v0=90673), euler #=-46 (162557,484771,322168) : difference with theory (-51) = -5 CORRECTING DEFECT 49 (vertices=158, convex hull=142, v0=90691) After retessellation of defect 49 (v0=90691), euler #=-46 (162614,485014,322354) : difference with theory (-50) = -4 CORRECTING DEFECT 50 (vertices=36, convex hull=66, v0=93452) After retessellation of defect 50 (v0=93452), euler #=-45 (162632,485090,322413) : difference with theory (-49) = -4 CORRECTING DEFECT 51 (vertices=114, convex hull=105, v0=94033) After retessellation of defect 51 (v0=94033), euler #=-44 (162672,485256,322540) : difference with theory (-48) = -4 CORRECTING DEFECT 52 (vertices=123, convex hull=91, v0=94392) After retessellation of defect 52 (v0=94392), euler #=-43 (162715,485426,322668) : difference with theory (-47) = -4 CORRECTING DEFECT 53 (vertices=895, convex hull=146, v0=101437) After retessellation of defect 53 (v0=101437), euler #=-42 (162769,485657,322846) : difference with theory (-46) = -4 CORRECTING DEFECT 54 (vertices=32, convex hull=38, v0=101458) After retessellation of defect 54 (v0=101458), euler #=-41 (162772,485684,322871) : difference with theory (-45) = -4 CORRECTING DEFECT 55 (vertices=19, convex hull=29, v0=102378) After retessellation of defect 55 (v0=102378), euler #=-40 (162775,485700,322885) : difference with theory (-44) = -4 CORRECTING DEFECT 56 (vertices=43, convex hull=37, v0=104074) After retessellation of defect 56 (v0=104074), euler #=-39 (162779,485726,322908) : difference with theory (-43) = -4 CORRECTING DEFECT 57 (vertices=1255, convex hull=311, v0=104364) After retessellation of defect 57 (v0=104364), euler #=-38 (163005,486562,323519) : difference with theory (-42) = -4 CORRECTING DEFECT 58 (vertices=32, convex hull=44, v0=105703) After retessellation of defect 58 (v0=105703), euler #=-37 (163021,486623,323565) : difference with theory (-41) = -4 CORRECTING DEFECT 59 (vertices=55, convex hull=61, v0=106032) After retessellation of defect 59 (v0=106032), euler #=-36 (163055,486750,323659) : difference with theory (-40) = -4 CORRECTING DEFECT 60 (vertices=35, convex hull=82, v0=106699) After retessellation of defect 60 (v0=106699), euler #=-35 (163070,486824,323719) : difference with theory (-39) = -4 CORRECTING DEFECT 61 (vertices=91, convex hull=126, v0=106766) After retessellation of defect 61 (v0=106766), euler #=-34 (163093,486947,323820) : difference with theory (-38) = -4 CORRECTING DEFECT 62 (vertices=10, convex hull=15, v0=108216) After retessellation of defect 62 (v0=108216), euler #=-33 (163094,486956,323829) : difference with theory (-37) = -4 CORRECTING DEFECT 63 (vertices=130, convex hull=37, v0=108784) After retessellation of defect 63 (v0=108784), euler #=-32 (163104,486997,323861) : difference with theory (-36) = -4 CORRECTING DEFECT 64 (vertices=25, convex hull=72, v0=109094) After retessellation of defect 64 (v0=109094), euler #=-31 (163118,487066,323917) : difference with theory (-35) = -4 CORRECTING DEFECT 65 (vertices=119, convex hull=154, v0=109223) After retessellation of defect 65 (v0=109223), euler #=-30 (163156,487254,324068) : difference with theory (-34) = -4 CORRECTING DEFECT 66 (vertices=1473, convex hull=583, v0=109735) XL defect detected... After retessellation of defect 66 (v0=109735), euler #=-31 (163364,488194,324799) : difference with theory (-33) = -2 CORRECTING DEFECT 67 (vertices=20, convex hull=52, v0=115296) After retessellation of defect 67 (v0=115296), euler #=-30 (163374,488243,324839) : difference with theory (-32) = -2 CORRECTING DEFECT 68 (vertices=41, convex hull=70, v0=116131) After retessellation of defect 68 (v0=116131), euler #=-29 (163397,488340,324914) : difference with theory (-31) = -2 CORRECTING DEFECT 69 (vertices=82, convex hull=125, v0=121326) After retessellation of defect 69 (v0=121326), euler #=-28 (163439,488523,325056) : difference with theory (-30) = -2 CORRECTING DEFECT 70 (vertices=2129, convex hull=777, v0=122199) XL defect detected... After retessellation of defect 70 (v0=122199), euler #=-29 (164084,490895,326782) : difference with theory (-29) = 0 CORRECTING DEFECT 71 (vertices=1604, convex hull=592, v0=126769) XL defect detected... After retessellation of defect 71 (v0=126769), euler #=-28 (164516,492512,327968) : difference with theory (-28) = 0 CORRECTING DEFECT 72 (vertices=17, convex hull=29, v0=130383) After retessellation of defect 72 (v0=130383), euler #=-27 (164519,492528,327982) : difference with theory (-27) = 0 CORRECTING DEFECT 73 (vertices=649, convex hull=366, v0=130457) After retessellation of defect 73 (v0=130457), euler #=-26 (164628,493041,328387) : difference with theory (-26) = 0 CORRECTING DEFECT 74 (vertices=49, convex hull=76, v0=132923) After retessellation of defect 74 (v0=132923), euler #=-25 (164637,493098,328436) : difference with theory (-25) = 0 CORRECTING DEFECT 75 (vertices=48, convex hull=66, v0=134859) After retessellation of defect 75 (v0=134859), euler #=-24 (164655,493178,328499) : difference with theory (-24) = 0 CORRECTING DEFECT 76 (vertices=27, convex hull=47, v0=134880) After retessellation of defect 76 (v0=134880), euler #=-23 (164669,493235,328543) : difference with theory (-23) = 0 CORRECTING DEFECT 77 (vertices=46, convex hull=70, v0=141204) After retessellation of defect 77 (v0=141204), euler #=-22 (164692,493333,328619) : difference with theory (-22) = 0 CORRECTING DEFECT 78 (vertices=38, convex hull=69, v0=141828) After retessellation of defect 78 (v0=141828), euler #=-21 (164711,493416,328684) : difference with theory (-21) = 0 CORRECTING DEFECT 79 (vertices=37, convex hull=32, v0=144433) After retessellation of defect 79 (v0=144433), euler #=-20 (164720,493453,328713) : difference with theory (-20) = 0 CORRECTING DEFECT 80 (vertices=512, convex hull=161, v0=149124) After retessellation of defect 80 (v0=149124), euler #=-19 (164767,493673,328887) : difference with theory (-19) = 0 CORRECTING DEFECT 81 (vertices=54, convex hull=38, v0=149353) After retessellation of defect 81 (v0=149353), euler #=-18 (164775,493711,328918) : difference with theory (-18) = 0 CORRECTING DEFECT 82 (vertices=36, convex hull=66, v0=150090) After retessellation of defect 82 (v0=150090), euler #=-17 (164785,493765,328963) : difference with theory (-17) = 0 CORRECTING DEFECT 83 (vertices=31, convex hull=42, v0=151509) After retessellation of defect 83 (v0=151509), euler #=-16 (164799,493824,329009) : difference with theory (-16) = 0 CORRECTING DEFECT 84 (vertices=29, convex hull=80, v0=154273) After retessellation of defect 84 (v0=154273), euler #=-15 (164817,493907,329075) : difference with theory (-15) = 0 CORRECTING DEFECT 85 (vertices=35, convex hull=33, v0=157124) After retessellation of defect 85 (v0=157124), euler #=-14 (164819,493926,329093) : difference with theory (-14) = 0 CORRECTING DEFECT 86 (vertices=34, convex hull=62, v0=160182) After retessellation of defect 86 (v0=160182), euler #=-13 (164832,493989,329144) : difference with theory (-13) = 0 CORRECTING DEFECT 87 (vertices=46, convex hull=99, v0=161060) After retessellation of defect 87 (v0=161060), euler #=-12 (164859,494114,329243) : difference with theory (-12) = 0 CORRECTING DEFECT 88 (vertices=50, convex hull=87, v0=163969) After retessellation of defect 88 (v0=163969), euler #=-11 (164894,494257,329352) : difference with theory (-11) = 0 CORRECTING DEFECT 89 (vertices=48, convex hull=83, v0=165360) After retessellation of defect 89 (v0=165360), euler #=-10 (164924,494385,329451) : difference with theory (-10) = 0 CORRECTING DEFECT 90 (vertices=18, convex hull=20, v0=166231) After retessellation of defect 90 (v0=166231), euler #=-9 (164924,494391,329458) : difference with theory (-9) = 0 CORRECTING DEFECT 91 (vertices=48, convex hull=42, v0=168051) After retessellation of defect 91 (v0=168051), euler #=-8 (164927,494418,329483) : difference with theory (-8) = 0 CORRECTING DEFECT 92 (vertices=150, convex hull=85, v0=169012) After retessellation of defect 92 (v0=169012), euler #=-7 (164943,494504,329554) : difference with theory (-7) = 0 CORRECTING DEFECT 93 (vertices=58, convex hull=94, v0=171278) After retessellation of defect 93 (v0=171278), euler #=-6 (164970,494623,329647) : difference with theory (-6) = 0 CORRECTING DEFECT 94 (vertices=11, convex hull=19, v0=173430) After retessellation of defect 94 (v0=173430), euler #=-5 (164971,494633,329657) : difference with theory (-5) = 0 CORRECTING DEFECT 95 (vertices=42, convex hull=20, v0=174261) After retessellation of defect 95 (v0=174261), euler #=-4 (164973,494646,329669) : difference with theory (-4) = 0 CORRECTING DEFECT 96 (vertices=99, convex hull=100, v0=175048) After retessellation of defect 96 (v0=175048), euler #=-3 (165006,494794,329785) : difference with theory (-3) = 0 CORRECTING DEFECT 97 (vertices=104, convex hull=95, v0=176136) After retessellation of defect 97 (v0=176136), euler #=-2 (165045,494956,329909) : difference with theory (-2) = 0 CORRECTING DEFECT 98 (vertices=180, convex hull=150, v0=180352) After retessellation of defect 98 (v0=180352), euler #=-1 (165109,495222,330112) : difference with theory (-1) = 0 CORRECTING DEFECT 99 (vertices=172, convex hull=122, v0=180447) After retessellation of defect 99 (v0=180447), euler #=0 (165155,495416,330261) : difference with theory (0) = 0 CORRECTING DEFECT 100 (vertices=42, convex hull=24, v0=180967) After retessellation of defect 100 (v0=180967), euler #=1 (165156,495426,330271) : difference with theory (1) = 0 CORRECTING DEFECT 101 (vertices=52, convex hull=92, v0=183295) After retessellation of defect 101 (v0=183295), euler #=2 (165183,495543,330362) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.32 (0.02-->28.62) (max @ vno 26853 --> 51271) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.32 (0.02-->28.62) (max @ vno 26853 --> 51271) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 263 mutations (32.5%), 545 crossovers (67.5%), 2111 vertices were eliminated building final representation... 18597 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=165183, nf=330362, ne=495543, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 226.2 minutes 0 defective edges removing intersecting faces 000: 1980 intersecting 001: 60 intersecting 002: 2 intersecting mris_fix_topology utimesec 13573.626495 mris_fix_topology stimesec 0.542917 mris_fix_topology ru_maxrss 682248 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 71948 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 35984 mris_fix_topology ru_oublock 16536 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 479 mris_fix_topology ru_nivcsw 21178 FSRUNTIME@ mris_fix_topology rh 3.7701 hours 1 threads PIDs (16546 16549) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 159921 - 479757 + 319838 = 2 --> 0 holes F =2V-4: 319838 = 319842-4 (0) 2E=3F: 959514 = 959514 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 165183 - 495543 + 330362 = 2 --> 0 holes F =2V-4: 330362 = 330366-4 (0) 2E=3F: 991086 = 991086 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 265 intersecting 001: 15 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 670 intersecting 001: 75 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Oct 8 07:54:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 lh #-------------------------------------------- #@# Make White Surf rh Sun Oct 8 07:54:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 rh Waiting for PID 25932 of (25932 25935) to complete... Waiting for PID 25935 of (25932 25935) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... 17660 bright wm thresholded. 2039 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.orig... computing class statistics... border white: 320647 voxels (1.91%) border gray 377071 voxels (2.25%) WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0] GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.4 (was 70) setting MAX_BORDER_WHITE to 106.8 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 91.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 58.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.3 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.24 (0.02-->6.08) (max @ vno 56130 --> 60727) face area 0.28 +- 0.14 (0.00-->9.12) mean absolute distance = 0.68 +- 0.85 4499 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=99+-6.1, GM=69+-7.0 mean inside = 91.5, mean outside = 75.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=81.2, 202 (202) missing vertices, mean dist 0.2 [0.6 (%40.1)->0.7 (%59.9))] %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.27 (0.09-->6.24) (max @ vno 54871 --> 60605) face area 0.28 +- 0.14 (0.00-->9.51) mean absolute distance = 0.37 +- 0.66 5058 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3082067.2, rms=8.847 001: dt: 0.5000, sse=1891597.5, rms=6.396 (27.704%) 002: dt: 0.5000, sse=1387078.4, rms=4.957 (22.502%) 003: dt: 0.5000, sse=1172859.1, rms=4.201 (15.248%) 004: dt: 0.5000, sse=1078760.6, rms=3.809 (9.326%) 005: dt: 0.5000, sse=1025619.2, rms=3.573 (6.198%) 006: dt: 0.5000, sse=981190.0, rms=3.375 (5.544%) 007: dt: 0.5000, sse=958772.1, rms=3.266 (3.236%) 008: dt: 0.5000, sse=943257.4, rms=3.177 (2.717%) rms = 3.14, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=938490.4, rms=3.140 (1.182%) 010: dt: 0.2500, sse=795710.2, rms=2.180 (30.575%) 011: dt: 0.2500, sse=771011.6, rms=1.976 (9.335%) 012: dt: 0.2500, sse=764212.8, rms=1.923 (2.693%) rms = 1.89, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=760691.6, rms=1.892 (1.598%) rms = 1.86, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=756203.1, rms=1.862 (1.597%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... mean border=83.1, 248 (80) missing vertices, mean dist -0.2 [0.4 (%63.8)->0.3 (%36.2))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.26 (0.05-->6.74) (max @ vno 54871 --> 60605) face area 0.35 +- 0.18 (0.00-->13.17) mean absolute distance = 0.32 +- 0.49 4911 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1228946.9, rms=3.734 015: dt: 0.5000, sse=1016613.8, rms=2.614 (29.984%) 016: dt: 0.5000, sse=985590.4, rms=2.483 (5.028%) rms = 2.54, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=918147.9, rms=1.964 (20.909%) 018: dt: 0.2500, sse=888911.6, rms=1.686 (14.136%) 019: dt: 0.2500, sse=895696.8, rms=1.628 (3.465%) rms = 1.60, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=889456.4, rms=1.603 (1.521%) rms = 1.56, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=876294.9, rms=1.561 (2.600%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=84.4, 272 (57) missing vertices, mean dist -0.1 [0.4 (%58.7)->0.2 (%41.3))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.26 (0.04-->6.92) (max @ vno 60727 --> 56130) face area 0.34 +- 0.18 (0.00-->13.38) mean absolute distance = 0.31 +- 0.43 4211 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=980696.7, rms=2.505 022: dt: 0.5000, sse=930464.1, rms=2.096 (16.345%) rms = 2.17, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=877605.4, rms=1.683 (19.700%) 024: dt: 0.2500, sse=860596.7, rms=1.496 (11.082%) rms = 1.45, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=856533.9, rms=1.453 (2.862%) rms = 1.41, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=850404.4, rms=1.412 (2.877%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=85.0, 264 (47) missing vertices, mean dist -0.1 [0.3 (%52.7)->0.3 (%47.3))] %84 local maxima, %11 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-6.0.0/0050352/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=878171.2, rms=1.765 027: dt: 0.5000, sse=865516.9, rms=1.611 (8.763%) rms = 1.93, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=831873.9, rms=1.282 (20.413%) 029: dt: 0.2500, sse=830962.7, rms=1.206 (5.948%) rms = 1.17, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=832184.2, rms=1.172 (2.816%) rms = 1.13, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=817161.9, rms=1.129 (3.681%) positioning took 0.7 minutes generating cortex label... 12 non-cortical segments detected only using segment with 8687 vertices erasing segment 1 (vno[0] = 75424) erasing segment 2 (vno[0] = 93729) erasing segment 3 (vno[0] = 97178) erasing segment 4 (vno[0] = 97732) erasing segment 5 (vno[0] = 102244) erasing segment 6 (vno[0] = 104586) erasing segment 7 (vno[0] = 110172) erasing segment 8 (vno[0] = 111346) erasing segment 9 (vno[0] = 112461) erasing segment 10 (vno[0] = 112487) erasing segment 11 (vno[0] = 157738) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.area vertex spacing 0.90 +- 0.27 (0.03-->7.14) (max @ vno 56130 --> 60727) face area 0.34 +- 0.18 (0.00-->13.23) refinement took 5.8 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... 17660 bright wm thresholded. 2039 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.orig... computing class statistics... border white: 320647 voxels (1.91%) border gray 377071 voxels (2.25%) WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0] GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.4 (was 70) setting MAX_BORDER_WHITE to 105.8 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 50.9 (was 40) setting MAX_GRAY to 90.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.3 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.25 (0.01-->6.59) (max @ vno 78197 --> 162389) face area 0.28 +- 0.14 (0.00-->5.58) mean absolute distance = 0.67 +- 0.85 4694 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=98+-6.1, GM=72+-6.1 mean inside = 91.3, mean outside = 76.8 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=83.3, 281 (281) missing vertices, mean dist 0.1 [0.7 (%45.7)->0.7 (%54.3))] %75 local maxima, %21 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 0.90 +- 0.27 (0.05-->6.73) (max @ vno 108009 --> 163207) face area 0.28 +- 0.14 (0.00-->6.30) mean absolute distance = 0.39 +- 0.67 5920 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2532878.8, rms=7.445 001: dt: 0.5000, sse=1471837.1, rms=5.038 (32.338%) 002: dt: 0.5000, sse=1075899.8, rms=3.608 (28.370%) 003: dt: 0.5000, sse=940748.9, rms=2.980 (17.415%) 004: dt: 0.5000, sse=900906.0, rms=2.756 (7.520%) 005: dt: 0.5000, sse=883643.8, rms=2.669 (3.137%) rms = 2.64, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=883764.4, rms=2.645 (0.931%) 007: dt: 0.2500, sse=773817.1, rms=1.790 (32.303%) 008: dt: 0.2500, sse=757897.6, rms=1.627 (9.133%) rms = 1.60, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=757189.0, rms=1.599 (1.699%) rms = 1.58, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=752244.0, rms=1.575 (1.491%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=85.1, 269 (73) missing vertices, mean dist -0.2 [0.5 (%63.5)->0.3 (%36.5))] %79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.27 (0.07-->7.48) (max @ vno 108009 --> 163207) face area 0.34 +- 0.17 (0.00-->8.98) mean absolute distance = 0.33 +- 0.51 5228 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1178558.2, rms=3.371 011: dt: 0.5000, sse=982478.4, rms=2.257 (33.041%) 012: dt: 0.5000, sse=953683.6, rms=2.086 (7.596%) rms = 2.13, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=906935.5, rms=1.704 (18.306%) 014: dt: 0.2500, sse=889747.2, rms=1.505 (11.657%) rms = 1.46, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=890636.4, rms=1.462 (2.872%) rms = 1.43, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=884202.3, rms=1.434 (1.918%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.1, 277 (46) missing vertices, mean dist -0.1 [0.4 (%57.6)->0.3 (%42.4))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.27 (0.05-->8.01) (max @ vno 108009 --> 163207) face area 0.33 +- 0.17 (0.00-->9.26) mean absolute distance = 0.32 +- 0.43 4522 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=974259.8, rms=2.280 017: dt: 0.5000, sse=921469.2, rms=1.811 (20.545%) rms = 1.83, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=883277.1, rms=1.517 (16.252%) 019: dt: 0.2500, sse=872877.5, rms=1.368 (9.818%) rms = 1.33, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=869855.9, rms=1.332 (2.640%) rms = 1.31, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=863920.9, rms=1.307 (1.888%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=86.7, 328 (41) missing vertices, mean dist -0.0 [0.3 (%52.3)->0.3 (%47.7))] %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-6.0.0/0050352/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=883245.9, rms=1.585 022: dt: 0.5000, sse=878382.7, rms=1.314 (17.056%) rms = 1.65, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=841154.0, rms=1.094 (16.745%) rms = 1.08, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=855674.2, rms=1.082 (1.162%) rms = 1.04, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=833807.8, rms=1.038 (4.021%) positioning took 0.6 minutes generating cortex label... 6 non-cortical segments detected only using segment with 7856 vertices erasing segment 1 (vno[0] = 115541) erasing segment 2 (vno[0] = 116581) erasing segment 3 (vno[0] = 116654) erasing segment 4 (vno[0] = 117658) erasing segment 5 (vno[0] = 164558) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.area vertex spacing 0.89 +- 0.27 (0.03-->8.41) (max @ vno 108009 --> 163207) face area 0.33 +- 0.17 (0.00-->9.70) refinement took 5.3 minutes PIDs (25932 25935) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sun Oct 8 08:00:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sun Oct 8 08:00:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 26264 of (26264 26267) to complete... Waiting for PID 26267 of (26264 26267) 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 (26264 26267) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sun Oct 8 08:00:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sun Oct 8 08:00:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 26313 of (26313 26316) to complete... Waiting for PID 26316 of (26313 26316) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 48.6 mm, total surface area = 96635 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=0.130 (target=0.015) step 010: RMS=0.100 (target=0.015) step 015: RMS=0.084 (target=0.015) step 020: RMS=0.071 (target=0.015) step 025: RMS=0.060 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.044 (target=0.015) step 040: RMS=0.040 (target=0.015) step 045: RMS=0.035 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. inflation took 0.8 minutes mris_inflate utimesec 49.088537 mris_inflate stimesec 0.105983 mris_inflate ru_maxrss 234812 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 34239 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11248 mris_inflate ru_oublock 12528 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2264 mris_inflate ru_nivcsw 3943 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 48.8 mm, total surface area = 97735 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.188 (target=0.015) step 005: RMS=0.133 (target=0.015) step 010: RMS=0.106 (target=0.015) step 015: RMS=0.089 (target=0.015) step 020: RMS=0.075 (target=0.015) step 025: RMS=0.064 (target=0.015) step 030: RMS=0.057 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.044 (target=0.015) step 045: RMS=0.039 (target=0.015) step 050: RMS=0.036 (target=0.015) step 055: RMS=0.033 (target=0.015) step 060: RMS=0.031 (target=0.015) inflation complete. inflation took 0.8 minutes mris_inflate utimesec 50.675296 mris_inflate stimesec 0.115982 mris_inflate ru_maxrss 242716 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 35192 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11624 mris_inflate ru_oublock 12936 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2232 mris_inflate ru_nivcsw 3813 PIDs (26313 26316) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sun Oct 8 08:01:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Sun Oct 8 08:01:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 26427 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... Waiting for PID 26430 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... Waiting for PID 26433 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... Waiting for PID 26436 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... Waiting for PID 26439 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... Waiting for PID 26442 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... Waiting for PID 26445 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... Waiting for PID 26448 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... Waiting for PID 26451 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... Waiting for PID 26454 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... Waiting for PID 26457 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... Waiting for PID 26460 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 18.035*4pi (226.639) --> -17 handles ICI = 281.1, FI = 2023.5, variation=34940.246 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 202 vertices thresholded to be in k1 ~ [-0.34 0.79], k2 ~ [-0.12 0.08] total integrated curvature = 0.289*4pi (3.628) --> 1 handles ICI = 1.5, FI = 11.0, variation=183.930 139 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 165 vertices thresholded to be in [-0.17 0.36] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.025 done. mris_curvature -w rh.white.preaparc total integrated curvature = 26.619*4pi (334.505) --> -26 handles ICI = 326.0, FI = 2252.8, variation=39306.423 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 228 vertices thresholded to be in k1 ~ [-0.47 0.96], k2 ~ [-0.15 0.08] total integrated curvature = 0.252*4pi (3.169) --> 1 handles ICI = 1.5, FI = 12.1, variation=198.815 178 vertices thresholded to be in [-0.04 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 162 vertices thresholded to be in [-0.21 0.40] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.027 done. PIDs (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sun Oct 8 08:02:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050352 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 [ 0050352/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 [ 285 ] Gb_filter = 0 #----------------------------------------- #@# Curvature Stats rh Sun Oct 8 08:03:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050352 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 [ 0050352/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 [ 326 ] Gb_filter = 0 WARN: S lookup min: -0.429441 WARN: S explicit min: 0.000000 vertex = 384 #-------------------------------------------- #@# Sphere lh Sun Oct 8 08:03:07 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sun Oct 8 08:03:07 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 26628 of (26628 26631) to complete... Waiting for PID 26631 of (26628 26631) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0.275... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.03 pass 1: epoch 2 of 3 starting distance error %19.95 unfolding complete - removing small folds... starting distance error %19.82 removing remaining folds... final distance error %19.85 MRISunfold() return, current seed 1234 -01: dt=0.0000, 191 negative triangles 265: dt=0.9900, 191 negative triangles 266: dt=0.9900, 111 negative triangles 267: dt=0.9900, 91 negative triangles 268: dt=0.9900, 64 negative triangles 269: dt=0.9900, 65 negative triangles 270: dt=0.9900, 62 negative triangles 271: dt=0.9900, 44 negative triangles 272: dt=0.9900, 39 negative triangles 273: dt=0.9900, 35 negative triangles 274: dt=0.9900, 22 negative triangles 275: dt=0.9900, 19 negative triangles 276: dt=0.9900, 20 negative triangles 277: dt=0.9900, 22 negative triangles 278: dt=0.9900, 16 negative triangles 279: dt=0.9900, 16 negative triangles 280: dt=0.9900, 16 negative triangles 281: dt=0.9900, 13 negative triangles 282: dt=0.9900, 14 negative triangles 283: dt=0.9900, 8 negative triangles 284: dt=0.9900, 6 negative triangles 285: dt=0.9900, 10 negative triangles 286: dt=0.9900, 5 negative triangles 287: dt=0.9900, 3 negative triangles 288: dt=0.9900, 2 negative triangles 289: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.31 hours mris_sphere utimesec 4711.910680 mris_sphere stimesec 1.819723 mris_sphere ru_maxrss 328888 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 57908 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 11296 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 171646 mris_sphere ru_nivcsw 378217 FSRUNTIME@ mris_sphere 1.3070 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0.274... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.19 pass 1: epoch 2 of 3 starting distance error %20.07 unfolding complete - removing small folds... starting distance error %19.89 removing remaining folds... final distance error %19.92 MRISunfold() return, current seed 1234 -01: dt=0.0000, 389 negative triangles 249: dt=0.9900, 389 negative triangles 250: dt=0.9900, 203 negative triangles 251: dt=0.9900, 157 negative triangles 252: dt=0.9900, 145 negative triangles 253: dt=0.9900, 141 negative triangles 254: dt=0.9900, 128 negative triangles 255: dt=0.9900, 133 negative triangles 256: dt=0.9900, 116 negative triangles 257: dt=0.9900, 112 negative triangles 258: dt=0.9900, 104 negative triangles 259: dt=0.9900, 105 negative triangles 260: dt=0.9900, 100 negative triangles 261: dt=0.9900, 97 negative triangles 262: dt=0.9900, 89 negative triangles 263: dt=0.9900, 82 negative triangles 264: dt=0.9900, 70 negative triangles 265: dt=0.9900, 74 negative triangles 266: dt=0.9900, 67 negative triangles 267: dt=0.9900, 62 negative triangles 268: dt=0.9900, 53 negative triangles 269: dt=0.9900, 57 negative triangles 270: dt=0.9900, 45 negative triangles 271: dt=0.9900, 40 negative triangles 272: dt=0.9900, 42 negative triangles 273: dt=0.9900, 35 negative triangles 274: dt=0.9900, 28 negative triangles 275: dt=0.9900, 23 negative triangles 276: dt=0.9900, 19 negative triangles 277: dt=0.9900, 18 negative triangles 278: dt=0.9900, 11 negative triangles 279: dt=0.9900, 8 negative triangles 280: dt=0.9900, 9 negative triangles 281: dt=0.9900, 7 negative triangles 282: dt=0.9900, 6 negative triangles 283: dt=0.9900, 3 negative triangles 284: dt=0.9900, 3 negative triangles 285: dt=0.9900, 7 negative triangles 286: dt=0.9900, 7 negative triangles 287: dt=0.9900, 1 negative triangles 288: dt=0.9900, 2 negative triangles 289: dt=0.9900, 5 negative triangles 290: dt=0.9900, 2 negative triangles 291: dt=0.9900, 1 negative triangles 292: dt=0.9900, 2 negative triangles 293: dt=0.9900, 1 negative triangles 294: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.30 hours mris_sphere utimesec 4694.641306 mris_sphere stimesec 1.756732 mris_sphere ru_maxrss 339468 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 59532 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 11680 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 166518 mris_sphere ru_nivcsw 377580 FSRUNTIME@ mris_sphere 1.3044 hours 1 threads PIDs (26628 26631) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sun Oct 8 09:21:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Sun Oct 8 09:21:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 29352 of (29352 29355) to complete... Waiting for PID 29355 of (29352 29355) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 5.778 curvature mean = 0.029, std = 0.820 curvature mean = 0.017, std = 0.856 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, 0.00, 8.00) sse = 345354.8, tmin=2.4124 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 325031.6, tmin=3.6389 d=8.00 min @ (2.00, 0.00, -2.00) sse = 319974.4, tmin=4.8967 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 319718.5, tmin=6.1683 d=2.00 min @ (0.50, 0.50, 0.50) sse = 319282.7, tmin=7.4417 d=1.00 min @ (0.00, -0.25, 0.00) sse = 319194.3, tmin=8.6926 tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 9.93 min curvature mean = -0.013, std = 0.823 curvature mean = 0.005, std = 0.942 curvature mean = -0.021, std = 0.831 curvature mean = 0.002, std = 0.976 curvature mean = -0.025, std = 0.831 curvature mean = 0.000, std = 0.989 2 Reading smoothwm curvature mean = -0.035, std = 0.298 curvature mean = 0.034, std = 0.244 curvature mean = 0.069, std = 0.325 curvature mean = 0.031, std = 0.301 curvature mean = 0.053, std = 0.493 curvature mean = 0.030, std = 0.325 curvature mean = 0.032, std = 0.636 curvature mean = 0.030, std = 0.336 curvature mean = 0.013, std = 0.751 MRISregister() return, current seed 0 -01: dt=0.0000, 162 negative triangles 139: dt=0.9900, 162 negative triangles 140: dt=0.9405, 207 negative triangles expanding nbhd size to 1 141: dt=0.9900, 179 negative triangles 142: dt=0.9900, 145 negative triangles 143: dt=0.9900, 142 negative triangles 144: dt=0.9900, 143 negative triangles 145: dt=0.9900, 133 negative triangles 146: dt=0.9900, 130 negative triangles 147: dt=0.9900, 116 negative triangles 148: dt=0.9900, 127 negative triangles 149: dt=0.9900, 116 negative triangles 150: dt=0.9900, 108 negative triangles 151: dt=0.9900, 106 negative triangles 152: dt=0.9900, 102 negative triangles 153: dt=0.9900, 100 negative triangles 154: dt=0.9900, 95 negative triangles 155: dt=0.9900, 88 negative triangles 156: dt=0.9900, 83 negative triangles 157: dt=0.9900, 85 negative triangles 158: dt=0.9900, 74 negative triangles 159: dt=0.9900, 72 negative triangles 160: dt=0.9900, 75 negative triangles 161: dt=0.9900, 69 negative triangles 162: dt=0.9900, 62 negative triangles 163: dt=0.9900, 53 negative triangles 164: dt=0.9900, 57 negative triangles 165: dt=0.9900, 52 negative triangles 166: dt=0.9900, 47 negative triangles 167: dt=0.9900, 47 negative triangles 168: dt=0.9900, 44 negative triangles 169: dt=0.9900, 47 negative triangles 170: dt=0.9900, 43 negative triangles 171: dt=0.9900, 41 negative triangles 172: dt=0.9900, 40 negative triangles 173: dt=0.9900, 38 negative triangles 174: dt=0.9900, 35 negative triangles 175: dt=0.9900, 35 negative triangles 176: dt=0.9900, 28 negative triangles 177: dt=0.9900, 26 negative triangles 178: dt=0.9900, 17 negative triangles 179: dt=0.9900, 22 negative triangles 180: dt=0.9900, 22 negative triangles 181: dt=0.9900, 19 negative triangles 182: dt=0.9900, 16 negative triangles 183: dt=0.9900, 15 negative triangles 184: dt=0.9900, 13 negative triangles 185: dt=0.9900, 14 negative triangles 186: dt=0.9900, 12 negative triangles 187: dt=0.9900, 13 negative triangles 188: dt=0.9900, 9 negative triangles 189: dt=0.9900, 14 negative triangles 190: dt=0.9900, 11 negative triangles 191: dt=0.9900, 10 negative triangles 192: dt=0.9900, 10 negative triangles 193: dt=0.9900, 13 negative triangles 194: dt=0.9900, 8 negative triangles 195: dt=0.9900, 7 negative triangles 196: dt=0.9900, 6 negative triangles 197: dt=0.9900, 2 negative triangles 198: dt=0.9900, 5 negative triangles 199: dt=0.9900, 4 negative triangles 200: dt=0.9900, 1 negative triangles 201: dt=0.9900, 3 negative triangles 202: dt=0.9900, 2 negative triangles 203: dt=0.9900, 1 negative triangles 204: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.77 hours mris_register utimesec 6351.960355 mris_register stimesec 5.284196 mris_register ru_maxrss 289340 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 41427 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 11344 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 459768 mris_register ru_nivcsw 292004 FSRUNTIME@ mris_register 1.7656 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 5.765 curvature mean = 0.022, std = 0.803 curvature mean = 0.020, std = 0.854 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 377729.0, tmin=1.2466 d=16.00 min @ (0.00, -4.00, 0.00) sse = 355968.7, tmin=3.7840 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 355588.5, tmin=5.0671 d=4.00 min @ (1.00, 0.00, 0.00) sse = 354644.7, tmin=6.3627 d=2.00 min @ (0.00, 0.50, -0.50) sse = 354321.5, tmin=7.6612 d=1.00 min @ (0.00, 0.00, 0.25) sse = 354289.4, tmin=8.9429 d=0.50 min @ (0.00, -0.12, 0.00) sse = 354264.6, tmin=10.2319 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 10.23 min curvature mean = -0.014, std = 0.806 curvature mean = 0.005, std = 0.942 curvature mean = -0.021, std = 0.813 curvature mean = 0.002, std = 0.975 curvature mean = -0.024, std = 0.813 curvature mean = 0.000, std = 0.989 2 Reading smoothwm curvature mean = -0.041, std = 0.359 curvature mean = 0.029, std = 0.239 curvature mean = 0.068, std = 0.269 curvature mean = 0.021, std = 0.297 curvature mean = 0.053, std = 0.406 curvature mean = 0.020, std = 0.324 curvature mean = 0.035, std = 0.525 curvature mean = 0.019, std = 0.335 curvature mean = 0.016, std = 0.632 MRISregister() return, current seed 0 -01: dt=0.0000, 362 negative triangles 137: dt=0.9900, 362 negative triangles expanding nbhd size to 1 138: dt=0.9900, 391 negative triangles 139: dt=0.9900, 351 negative triangles 140: dt=0.9900, 323 negative triangles 141: dt=0.9900, 325 negative triangles 142: dt=0.9900, 323 negative triangles 143: dt=0.9900, 301 negative triangles 144: dt=0.9900, 287 negative triangles 145: dt=0.9900, 275 negative triangles 146: dt=0.9900, 254 negative triangles 147: dt=0.9900, 243 negative triangles 148: dt=0.9900, 224 negative triangles 149: dt=0.9900, 218 negative triangles 150: dt=0.9900, 208 negative triangles 151: dt=0.9900, 200 negative triangles 152: dt=0.9900, 182 negative triangles 153: dt=0.9900, 184 negative triangles 154: dt=0.9900, 172 negative triangles 155: dt=0.9900, 168 negative triangles 156: dt=0.9900, 157 negative triangles 157: dt=0.9900, 142 negative triangles 158: dt=0.9900, 142 negative triangles 159: dt=0.9900, 142 negative triangles 160: dt=0.9900, 122 negative triangles 161: dt=0.9900, 114 negative triangles 162: dt=0.9900, 106 negative triangles 163: dt=0.9900, 101 negative triangles 164: dt=0.9900, 98 negative triangles 165: dt=0.9900, 91 negative triangles 166: dt=0.9900, 86 negative triangles 167: dt=0.9900, 78 negative triangles 168: dt=0.9900, 78 negative triangles 169: dt=0.9900, 71 negative triangles 170: dt=0.9900, 73 negative triangles 171: dt=0.9900, 61 negative triangles 172: dt=0.9900, 67 negative triangles 173: dt=0.9900, 64 negative triangles 174: dt=0.9900, 57 negative triangles 175: dt=0.9900, 54 negative triangles 176: dt=0.9900, 57 negative triangles 177: dt=0.9900, 51 negative triangles 178: dt=0.9900, 55 negative triangles 179: dt=0.9900, 49 negative triangles 180: dt=0.9900, 51 negative triangles 181: dt=0.9900, 46 negative triangles 182: dt=0.9900, 42 negative triangles 183: dt=0.9900, 46 negative triangles 184: dt=0.9900, 45 negative triangles 185: dt=0.9900, 46 negative triangles 186: dt=0.9900, 42 negative triangles 187: dt=0.9900, 39 negative triangles 188: dt=0.9900, 38 negative triangles 189: dt=0.9900, 38 negative triangles 190: dt=0.9900, 36 negative triangles 191: dt=0.9900, 35 negative triangles 192: dt=0.9900, 34 negative triangles 193: dt=0.9900, 32 negative triangles 194: dt=0.9900, 33 negative triangles 195: dt=0.9900, 32 negative triangles 196: dt=0.9900, 31 negative triangles 197: dt=0.9900, 31 negative triangles 198: dt=0.9900, 34 negative triangles 199: dt=0.9900, 33 negative triangles 200: dt=0.9900, 31 negative triangles 201: dt=0.9900, 30 negative triangles 202: dt=0.9900, 30 negative triangles 203: dt=0.9900, 30 negative triangles 204: dt=0.9900, 30 negative triangles 205: dt=0.9900, 29 negative triangles 206: dt=0.9900, 28 negative triangles 207: dt=0.9900, 27 negative triangles 208: dt=0.9900, 28 negative triangles 209: dt=0.9900, 28 negative triangles 210: dt=0.9900, 28 negative triangles 211: dt=0.9900, 26 negative triangles 212: dt=0.9900, 26 negative triangles 213: dt=0.9900, 26 negative triangles 214: dt=0.9900, 25 negative triangles 215: dt=0.9900, 25 negative triangles 216: dt=0.9900, 25 negative triangles 217: dt=0.9900, 27 negative triangles 218: dt=0.9900, 27 negative triangles 219: dt=0.9900, 26 negative triangles 220: dt=0.9900, 25 negative triangles 221: dt=0.9900, 25 negative triangles 222: dt=0.9900, 26 negative triangles 223: dt=0.9900, 26 negative triangles 224: dt=0.9405, 27 negative triangles 225: dt=0.9405, 24 negative triangles 226: dt=0.9405, 24 negative triangles 227: dt=0.9405, 25 negative triangles 228: dt=0.9405, 23 negative triangles 229: dt=0.9405, 23 negative triangles 230: dt=0.9405, 23 negative triangles 231: dt=0.9405, 21 negative triangles 232: dt=0.9405, 21 negative triangles 233: dt=0.9405, 21 negative triangles 234: dt=0.9405, 23 negative triangles 235: dt=0.9405, 21 negative triangles 236: dt=0.9405, 21 negative triangles 237: dt=0.9405, 22 negative triangles 238: dt=0.9405, 21 negative triangles 239: dt=0.9405, 21 negative triangles 240: dt=0.9405, 19 negative triangles 241: dt=0.9405, 20 negative triangles 242: dt=0.9405, 21 negative triangles 243: dt=0.9405, 21 negative triangles 244: dt=0.9405, 20 negative triangles 245: dt=0.9405, 19 negative triangles 246: dt=0.9405, 19 negative triangles 247: dt=0.9405, 20 negative triangles 248: dt=0.9405, 22 negative triangles 249: dt=0.9405, 19 negative triangles 250: dt=0.8935, 19 negative triangles 251: dt=0.8935, 21 negative triangles 252: dt=0.8935, 22 negative triangles 253: dt=0.8935, 19 negative triangles 254: dt=0.8935, 19 negative triangles 255: dt=0.8935, 17 negative triangles 256: dt=0.8935, 21 negative triangles 257: dt=0.8935, 20 negative triangles 258: dt=0.8935, 20 negative triangles 259: dt=0.8935, 17 negative triangles 260: dt=0.8935, 15 negative triangles 261: dt=0.8935, 15 negative triangles 262: dt=0.8935, 15 negative triangles 263: dt=0.8935, 16 negative triangles 264: dt=0.8935, 16 negative triangles 265: dt=0.8935, 16 negative triangles 266: dt=0.8935, 15 negative triangles 267: dt=0.8935, 16 negative triangles 268: dt=0.8935, 15 negative triangles 269: dt=0.8935, 15 negative triangles 270: dt=0.8488, 15 negative triangles 271: dt=0.8488, 16 negative triangles 272: dt=0.8488, 15 negative triangles 273: dt=0.8488, 15 negative triangles 274: dt=0.8488, 15 negative triangles 275: dt=0.8488, 15 negative triangles 276: dt=0.8488, 14 negative triangles 277: dt=0.8488, 14 negative triangles 278: dt=0.8488, 14 negative triangles 279: dt=0.8488, 15 negative triangles 280: dt=0.8488, 14 negative triangles 281: dt=0.8488, 13 negative triangles 282: dt=0.8488, 13 negative triangles 283: dt=0.8488, 14 negative triangles 284: dt=0.8488, 14 negative triangles 285: dt=0.8488, 13 negative triangles 286: dt=0.8488, 12 negative triangles 287: dt=0.8488, 13 negative triangles 288: dt=0.8488, 13 negative triangles 289: dt=0.8488, 12 negative triangles 290: dt=0.8488, 10 negative triangles 291: dt=0.8488, 10 negative triangles 292: dt=0.8488, 12 negative triangles 293: dt=0.8488, 10 negative triangles 294: dt=0.8488, 10 negative triangles 295: dt=0.8488, 9 negative triangles 296: dt=0.8488, 10 negative triangles 297: dt=0.8488, 10 negative triangles 298: dt=0.8488, 9 negative triangles 299: dt=0.8488, 10 negative triangles 300: dt=0.8488, 9 negative triangles 301: dt=0.8488, 9 negative triangles 302: dt=0.8488, 9 negative triangles 303: dt=0.8488, 9 negative triangles 304: dt=0.8488, 8 negative triangles 305: dt=0.8488, 8 negative triangles 306: dt=0.8488, 6 negative triangles 307: dt=0.8488, 6 negative triangles 308: dt=0.8488, 8 negative triangles 309: dt=0.8488, 5 negative triangles 310: dt=0.8488, 5 negative triangles 311: dt=0.8488, 5 negative triangles 312: dt=0.8488, 5 negative triangles 313: dt=0.8488, 6 negative triangles 314: dt=0.8488, 6 negative triangles 315: dt=0.8488, 5 negative triangles 316: dt=0.8488, 3 negative triangles 317: dt=0.8488, 3 negative triangles 318: dt=0.8488, 3 negative triangles 319: dt=0.8488, 2 negative triangles 320: dt=0.8488, 2 negative triangles 321: dt=0.8488, 2 negative triangles 322: dt=0.8488, 1 negative triangles 323: dt=0.8488, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.85 hours mris_register utimesec 6859.043266 mris_register stimesec 5.310192 mris_register ru_maxrss 296560 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 41995 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 11736 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 470326 mris_register ru_nivcsw 283907 FSRUNTIME@ mris_register 1.8520 hours 1 threads PIDs (29352 29355) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 11:12:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 11:12:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 1039 of (1039 1042) to complete... Waiting for PID 1042 of (1039 1042) 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 (1039 1042) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 11:12:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Sun Oct 8 11:12:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 1084 of (1084 1087) to complete... Waiting for PID 1087 of (1084 1087) 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 (1084 1087) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 11:12:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Sun Oct 8 11:12:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 1131 of (1131 1134) to complete... Waiting for PID 1134 of (1131 1134) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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... 1134 labels changed using aseg relabeling using gibbs priors... 000: 3637 changed, 159921 examined... 001: 846 changed, 14944 examined... 002: 206 changed, 4666 examined... 003: 66 changed, 1266 examined... 004: 26 changed, 377 examined... 005: 14 changed, 160 examined... 006: 4 changed, 68 examined... 007: 4 changed, 28 examined... 008: 2 changed, 17 examined... 009: 5 changed, 14 examined... 010: 0 changed, 16 examined... 254 labels changed using aseg 000: 136 total segments, 88 labels (376 vertices) changed 001: 48 total segments, 3 labels (6 vertices) changed 002: 45 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2165 vertices marked for relabeling... 2165 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 16 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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... 1295 labels changed using aseg relabeling using gibbs priors... 000: 3003 changed, 165183 examined... 001: 719 changed, 12988 examined... 002: 183 changed, 4005 examined... 003: 58 changed, 1085 examined... 004: 27 changed, 371 examined... 005: 6 changed, 160 examined... 006: 2 changed, 35 examined... 007: 1 changed, 14 examined... 008: 1 changed, 7 examined... 009: 1 changed, 7 examined... 010: 1 changed, 7 examined... 011: 1 changed, 7 examined... 012: 0 changed, 7 examined... 169 labels changed using aseg 000: 104 total segments, 66 labels (298 vertices) changed 001: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2155 vertices marked for relabeling... 2155 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 16 seconds. PIDs (1131 1134) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 11:13:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 11:13:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 rh Waiting for PID 1182 of (1182 1185) to complete... Waiting for PID 1185 of (1182 1185) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... 17660 bright wm thresholded. 2039 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.orig... computing class statistics... border white: 320647 voxels (1.91%) border gray 377071 voxels (2.25%) WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0] GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.4 (was 70) setting MAX_BORDER_WHITE to 106.8 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 91.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 58.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.3 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=99+-6.1, GM=69+-7.0 mean inside = 91.5, mean outside = 75.7 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.27 (0.03-->7.14) (max @ vno 56130 --> 60727) face area 0.34 +- 0.18 (0.00-->13.14) mean absolute distance = 0.53 +- 0.83 4140 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 20 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 120 points - only 0.00% unknown deleting segment 4 with 90 points - only 0.00% unknown deleting segment 6 with 225 points - only 0.00% unknown deleting segment 8 with 35 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown deleting segment 12 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown deleting segment 14 with 123 points - only 0.00% unknown removing 3 vertex label from ripped group mean border=81.0, 275 (275) missing vertices, mean dist 0.3 [0.6 (%22.9)->0.5 (%77.1))] %69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.27 (0.07-->6.86) (max @ vno 54871 --> 65504) face area 0.34 +- 0.18 (0.00-->12.46) mean absolute distance = 0.37 +- 0.65 4881 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1860433.5, rms=5.948 001: dt: 0.5000, sse=1218953.2, rms=3.797 (36.168%) 002: dt: 0.5000, sse=1052613.9, rms=3.018 (20.523%) 003: dt: 0.5000, sse=1023272.9, rms=2.873 (4.800%) 004: dt: 0.5000, sse=1011710.2, rms=2.778 (3.287%) rms = 2.85, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=915516.4, rms=2.138 (23.035%) 006: dt: 0.2500, sse=882689.1, rms=1.827 (14.571%) 007: dt: 0.2500, sse=874442.1, rms=1.755 (3.953%) rms = 1.73, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=872185.0, rms=1.732 (1.310%) rms = 1.70, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=868741.6, rms=1.696 (2.044%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 17 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 112 points - only 0.00% unknown deleting segment 3 with 72 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 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 74 points - only 0.00% unknown deleting segment 7 with 35 points - only 0.00% unknown deleting segment 8 with 37 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 107 points - only 0.00% unknown mean border=83.1, 215 (105) missing vertices, mean dist -0.2 [0.4 (%63.9)->0.3 (%36.1))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.27 (0.05-->7.03) (max @ vno 54871 --> 65504) face area 0.35 +- 0.19 (0.00-->13.62) mean absolute distance = 0.32 +- 0.49 5031 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1197210.9, rms=3.535 010: dt: 0.5000, sse=1002927.2, rms=2.429 (31.283%) 011: dt: 0.5000, sse=980718.8, rms=2.327 (4.183%) rms = 2.44, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=913009.9, rms=1.804 (22.480%) 013: dt: 0.2500, sse=891020.9, rms=1.545 (14.373%) rms = 1.51, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=888721.8, rms=1.513 (2.045%) rms = 1.48, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=882428.0, rms=1.483 (2.027%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 17 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 115 points - only 0.00% unknown deleting segment 3 with 73 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 166 points - only 0.00% unknown deleting segment 6 with 43 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 40 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 105 points - only 0.00% unknown mean border=84.4, 236 (77) missing vertices, mean dist -0.1 [0.4 (%59.0)->0.2 (%41.0))] %81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.27 (0.04-->7.03) (max @ vno 54871 --> 65504) face area 0.34 +- 0.18 (0.00-->13.46) mean absolute distance = 0.31 +- 0.43 4151 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=983497.1, rms=2.471 016: dt: 0.5000, sse=943433.1, rms=2.062 (16.528%) rms = 2.14, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=885016.3, rms=1.647 (20.141%) 018: dt: 0.2500, sse=890783.4, rms=1.461 (11.320%) rms = 1.41, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=860965.7, rms=1.412 (3.306%) rms = 1.37, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=854889.4, rms=1.375 (2.666%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 17 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 119 points - only 0.00% unknown deleting segment 3 with 74 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown deleting segment 5 with 172 points - only 0.00% unknown deleting segment 6 with 43 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 40 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 108 points - only 0.00% unknown mean border=85.0, 247 (64) missing vertices, mean dist -0.1 [0.3 (%52.7)->0.3 (%47.3))] %84 local maxima, %11 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-6.0.0/0050352/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=882570.6, rms=1.744 021: dt: 0.5000, sse=875049.6, rms=1.582 (9.302%) rms = 1.90, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=836627.6, rms=1.242 (21.473%) 023: dt: 0.2500, sse=837364.1, rms=1.192 (4.035%) rms = 1.15, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=827933.8, rms=1.146 (3.908%) rms = 1.10, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=823017.5, rms=1.099 (4.073%) positioning took 0.7 minutes generating cortex label... 9 non-cortical segments detected only using segment with 8702 vertices erasing segment 1 (vno[0] = 97732) erasing segment 2 (vno[0] = 102244) erasing segment 3 (vno[0] = 104586) erasing segment 4 (vno[0] = 107961) erasing segment 5 (vno[0] = 110172) erasing segment 6 (vno[0] = 111346) erasing segment 7 (vno[0] = 112461) erasing segment 8 (vno[0] = 112487) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.area vertex spacing 0.90 +- 0.27 (0.05-->6.97) (max @ vno 98357 --> 157869) face area 0.34 +- 0.18 (0.00-->13.04) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 80 points - only 0.00% unknown deleting segment 1 with 13 points - only 0.00% unknown deleting segment 3 with 36 points - only 0.00% unknown deleting segment 5 with 20 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown deleting segment 7 with 25 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 50.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=57.5, 264 (264) missing vertices, mean dist 1.6 [1.1 (%0.0)->2.9 (%100.0))] %13 local maxima, %37 large gradients and %45 min vals, 692 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=25308272.0, rms=28.348 001: dt: 0.0500, sse=22638340.0, rms=26.761 (5.598%) 002: dt: 0.0500, sse=20707266.0, rms=25.552 (4.519%) 003: dt: 0.0500, sse=19205946.0, rms=24.570 (3.841%) 004: dt: 0.0500, sse=17974636.0, rms=23.735 (3.400%) 005: dt: 0.0500, sse=16924140.0, rms=22.998 (3.104%) 006: dt: 0.0500, sse=16002985.0, rms=22.332 (2.897%) 007: dt: 0.0500, sse=15178845.0, rms=21.719 (2.747%) 008: dt: 0.0500, sse=14430951.0, rms=21.146 (2.634%) 009: dt: 0.0500, sse=13743778.0, rms=20.607 (2.552%) 010: dt: 0.0500, sse=13108337.0, rms=20.095 (2.485%) positioning took 1.1 minutes mean border=57.3, 235 (154) missing vertices, mean dist 1.3 [0.5 (%0.0)->2.4 (%100.0))] %14 local maxima, %38 large gradients and %44 min vals, 633 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=14032075.0, rms=20.834 011: dt: 0.0500, sse=13433637.0, rms=20.358 (2.286%) 012: dt: 0.0500, sse=12874301.0, rms=19.902 (2.237%) 013: dt: 0.0500, sse=12349945.0, rms=19.465 (2.194%) 014: dt: 0.0500, sse=11857777.0, rms=19.046 (2.153%) 015: dt: 0.0500, sse=11395210.0, rms=18.644 (2.114%) 016: dt: 0.0500, sse=10960952.0, rms=18.258 (2.071%) 017: dt: 0.0500, sse=10553168.0, rms=17.887 (2.028%) 018: dt: 0.0500, sse=10170341.0, rms=17.533 (1.983%) 019: dt: 0.0500, sse=9810546.0, rms=17.192 (1.940%) 020: dt: 0.0500, sse=9472828.0, rms=16.867 (1.894%) positioning took 1.1 minutes mean border=57.2, 268 (119) missing vertices, mean dist 1.1 [0.1 (%1.4)->2.1 (%98.6))] %14 local maxima, %37 large gradients and %44 min vals, 602 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=9571632.0, rms=16.968 021: dt: 0.0500, sse=9245767.0, rms=16.649 (1.876%) 022: dt: 0.0500, sse=8940497.0, rms=16.345 (1.825%) 023: dt: 0.0500, sse=8652347.0, rms=16.053 (1.788%) 024: dt: 0.0500, sse=8382553.0, rms=15.775 (1.736%) 025: dt: 0.0500, sse=8129841.0, rms=15.509 (1.684%) 026: dt: 0.0500, sse=7892888.5, rms=15.256 (1.634%) 027: dt: 0.0500, sse=7669313.0, rms=15.012 (1.593%) 028: dt: 0.0500, sse=7456474.5, rms=14.777 (1.567%) 029: dt: 0.0500, sse=7253870.0, rms=14.550 (1.540%) 030: dt: 0.0500, sse=7061353.5, rms=14.330 (1.510%) positioning took 1.1 minutes mean border=57.2, 321 (99) missing vertices, mean dist 0.9 [0.1 (%11.0)->2.0 (%89.0))] %14 local maxima, %38 large gradients and %43 min vals, 601 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=7135658.5, rms=14.414 031: dt: 0.5000, sse=5781775.5, rms=12.777 (11.363%) 032: dt: 0.5000, sse=4890548.0, rms=11.564 (9.492%) 033: dt: 0.5000, sse=4245457.0, rms=10.601 (8.326%) 034: dt: 0.5000, sse=3765931.5, rms=9.817 (7.399%) 035: dt: 0.5000, sse=3374981.5, rms=9.130 (6.990%) 036: dt: 0.5000, sse=3036233.5, rms=8.488 (7.037%) 037: dt: 0.5000, sse=2733787.8, rms=7.875 (7.215%) 038: dt: 0.5000, sse=2472625.8, rms=7.302 (7.282%) 039: dt: 0.5000, sse=2252052.8, rms=6.785 (7.081%) 040: dt: 0.5000, sse=2083718.1, rms=6.357 (6.304%) 041: dt: 0.5000, sse=1957419.4, rms=6.021 (5.295%) 042: dt: 0.5000, sse=1878639.0, rms=5.796 (3.725%) 043: dt: 0.5000, sse=1823120.5, rms=5.637 (2.754%) 044: dt: 0.5000, sse=1789904.5, rms=5.535 (1.812%) 045: dt: 0.5000, sse=1765039.5, rms=5.461 (1.326%) rms = 5.42, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1753900.0, rms=5.424 (0.681%) 047: dt: 0.2500, sse=1666929.5, rms=5.114 (5.721%) 048: dt: 0.2500, sse=1642357.4, rms=5.032 (1.600%) rms = 5.03, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1641327.5, rms=5.026 (0.112%) 050: dt: 0.1250, sse=1623718.8, rms=4.963 (1.264%) rms = 4.95, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1620277.9, rms=4.951 (0.233%) positioning took 3.2 minutes mean border=56.3, 3115 (28) missing vertices, mean dist 0.2 [0.2 (%47.8)->0.7 (%52.2))] %22 local maxima, %32 large gradients and %39 min vals, 322 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=1840226.4, rms=5.043 052: dt: 0.5000, sse=1730001.0, rms=4.685 (7.089%) 053: dt: 0.5000, sse=1655061.0, rms=4.441 (5.209%) rms = 4.51, time step reduction 1 of 3 to 0.250... 054: dt: 0.2500, sse=1571264.8, rms=4.080 (8.130%) 055: dt: 0.2500, sse=1546017.9, rms=3.962 (2.905%) rms = 3.94, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1540530.9, rms=3.939 (0.586%) 057: dt: 0.1250, sse=1518452.0, rms=3.836 (2.611%) rms = 3.81, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1513212.5, rms=3.814 (0.564%) positioning took 1.4 minutes mean border=55.9, 3568 (21) missing vertices, mean dist 0.1 [0.2 (%49.2)->0.5 (%50.8))] %29 local maxima, %27 large gradients and %38 min vals, 403 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=1559771.0, rms=3.996 rms = 4.20, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1533505.9, rms=3.882 (2.835%) rms = 3.84, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=1520918.6, rms=3.835 (1.212%) 061: dt: 0.1250, sse=1509364.4, rms=3.781 (1.413%) rms = 3.76, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=1502854.0, rms=3.755 (0.677%) positioning took 0.9 minutes mean border=55.4, 7211 (21) missing vertices, mean dist 0.1 [0.2 (%48.6)->0.4 (%51.4))] %33 local maxima, %22 large gradients and %36 min vals, 439 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-6.0.0/0050352/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1530470.5, rms=3.858 rms = 3.93, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=1508682.0, rms=3.765 (2.412%) 064: dt: 0.2500, sse=1484530.5, rms=3.677 (2.330%) rms = 3.63, time step reduction 2 of 3 to 0.125... 065: dt: 0.2500, sse=1471231.2, rms=3.627 (1.356%) 066: dt: 0.1250, sse=1453012.9, rms=3.539 (2.421%) rms = 3.51, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1445074.5, rms=3.507 (0.911%) positioning took 1.2 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.area.pial vertex spacing 1.01 +- 0.46 (0.05-->8.40) (max @ vno 157872 --> 98357) face area 0.40 +- 0.34 (0.00-->9.18) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 159921 vertices processed 25000 of 159921 vertices processed 50000 of 159921 vertices processed 75000 of 159921 vertices processed 100000 of 159921 vertices processed 125000 of 159921 vertices processed 150000 of 159921 vertices processed 0 of 159921 vertices processed 25000 of 159921 vertices processed 50000 of 159921 vertices processed 75000 of 159921 vertices processed 100000 of 159921 vertices processed 125000 of 159921 vertices processed 150000 of 159921 vertices processed thickness calculation complete, 422:976 truncations. 33870 vertices at 0 distance 105995 vertices at 1 distance 96590 vertices at 2 distance 44343 vertices at 3 distance 15718 vertices at 4 distance 5428 vertices at 5 distance 2027 vertices at 6 distance 882 vertices at 7 distance 366 vertices at 8 distance 191 vertices at 9 distance 97 vertices at 10 distance 63 vertices at 11 distance 48 vertices at 12 distance 32 vertices at 13 distance 33 vertices at 14 distance 20 vertices at 15 distance 13 vertices at 16 distance 11 vertices at 17 distance 20 vertices at 18 distance 18 vertices at 19 distance 19 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.thickness positioning took 17.7 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... 17660 bright wm thresholded. 2039 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.orig... computing class statistics... border white: 320647 voxels (1.91%) border gray 377071 voxels (2.25%) WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0] GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.4 (was 70) setting MAX_BORDER_WHITE to 105.8 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 50.9 (was 40) setting MAX_GRAY to 90.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.3 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=98+-6.1, GM=72+-6.1 mean inside = 91.3, mean outside = 76.8 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.27 (0.03-->8.41) (max @ vno 108009 --> 163207) face area 0.33 +- 0.17 (0.00-->9.65) mean absolute distance = 0.54 +- 0.85 4536 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 69 points - only 0.00% unknown deleting segment 2 with 14 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown deleting segment 4 with 245 points - only 0.00% unknown deleting segment 5 with 68 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 9 with 48 points - only 0.00% unknown mean border=83.2, 397 (395) missing vertices, mean dist 0.2 [0.6 (%24.2)->0.5 (%75.8))] %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.27 (0.02-->7.79) (max @ vno 108009 --> 163207) face area 0.33 +- 0.17 (0.00-->9.26) mean absolute distance = 0.39 +- 0.67 5808 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1698331.2, rms=5.326 001: dt: 0.5000, sse=1155934.9, rms=3.366 (36.794%) 002: dt: 0.5000, sse=1011278.4, rms=2.639 (21.618%) 003: dt: 0.5000, sse=984570.6, rms=2.483 (5.904%) 004: dt: 0.5000, sse=971679.3, rms=2.406 (3.094%) rms = 2.46, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=909869.0, rms=1.915 (20.420%) 006: dt: 0.2500, sse=889970.2, rms=1.674 (12.600%) 007: dt: 0.2500, sse=884931.4, rms=1.621 (3.136%) rms = 1.60, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=880575.8, rms=1.603 (1.136%) rms = 1.58, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=877829.0, rms=1.577 (1.581%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 18 points - only 0.00% unknown deleting segment 1 with 18 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 3 with 254 points - only 0.00% unknown deleting segment 4 with 66 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown deleting segment 6 with 48 points - only 0.00% unknown mean border=85.0, 324 (137) missing vertices, mean dist -0.2 [0.5 (%63.5)->0.3 (%36.5))] %79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.27 (0.06-->8.06) (max @ vno 108009 --> 163207) face area 0.34 +- 0.18 (0.00-->10.21) mean absolute distance = 0.33 +- 0.50 5672 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1159586.9, rms=3.229 010: dt: 0.5000, sse=988661.1, rms=2.131 (34.020%) 011: dt: 0.5000, sse=959757.2, rms=1.974 (7.334%) rms = 2.07, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=916613.5, rms=1.607 (18.625%) 013: dt: 0.2500, sse=903480.8, rms=1.430 (10.968%) rms = 1.40, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=893121.4, rms=1.405 (1.797%) rms = 1.38, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=893205.6, rms=1.385 (1.400%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 45 points - only 0.00% unknown deleting segment 1 with 27 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 3 with 234 points - only 0.00% unknown deleting segment 4 with 58 points - only 0.00% unknown deleting segment 5 with 47 points - only 0.00% unknown mean border=86.1, 369 (93) missing vertices, mean dist -0.1 [0.4 (%57.6)->0.3 (%42.4))] %83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.27 (0.09-->8.28) (max @ vno 108009 --> 163207) face area 0.34 +- 0.18 (0.00-->10.30) mean absolute distance = 0.31 +- 0.42 4387 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=973929.6, rms=2.231 016: dt: 0.5000, sse=924500.6, rms=1.772 (20.595%) rms = 1.79, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=888262.7, rms=1.475 (16.730%) 018: dt: 0.2500, sse=876876.8, rms=1.334 (9.564%) rms = 1.30, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=877732.0, rms=1.303 (2.335%) rms = 1.28, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=874149.6, rms=1.282 (1.581%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 35 points - only 0.00% unknown deleting segment 1 with 27 points - only 0.00% unknown deleting segment 2 with 12 points - only 0.00% unknown deleting segment 3 with 72 points - only 0.00% unknown deleting segment 4 with 242 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 47 points - only 0.00% unknown mean border=86.7, 439 (77) missing vertices, mean dist -0.0 [0.3 (%52.4)->0.3 (%47.6))] %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-6.0.0/0050352/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=894350.3, rms=1.576 021: dt: 0.5000, sse=875687.2, rms=1.303 (17.329%) rms = 1.64, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=846503.8, rms=1.085 (16.787%) rms = 1.07, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=845152.2, rms=1.069 (1.432%) rms = 1.03, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=845954.6, rms=1.031 (3.511%) positioning took 0.6 minutes generating cortex label... 7 non-cortical segments detected only using segment with 7827 vertices erasing segment 1 (vno[0] = 115541) erasing segment 2 (vno[0] = 116581) erasing segment 3 (vno[0] = 116654) erasing segment 4 (vno[0] = 117658) erasing segment 5 (vno[0] = 161798) erasing segment 6 (vno[0] = 164558) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.area vertex spacing 0.89 +- 0.28 (0.05-->8.65) (max @ vno 108009 --> 163207) face area 0.33 +- 0.18 (0.00-->10.30) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown deleting segment 2 with 27 points - only 0.00% unknown deleting segment 5 with 13 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 8 with 29 points - only 0.00% unknown deleting segment 9 with 29 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=60.7, 386 (386) missing vertices, mean dist 1.5 [0.9 (%0.0)->3.2 (%100.0))] %13 local maxima, %31 large gradients and %52 min vals, 708 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=23544016.0, rms=26.808 001: dt: 0.0500, sse=21158642.0, rms=25.364 (5.387%) 002: dt: 0.0500, sse=19439606.0, rms=24.269 (4.314%) 003: dt: 0.0500, sse=18106188.0, rms=23.385 (3.643%) 004: dt: 0.0500, sse=17012138.0, rms=22.634 (3.213%) 005: dt: 0.0500, sse=16080095.0, rms=21.974 (2.918%) 006: dt: 0.0500, sse=15263386.0, rms=21.378 (2.710%) 007: dt: 0.0500, sse=14532609.0, rms=20.831 (2.561%) 008: dt: 0.0500, sse=13868393.0, rms=20.320 (2.450%) 009: dt: 0.0500, sse=13257501.0, rms=19.839 (2.367%) 010: dt: 0.0500, sse=12691906.0, rms=19.383 (2.299%) positioning took 1.1 minutes mean border=60.6, 399 (223) missing vertices, mean dist 1.3 [0.3 (%0.1)->2.7 (%99.9))] %13 local maxima, %31 large gradients and %51 min vals, 659 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=13666072.0, rms=20.157 011: dt: 0.0500, sse=13131304.0, rms=19.734 (2.102%) 012: dt: 0.0500, sse=12630489.0, rms=19.328 (2.053%) 013: dt: 0.0500, sse=12159891.0, rms=18.940 (2.011%) 014: dt: 0.0500, sse=11716678.0, rms=18.566 (1.973%) 015: dt: 0.0500, sse=11299747.0, rms=18.207 (1.931%) 016: dt: 0.0500, sse=10906847.0, rms=17.863 (1.892%) 017: dt: 0.0500, sse=10535416.0, rms=17.531 (1.859%) 018: dt: 0.0500, sse=10185154.0, rms=17.212 (1.820%) 019: dt: 0.0500, sse=9854004.0, rms=16.905 (1.785%) 020: dt: 0.0500, sse=9540912.0, rms=16.609 (1.750%) positioning took 1.1 minutes mean border=60.5, 449 (186) missing vertices, mean dist 1.1 [0.1 (%1.1)->2.4 (%98.9))] %14 local maxima, %31 large gradients and %51 min vals, 605 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=9662268.0, rms=16.729 021: dt: 0.0500, sse=9360278.0, rms=16.440 (1.723%) 022: dt: 0.0500, sse=9075914.0, rms=16.164 (1.680%) 023: dt: 0.0500, sse=8806216.0, rms=15.898 (1.649%) 024: dt: 0.0500, sse=8552253.0, rms=15.643 (1.605%) 025: dt: 0.0500, sse=8312879.0, rms=15.398 (1.563%) 026: dt: 0.0500, sse=8087369.5, rms=15.164 (1.520%) 027: dt: 0.0500, sse=7873863.0, rms=14.939 (1.484%) 028: dt: 0.0500, sse=7670987.0, rms=14.722 (1.453%) 029: dt: 0.0500, sse=7477895.0, rms=14.512 (1.425%) 030: dt: 0.0500, sse=7294061.0, rms=14.309 (1.396%) positioning took 1.1 minutes mean border=60.5, 495 (166) missing vertices, mean dist 1.0 [0.1 (%8.1)->2.2 (%91.9))] %14 local maxima, %32 large gradients and %50 min vals, 594 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=7372661.5, rms=14.396 031: dt: 0.5000, sse=6077852.5, rms=12.890 (10.461%) 032: dt: 0.5000, sse=5201354.5, rms=11.754 (8.816%) 033: dt: 0.5000, sse=4577101.5, rms=10.872 (7.502%) 034: dt: 0.5000, sse=4091796.0, rms=10.128 (6.847%) 035: dt: 0.5000, sse=3686014.2, rms=9.463 (6.568%) 036: dt: 0.5000, sse=3328144.2, rms=8.834 (6.648%) 037: dt: 0.5000, sse=3000743.5, rms=8.219 (6.961%) 038: dt: 0.5000, sse=2703600.8, rms=7.617 (7.317%) 039: dt: 0.5000, sse=2457405.8, rms=7.083 (7.015%) 040: dt: 0.5000, sse=2257831.5, rms=6.616 (6.591%) 041: dt: 0.5000, sse=2112330.2, rms=6.255 (5.456%) 042: dt: 0.5000, sse=2011447.5, rms=5.989 (4.248%) 043: dt: 0.5000, sse=1941394.0, rms=5.800 (3.165%) 044: dt: 0.5000, sse=1897147.0, rms=5.673 (2.190%) 045: dt: 0.5000, sse=1862829.9, rms=5.576 (1.704%) 046: dt: 0.5000, sse=1840550.9, rms=5.509 (1.209%) rms = 5.48, time step reduction 1 of 3 to 0.250... 047: dt: 0.5000, sse=1829233.5, rms=5.476 (0.590%) 048: dt: 0.2500, sse=1758783.9, rms=5.228 (4.527%) 049: dt: 0.2500, sse=1734882.9, rms=5.155 (1.405%) rms = 5.16, time step reduction 2 of 3 to 0.125... rms = 5.13, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1728468.1, rms=5.133 (0.433%) positioning took 3.3 minutes mean border=59.9, 3726 (80) missing vertices, mean dist 0.2 [0.2 (%46.7)->0.8 (%53.3))] %22 local maxima, %27 large gradients and %45 min vals, 326 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=1890522.4, rms=5.077 051: dt: 0.5000, sse=1769510.8, rms=4.696 (7.507%) 052: dt: 0.5000, sse=1702250.6, rms=4.490 (4.378%) rms = 4.54, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1630112.0, rms=4.191 (6.678%) 054: dt: 0.2500, sse=1608542.9, rms=4.094 (2.305%) rms = 4.08, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1604928.6, rms=4.081 (0.321%) 056: dt: 0.1250, sse=1582783.6, rms=3.984 (2.363%) rms = 3.96, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1576792.2, rms=3.961 (0.585%) positioning took 1.6 minutes mean border=59.7, 4608 (59) missing vertices, mean dist 0.1 [0.2 (%49.2)->0.6 (%50.8))] %27 local maxima, %22 large gradients and %44 min vals, 416 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=1617004.6, rms=4.125 rms = 4.30, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1588824.6, rms=4.013 (2.723%) rms = 3.96, time step reduction 2 of 3 to 0.125... 059: dt: 0.2500, sse=1574283.1, rms=3.963 (1.241%) rms = 3.92, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1564297.1, rms=3.919 (1.116%) positioning took 0.8 minutes mean border=59.3, 8959 (57) missing vertices, mean dist 0.1 [0.2 (%47.8)->0.5 (%52.2))] %30 local maxima, %18 large gradients and %42 min vals, 488 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-6.0.0/0050352/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1581459.5, rms=3.981 rms = 4.02, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1556718.1, rms=3.883 (2.439%) 062: dt: 0.2500, sse=1528161.5, rms=3.787 (2.481%) rms = 3.75, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1515412.2, rms=3.746 (1.099%) 064: dt: 0.1250, sse=1496270.0, rms=3.660 (2.292%) rms = 3.63, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1487238.0, rms=3.626 (0.930%) positioning took 1.3 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.area.pial vertex spacing 0.99 +- 0.45 (0.07-->8.25) (max @ vno 111440 --> 109158) face area 0.39 +- 0.34 (0.00-->18.90) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 165183 vertices processed 25000 of 165183 vertices processed 50000 of 165183 vertices processed 75000 of 165183 vertices processed 100000 of 165183 vertices processed 125000 of 165183 vertices processed 150000 of 165183 vertices processed 0 of 165183 vertices processed 25000 of 165183 vertices processed 50000 of 165183 vertices processed 75000 of 165183 vertices processed 100000 of 165183 vertices processed 125000 of 165183 vertices processed 150000 of 165183 vertices processed thickness calculation complete, 583:1261 truncations. 32117 vertices at 0 distance 105552 vertices at 1 distance 99434 vertices at 2 distance 48548 vertices at 3 distance 18979 vertices at 4 distance 7284 vertices at 5 distance 2823 vertices at 6 distance 1178 vertices at 7 distance 547 vertices at 8 distance 268 vertices at 9 distance 165 vertices at 10 distance 91 vertices at 11 distance 60 vertices at 12 distance 57 vertices at 13 distance 43 vertices at 14 distance 28 vertices at 15 distance 27 vertices at 16 distance 16 vertices at 17 distance 28 vertices at 18 distance 24 vertices at 19 distance 43 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.thickness positioning took 18.4 minutes PIDs (1182 1185) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 11:31:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label Total face volume 282813 Total vertex volume 279572 (mask=0) #@# 0050352 lh 279572 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 11:31:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label Total face volume 289365 Total vertex volume 286560 (mask=0) #@# 0050352 rh 286560 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 11:31:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 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 = 466 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/ribbon.mgz mris_volmask took 14.24 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 11:45:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 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 0050352 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 11:45:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 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 0050352 rh pial Waiting for PID 2294 of (2294 2297 2300 2303) to complete... Waiting for PID 2297 of (2294 2297 2300 2303) to complete... Waiting for PID 2300 of (2294 2297 2300 2303) to complete... Waiting for PID 2303 of (2294 2297 2300 2303) 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 0050352 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813 Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 1461 999 2374 2.693 0.525 0.112 0.026 10 1.5 bankssts 1379 902 2794 2.736 0.810 0.147 0.031 21 1.7 caudalanteriorcingulate 4942 3281 9181 2.583 0.617 0.119 0.030 45 5.8 caudalmiddlefrontal 2515 1686 3664 1.999 0.541 0.151 0.051 38 5.2 cuneus 1146 725 2011 2.411 0.784 0.172 0.085 23 4.7 entorhinal 5233 3572 9651 2.386 0.655 0.141 0.050 74 10.8 fusiform 6776 4505 12637 2.390 0.634 0.131 0.035 79 9.7 inferiorparietal 5852 4013 13137 2.571 0.869 0.147 0.055 121 14.8 inferiortemporal 1456 988 2560 2.474 0.896 0.122 0.029 18 1.5 isthmuscingulate 8453 5658 14533 2.213 0.722 0.149 0.050 132 17.9 lateraloccipital 4767 3149 9526 2.723 0.789 0.138 0.047 66 9.7 lateralorbitofrontal 4558 3049 6686 1.961 0.591 0.151 0.055 74 10.2 lingual 3190 2294 6544 2.507 0.822 0.143 0.044 49 5.8 medialorbitofrontal 5018 3452 11876 2.704 0.758 0.125 0.033 54 6.6 middletemporal 1164 708 1885 2.307 0.669 0.101 0.038 14 2.0 parahippocampal 2615 1677 4592 2.493 0.652 0.141 0.045 34 5.2 paracentral 2389 1616 4528 2.498 0.589 0.112 0.026 21 2.5 parsopercularis 1186 795 2454 2.524 0.911 0.151 0.057 23 2.5 parsorbitalis 2251 1469 4891 2.765 0.761 0.122 0.032 23 2.8 parstriangularis 1781 1299 2094 1.848 0.493 0.163 0.053 24 4.0 pericalcarine 7057 4571 10110 2.028 0.622 0.125 0.036 73 10.5 postcentral 2305 1584 3732 2.310 0.639 0.145 0.040 31 3.7 posteriorcingulate 9679 6401 16271 2.425 0.686 0.124 0.038 96 15.4 precentral 6234 4227 11289 2.491 0.679 0.131 0.038 73 9.4 precuneus 1208 848 2799 2.941 0.771 0.136 0.037 16 1.9 rostralanteriorcingulate 10933 7514 21687 2.588 0.656 0.149 0.049 164 21.6 rostralmiddlefrontal 15000 9996 29561 2.700 0.748 0.143 0.049 187 30.7 superiorfrontal 10890 7134 16511 2.136 0.573 0.135 0.044 133 18.9 superiorparietal 6865 4721 14836 2.569 0.768 0.116 0.030 67 8.5 superiortemporal 6047 4181 12041 2.500 0.666 0.133 0.038 85 9.4 supramarginal 486 316 1377 3.076 0.787 0.196 0.084 13 1.9 frontalpole 947 700 2618 2.783 0.919 0.172 0.066 16 2.7 temporalpole 939 572 1268 2.143 0.548 0.141 0.051 10 1.9 transversetemporal 4161 2808 7835 2.926 0.814 0.128 0.042 49 6.9 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 0050352 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813 Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 1461 817 2374 2.693 0.525 0.119 0.036 19 2.1 bankssts 1379 1136 2794 2.736 0.810 0.154 0.041 36 2.3 caudalanteriorcingulate 4942 3763 9181 2.583 0.617 0.130 0.031 63 6.9 caudalmiddlefrontal 2515 2035 3664 1.999 0.541 0.138 0.037 31 4.1 cuneus 1146 986 2011 2.411 0.784 0.200 0.127 60 8.8 entorhinal 5233 4387 9651 2.386 0.655 0.165 0.047 96 11.6 fusiform 6776 5935 12637 2.390 0.634 0.166 0.043 99 14.1 inferiorparietal 5852 5758 13137 2.571 0.869 0.191 0.053 97 14.9 inferiortemporal 1456 1189 2560 2.474 0.896 0.154 0.045 23 2.6 isthmuscingulate 8453 7182 14533 2.213 0.722 0.157 0.043 155 17.0 lateraloccipital 4767 3775 9526 2.723 0.789 0.152 0.044 77 9.3 lateralorbitofrontal 4558 3821 6686 1.961 0.591 0.154 0.042 77 8.7 lingual 3190 2917 6544 2.507 0.822 0.174 0.048 54 7.0 medialorbitofrontal 5018 5135 11876 2.704 0.758 0.185 0.048 65 11.5 middletemporal 1164 937 1885 2.307 0.669 0.146 0.039 12 2.0 parahippocampal 2615 2029 4592 2.493 0.652 0.143 0.039 42 4.8 paracentral 2389 1973 4528 2.498 0.589 0.146 0.036 35 4.0 parsopercularis 1186 1088 2454 2.524 0.911 0.168 0.052 200 2.8 parsorbitalis 2251 1966 4891 2.765 0.761 0.169 0.045 36 4.8 parstriangularis 1781 1088 2094 1.848 0.493 0.134 0.041 29 3.1 pericalcarine 7057 5457 10110 2.028 0.622 0.132 0.033 67 10.3 postcentral 2305 1751 3732 2.310 0.639 0.152 0.040 53 4.4 posteriorcingulate 9679 7020 16271 2.425 0.686 0.120 0.030 123 12.8 precentral 6234 4854 11289 2.491 0.679 0.147 0.044 149 12.7 precuneus 1208 1119 2799 2.941 0.771 0.178 0.055 54 2.7 rostralanteriorcingulate 10933 9038 21687 2.588 0.656 0.161 0.043 184 21.9 rostralmiddlefrontal 15000 11635 29561 2.700 0.748 0.143 0.042 264 27.5 superiorfrontal 10890 8251 16511 2.136 0.573 0.139 0.038 154 18.3 superiorparietal 6865 6014 14836 2.569 0.768 0.141 0.033 75 10.2 superiortemporal 6047 5265 12041 2.500 0.666 0.155 0.037 77 10.2 supramarginal 486 513 1377 3.076 0.787 0.164 0.029 6 0.8 frontalpole 947 1258 2618 2.783 0.919 0.218 0.051 13 2.3 temporalpole 939 685 1268 2.143 0.548 0.137 0.041 9 1.7 transversetemporal 4161 2542 7835 2.926 0.814 0.126 0.037 78 6.3 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 0050352 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365 Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 1205 865 2413 2.854 0.528 0.093 0.019 6 0.9 bankssts 1393 920 2496 2.550 0.562 0.125 0.026 16 1.5 caudalanteriorcingulate 5034 3350 8709 2.558 0.589 0.128 0.049 64 10.2 caudalmiddlefrontal 2458 1590 3415 1.950 0.515 0.138 0.041 33 4.2 cuneus 862 533 1945 2.824 0.900 0.167 0.080 22 3.1 entorhinal 5294 3494 10625 2.667 0.776 0.134 0.046 68 10.4 fusiform 8832 5726 17049 2.619 0.694 0.133 0.045 115 15.7 inferiorparietal 6653 4352 14290 2.687 0.802 0.141 0.065 135 18.8 inferiortemporal 1431 944 2648 2.495 0.799 0.136 0.038 18 2.0 isthmuscingulate 7989 5151 12465 2.186 0.698 0.147 0.054 130 17.4 lateraloccipital 4793 3124 8219 2.466 0.774 0.139 0.054 75 10.9 lateralorbitofrontal 4841 3286 7356 2.069 0.556 0.148 0.047 68 8.8 lingual 3427 2254 6376 2.509 0.912 0.137 0.054 56 7.9 medialorbitofrontal 6429 4370 15378 2.950 0.717 0.139 0.048 87 12.5 middletemporal 1127 705 1893 2.400 0.727 0.105 0.026 9 1.1 parahippocampal 2737 1772 4181 2.259 0.624 0.130 0.053 36 6.2 paracentral 2415 1656 4667 2.576 0.564 0.118 0.034 25 3.2 parsopercularis 1903 1207 3932 2.669 0.822 0.160 0.066 40 5.1 parsorbitalis 2887 1940 6035 2.683 0.632 0.126 0.034 34 3.6 parstriangularis 2276 1563 2810 1.900 0.549 0.131 0.044 31 3.9 pericalcarine 6805 4389 9915 2.093 0.714 0.122 0.046 136 13.4 postcentral 2445 1663 4566 2.490 0.869 0.146 0.039 37 3.6 posteriorcingulate 9868 6484 15157 2.361 0.674 0.132 0.043 104 18.2 precentral 6542 4390 11989 2.512 0.668 0.131 0.037 74 9.8 precuneus 1058 712 2550 3.139 0.837 0.131 0.034 16 1.5 rostralanteriorcingulate 13658 9095 25754 2.496 0.674 0.145 0.053 201 29.4 rostralmiddlefrontal 14491 9415 28835 2.781 0.785 0.141 0.056 238 35.3 superiorfrontal 9451 6352 15822 2.289 0.659 0.137 0.046 137 19.6 superiorparietal 6563 4296 12078 2.546 0.692 0.130 0.054 88 15.2 superiortemporal 6067 3988 11430 2.673 0.619 0.131 0.042 106 11.1 supramarginal 507 305 1225 2.626 0.798 0.157 0.074 12 1.4 frontalpole 824 489 1611 2.528 0.816 0.167 0.076 17 2.8 temporalpole 675 420 839 2.156 0.710 0.145 0.050 11 1.4 transversetemporal 4096 2822 7843 3.060 0.722 0.136 0.043 50 6.7 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 0050352 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365 Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 1205 789 2413 2.854 0.528 0.108 0.026 14 1.4 bankssts 1393 1089 2496 2.550 0.562 0.152 0.035 41 2.4 caudalanteriorcingulate 5034 3475 8709 2.558 0.589 0.113 0.030 65 7.0 caudalmiddlefrontal 2458 2000 3415 1.950 0.515 0.146 0.038 28 4.2 cuneus 862 815 1945 2.824 0.900 0.164 0.046 12 1.9 entorhinal 5294 4360 10625 2.667 0.776 0.160 0.049 112 12.7 fusiform 8832 7175 17049 2.619 0.694 0.155 0.046 141 19.8 inferiorparietal 6653 5838 14290 2.687 0.802 0.162 0.049 350 14.7 inferiortemporal 1431 1139 2648 2.495 0.799 0.167 0.043 26 2.7 isthmuscingulate 7989 6247 12465 2.186 0.698 0.142 0.041 135 14.7 lateraloccipital 4793 3628 8219 2.466 0.774 0.162 0.048 81 10.8 lateralorbitofrontal 4841 4029 7356 2.069 0.556 0.155 0.041 68 9.0 lingual 3427 2939 6376 2.509 0.912 0.175 0.054 66 8.4 medialorbitofrontal 6429 6024 15378 2.950 0.717 0.163 0.043 114 12.5 middletemporal 1127 848 1893 2.400 0.727 0.135 0.034 15 1.7 parahippocampal 2737 1927 4181 2.259 0.624 0.129 0.033 37 4.1 paracentral 2415 2037 4667 2.576 0.564 0.144 0.035 27 3.7 parsopercularis 1903 1689 3932 2.669 0.822 0.156 0.041 25 3.4 parsorbitalis 2887 2570 6035 2.683 0.632 0.158 0.034 34 4.6 parstriangularis 2276 1479 2810 1.900 0.549 0.138 0.044 44 4.2 pericalcarine 6805 5214 9915 2.093 0.714 0.130 0.034 84 10.3 postcentral 2445 1995 4566 2.490 0.869 0.159 0.042 50 4.7 posteriorcingulate 9868 6535 15157 2.361 0.674 0.113 0.034 155 14.1 precentral 6542 5038 11989 2.512 0.668 0.147 0.039 109 11.5 precuneus 1058 971 2550 3.139 0.837 0.155 0.041 32 1.9 rostralanteriorcingulate 13658 11057 25754 2.496 0.674 0.152 0.041 267 26.1 rostralmiddlefrontal 14491 10927 28835 2.781 0.785 0.146 0.044 243 29.2 superiorfrontal 9451 7516 15822 2.289 0.659 0.144 0.040 168 17.0 superiorparietal 6563 5168 12078 2.546 0.692 0.145 0.039 109 11.8 superiortemporal 6067 4561 11430 2.673 0.619 0.143 0.039 115 11.1 supramarginal 507 568 1225 2.626 0.798 0.190 0.044 7 1.1 frontalpole 824 706 1611 2.528 0.816 0.180 0.068 34 2.3 temporalpole 675 410 839 2.156 0.710 0.128 0.041 10 1.1 transversetemporal 4096 2400 7843 3.060 0.722 0.134 0.047 87 8.6 insula PIDs (2294 2297 2300 2303) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 11:47:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 11:47:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 2403 of (2403 2406) to complete... Waiting for PID 2406 of (2403 2406) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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... 57 labels changed using aseg relabeling using gibbs priors... 000: 10261 changed, 159921 examined... 001: 2506 changed, 39819 examined... 002: 781 changed, 12993 examined... 003: 351 changed, 4484 examined... 004: 173 changed, 2002 examined... 005: 88 changed, 1017 examined... 006: 38 changed, 502 examined... 007: 11 changed, 212 examined... 008: 3 changed, 76 examined... 009: 2 changed, 16 examined... 010: 1 changed, 10 examined... 011: 0 changed, 8 examined... 33 labels changed using aseg 000: 295 total segments, 211 labels (2644 vertices) changed 001: 95 total segments, 12 labels (89 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 36 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1434 vertices marked for relabeling... 1434 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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... 1 labels changed using aseg relabeling using gibbs priors... 000: 10278 changed, 165183 examined... 001: 2413 changed, 40284 examined... 002: 705 changed, 12705 examined... 003: 297 changed, 3968 examined... 004: 130 changed, 1665 examined... 005: 63 changed, 781 examined... 006: 37 changed, 350 examined... 007: 20 changed, 208 examined... 008: 7 changed, 107 examined... 009: 5 changed, 41 examined... 010: 4 changed, 25 examined... 011: 1 changed, 20 examined... 012: 0 changed, 4 examined... 0 labels changed using aseg 000: 300 total segments, 216 labels (2581 vertices) changed 001: 95 total segments, 11 labels (45 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 49 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1584 vertices marked for relabeling... 1584 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 22 seconds. PIDs (2403 2406) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 11:47:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 11:47:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh white Waiting for PID 2452 of (2452 2455) to complete... Waiting for PID 2455 of (2452 2455) 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 0050352 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813 Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 1596 1066 3379 2.812 0.774 0.148 0.057 25 4.0 G&S_frontomargin 1680 1138 3104 2.186 0.759 0.151 0.056 26 3.9 G&S_occipital_inf 1818 1187 3333 2.351 0.823 0.148 0.049 26 3.9 G&S_paracentral 1983 1282 4103 2.573 0.623 0.130 0.035 25 2.6 G&S_subcentral 1011 702 3008 3.239 0.657 0.183 0.072 23 2.9 G&S_transv_frontopol 2810 1980 5844 2.704 0.690 0.132 0.035 31 4.3 G&S_cingul-Ant 1636 1110 3195 2.801 0.593 0.135 0.035 17 2.1 G&S_cingul-Mid-Ant 1722 1188 2617 2.264 0.582 0.131 0.035 17 2.5 G&S_cingul-Mid-Post 695 483 1605 2.703 0.761 0.166 0.051 14 1.4 G_cingul-Post-dorsal 253 180 596 2.723 0.948 0.139 0.041 3 0.3 G_cingul-Post-ventral 2168 1487 3545 2.049 0.642 0.158 0.059 36 5.3 G_cuneus 1177 782 2716 2.576 0.611 0.129 0.040 15 2.1 G_front_inf-Opercular 540 346 1289 2.601 0.807 0.159 0.054 10 1.3 G_front_inf-Orbital 1527 948 3768 2.866 0.725 0.132 0.037 20 2.1 G_front_inf-Triangul 6227 4146 14649 2.723 0.680 0.154 0.050 107 12.7 G_front_middle 10050 6575 21349 2.694 0.810 0.156 0.059 155 25.0 G_front_sup 794 550 1704 2.964 0.944 0.149 0.053 15 1.4 G_Ins_lg&S_cent_ins 827 546 2272 3.262 0.701 0.141 0.057 12 2.0 G_insular_short 2203 1480 5619 2.684 0.732 0.164 0.058 46 5.3 G_occipital_middle 1835 1137 3025 2.157 0.699 0.148 0.048 29 3.4 G_occipital_sup 2108 1436 4247 2.344 0.660 0.160 0.072 43 6.6 G_oc-temp_lat-fusifor 3455 2306 5361 1.932 0.620 0.165 0.066 67 9.5 G_oc-temp_med-Lingual 1984 1237 3381 2.302 0.758 0.153 0.071 38 6.7 G_oc-temp_med-Parahip 2893 1844 6447 2.580 0.835 0.155 0.067 61 7.8 G_orbital 2899 1884 6121 2.423 0.738 0.150 0.042 51 5.0 G_pariet_inf-Angular 3248 2190 7358 2.591 0.674 0.150 0.052 59 6.8 G_pariet_inf-Supramar 4691 3024 7612 2.075 0.553 0.141 0.054 68 10.2 G_parietal_sup 2660 1605 3913 2.072 0.633 0.132 0.045 31 4.9 G_postcentral 3976 2556 7278 2.423 0.731 0.133 0.048 44 8.1 G_precentral 3154 2136 7032 2.558 0.657 0.150 0.054 50 6.6 G_precuneus 1078 834 2743 2.539 0.800 0.174 0.053 29 2.3 G_rectus 1051 677 1598 2.399 0.968 0.129 0.052 15 2.0 G_subcallosal 701 414 970 2.048 0.445 0.150 0.058 10 1.5 G_temp_sup-G_T_transv 2223 1536 7197 3.025 0.836 0.146 0.044 34 4.0 G_temp_sup-Lateral 1103 802 2723 2.895 0.860 0.115 0.039 9 1.8 G_temp_sup-Plan_polar 1015 668 1679 2.307 0.510 0.078 0.019 5 0.8 G_temp_sup-Plan_tempo 3226 2202 9087 2.857 0.932 0.176 0.079 102 11.7 G_temporal_inf 2650 1752 7688 2.959 0.737 0.138 0.040 38 4.2 G_temporal_middle 292 193 354 2.150 0.544 0.112 0.023 2 0.2 Lat_Fis-ant-Horizont 361 266 534 2.451 0.673 0.094 0.013 2 0.2 Lat_Fis-ant-Vertical 1120 760 1417 2.427 0.616 0.106 0.022 6 0.9 Lat_Fis-post 2480 1676 4179 2.110 0.761 0.165 0.063 49 6.6 Pole_occipital 1767 1282 4730 2.685 0.882 0.168 0.063 30 4.9 Pole_temporal 2121 1497 2613 2.037 0.668 0.139 0.041 23 3.5 S_calcarine 3498 2419 3933 1.854 0.524 0.122 0.030 28 4.5 S_central 1302 899 1870 2.260 0.498 0.133 0.032 12 1.7 S_cingul-Marginalis 524 367 988 3.260 0.502 0.100 0.018 2 0.4 S_circular_insula_ant 1687 1150 2514 2.734 0.807 0.098 0.022 8 1.5 S_circular_insula_inf 1983 1361 3005 2.827 0.509 0.103 0.020 9 1.8 S_circular_insula_sup 1232 862 1899 2.469 0.618 0.117 0.028 9 1.4 S_collat_transv_ant 617 409 661 1.973 0.468 0.120 0.027 4 0.7 S_collat_transv_post 2499 1730 3547 2.206 0.489 0.119 0.033 22 3.2 S_front_inf 1936 1358 2894 2.425 0.590 0.131 0.033 17 2.5 S_front_middle 4859 3292 7788 2.588 0.528 0.113 0.030 34 5.8 S_front_sup 413 293 590 2.107 0.464 0.099 0.020 2 0.4 S_interm_prim-Jensen 3759 2525 4876 2.187 0.500 0.117 0.025 30 3.7 S_intrapariet&P_trans 1150 766 1371 2.011 0.405 0.119 0.028 9 1.3 S_oc_middle&Lunatus 1354 910 1803 2.203 0.483 0.116 0.032 9 1.7 S_oc_sup&transversal 805 562 1203 2.350 0.616 0.129 0.031 6 1.0 S_occipital_ant 1130 785 1563 2.104 0.525 0.092 0.016 5 0.7 S_oc-temp_lat 2117 1406 3216 2.312 0.523 0.101 0.020 13 1.5 S_oc-temp_med&Lingual 490 365 1202 3.246 0.770 0.165 0.047 8 1.0 S_orbital_lateral 726 528 908 2.022 0.605 0.119 0.027 5 0.8 S_orbital_med-olfact 1929 1315 3658 2.807 0.713 0.129 0.033 18 2.9 S_orbital-H_Shaped 2541 1703 3376 2.345 0.707 0.123 0.030 22 3.1 S_parieto_occipital 1415 910 1550 2.116 0.704 0.131 0.025 22 1.2 S_pericallosal 2719 1924 3637 2.123 0.509 0.123 0.029 23 3.2 S_postcentral 2570 1717 4205 2.517 0.525 0.101 0.025 22 2.8 S_precentral-inf-part 2005 1336 3030 2.640 0.566 0.117 0.031 15 2.8 S_precentral-sup-part 669 465 1198 2.656 1.044 0.124 0.026 4 0.8 S_suborbital 1173 802 1714 2.297 0.555 0.120 0.024 10 1.1 S_subparietal 2004 1377 3123 2.186 0.583 0.112 0.026 14 2.2 S_temporal_inf 6392 4403 10512 2.422 0.576 0.112 0.025 49 6.6 S_temporal_sup 519 342 758 2.390 0.467 0.130 0.031 4 0.7 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 0050352 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365 Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 1308 877 2462 2.458 0.631 0.152 0.051 19 2.8 G&S_frontomargin 1180 763 1992 2.235 0.611 0.151 0.053 19 2.3 G&S_occipital_inf 1721 1107 2685 2.099 0.657 0.136 0.056 25 3.8 G&S_paracentral 1787 1096 3382 2.613 0.623 0.125 0.064 86 5.3 G&S_subcentral 1739 1112 3380 2.349 0.660 0.175 0.083 34 6.2 G&S_transv_frontopol 3648 2463 7363 2.828 0.807 0.129 0.039 45 5.8 G&S_cingul-Ant 1622 1120 3267 2.838 0.692 0.110 0.024 12 1.5 G&S_cingul-Mid-Ant 1898 1271 3234 2.606 0.717 0.139 0.041 21 3.1 G&S_cingul-Mid-Post 605 416 1788 3.016 0.993 0.170 0.059 10 1.4 G_cingul-Post-dorsal 316 215 682 2.512 0.878 0.137 0.055 4 0.6 G_cingul-Post-ventral 2328 1480 3302 1.968 0.532 0.145 0.047 41 4.5 G_cuneus 1417 934 3140 2.574 0.530 0.128 0.043 21 2.2 G_front_inf-Opercular 611 365 1262 2.501 0.562 0.152 0.066 13 1.7 G_front_inf-Orbital 1304 848 3441 2.891 0.662 0.144 0.044 20 2.1 G_front_inf-Triangul 7343 4626 15602 2.582 0.765 0.159 0.073 154 22.0 G_front_middle 9699 6046 20898 2.764 0.863 0.153 0.073 214 31.5 G_front_sup 780 542 1737 3.237 0.860 0.150 0.051 12 1.5 G_Ins_lg&S_cent_ins 870 560 1877 3.107 0.726 0.149 0.056 15 1.9 G_insular_short 2713 1750 6675 2.753 0.881 0.160 0.071 58 7.7 G_occipital_middle 1767 1107 3761 2.593 0.834 0.135 0.052 26 4.0 G_occipital_sup 2420 1518 5911 2.871 0.896 0.151 0.056 40 5.3 G_oc-temp_lat-fusifor 3240 2150 5426 2.088 0.577 0.152 0.052 53 6.6 G_oc-temp_med-Lingual 1669 1031 3592 2.753 0.840 0.148 0.069 35 4.8 G_oc-temp_med-Parahip 4011 2569 8341 2.495 0.819 0.164 0.075 94 12.6 G_orbital 3676 2289 7628 2.580 0.702 0.147 0.059 63 8.3 G_pariet_inf-Angular 2967 1898 6463 2.646 0.701 0.150 0.065 84 8.7 G_pariet_inf-Supramar 2823 1952 5095 2.124 0.618 0.156 0.067 69 8.8 G_parietal_sup 2396 1493 3820 2.046 0.769 0.136 0.052 32 5.2 G_postcentral 4059 2479 6383 2.227 0.754 0.148 0.061 62 10.9 G_precentral 2829 1810 6587 2.683 0.668 0.147 0.054 48 6.4 G_precuneus 1038 670 1995 2.189 0.822 0.148 0.061 18 2.9 G_rectus 616 425 1021 2.687 1.024 0.156 0.079 15 1.7 G_subcallosal 589 338 817 2.316 0.765 0.144 0.057 10 1.3 G_temp_sup-G_T_transv 2449 1525 5508 2.672 0.802 0.148 0.072 45 7.2 G_temp_sup-Lateral 1332 883 2304 2.457 0.681 0.157 0.071 22 4.5 G_temp_sup-Plan_polar 1246 843 2102 2.393 0.567 0.120 0.050 12 3.0 G_temp_sup-Plan_tempo 3988 2556 9713 2.704 0.872 0.162 0.086 110 15.7 G_temporal_inf 3794 2574 10354 2.951 0.753 0.150 0.058 64 8.5 G_temporal_middle 328 247 471 2.307 0.509 0.105 0.021 2 0.2 Lat_Fis-ant-Horizont 305 230 482 2.332 0.468 0.107 0.018 2 0.2 Lat_Fis-ant-Vertical 1629 1108 2401 2.663 0.600 0.120 0.026 14 1.6 Lat_Fis-post 3700 2373 4853 1.924 0.569 0.149 0.055 61 8.3 Pole_occipital 1520 981 4203 2.897 0.926 0.181 0.096 41 6.7 Pole_temporal 2200 1554 2806 2.015 0.618 0.129 0.036 21 3.3 S_calcarine 3671 2507 4165 1.987 0.600 0.118 0.031 27 4.5 S_central 1315 912 1855 2.131 0.522 0.097 0.021 6 1.0 S_cingul-Marginalis 817 548 1416 3.396 0.595 0.113 0.023 5 0.8 S_circular_insula_ant 1315 878 1977 2.749 0.711 0.102 0.026 9 1.5 S_circular_insula_inf 1657 1147 2712 2.864 0.481 0.105 0.020 8 1.4 S_circular_insula_sup 1265 877 2008 2.544 0.597 0.105 0.026 8 1.3 S_collat_transv_ant 542 389 693 2.001 0.485 0.130 0.029 5 0.7 S_collat_transv_post 2684 1896 4269 2.509 0.485 0.115 0.025 19 2.7 S_front_inf 3756 2603 5734 2.350 0.555 0.124 0.036 30 5.0 S_front_middle 3932 2779 6641 2.772 0.539 0.116 0.028 25 4.5 S_front_sup 506 342 739 2.721 0.530 0.109 0.027 3 0.5 S_interm_prim-Jensen 4193 2817 6009 2.407 0.629 0.121 0.029 33 5.1 S_intrapariet&P_trans 1117 776 1372 1.973 0.393 0.137 0.029 12 1.4 S_oc_middle&Lunatus 1502 1023 2088 2.271 0.451 0.118 0.027 11 1.7 S_oc_sup&transversal 805 555 1109 2.320 0.449 0.126 0.031 6 1.1 S_occipital_ant 1557 1067 2246 2.532 0.563 0.107 0.023 9 1.4 S_oc-temp_lat 2262 1544 2887 2.149 0.525 0.105 0.019 13 1.7 S_oc-temp_med&Lingual 638 447 943 2.436 0.530 0.119 0.025 4 0.6 S_orbital_lateral 736 512 901 1.959 0.474 0.112 0.025 5 0.7 S_orbital_med-olfact 1805 1198 3094 2.566 0.721 0.122 0.036 16 2.4 S_orbital-H_Shaped 2984 2015 4143 2.246 0.596 0.124 0.030 26 3.6 S_parieto_occipital 1878 1221 2192 2.290 0.777 0.135 0.022 29 1.5 S_pericallosal 2505 1722 3434 2.314 0.572 0.132 0.034 25 3.5 S_postcentral 2465 1710 4096 2.656 0.549 0.109 0.024 17 2.3 S_precentral-inf-part 1966 1386 2932 2.478 0.511 0.113 0.024 12 2.1 S_precentral-sup-part 263 176 482 2.394 0.522 0.117 0.028 2 0.4 S_suborbital 1288 885 2318 2.737 0.689 0.127 0.032 12 1.5 S_subparietal 1650 1119 2577 2.733 0.544 0.115 0.025 11 1.6 S_temporal_inf 6233 4213 10930 2.809 0.561 0.102 0.022 38 5.5 S_temporal_sup 257 184 389 2.378 0.497 0.106 0.025 1 0.3 S_temporal_transverse PIDs (2452 2455) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 11:48:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 11:48:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 2525 of (2525 2528) to complete... Waiting for PID 2528 of (2525 2528) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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... 1377 labels changed using aseg relabeling using gibbs priors... 000: 2293 changed, 159921 examined... 001: 537 changed, 10466 examined... 002: 180 changed, 3010 examined... 003: 82 changed, 1028 examined... 004: 48 changed, 464 examined... 005: 38 changed, 256 examined... 006: 25 changed, 194 examined... 007: 21 changed, 124 examined... 008: 12 changed, 109 examined... 009: 11 changed, 70 examined... 010: 10 changed, 65 examined... 011: 9 changed, 63 examined... 012: 7 changed, 56 examined... 013: 2 changed, 35 examined... 014: 1 changed, 14 examined... 015: 1 changed, 7 examined... 016: 1 changed, 7 examined... 017: 1 changed, 6 examined... 018: 1 changed, 7 examined... 019: 2 changed, 6 examined... 020: 3 changed, 9 examined... 021: 2 changed, 17 examined... 022: 0 changed, 11 examined... 350 labels changed using aseg 000: 75 total segments, 42 labels (402 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1017 vertices marked for relabeling... 1017 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 17 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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... 1236 labels changed using aseg relabeling using gibbs priors... 000: 2187 changed, 165183 examined... 001: 546 changed, 10201 examined... 002: 164 changed, 3073 examined... 003: 66 changed, 1002 examined... 004: 32 changed, 365 examined... 005: 18 changed, 177 examined... 006: 16 changed, 99 examined... 007: 7 changed, 69 examined... 008: 2 changed, 33 examined... 009: 3 changed, 14 examined... 010: 1 changed, 20 examined... 011: 0 changed, 7 examined... 199 labels changed using aseg 000: 53 total segments, 20 labels (169 vertices) changed 001: 34 total segments, 1 labels (2 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1285 vertices marked for relabeling... 1285 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 17 seconds. PIDs (2525 2528) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 11:48:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 11:48:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh white Waiting for PID 2576 of (2576 2579) to complete... Waiting for PID 2579 of (2576 2579) 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 0050352 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813 Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 1984 1295 3801 2.718 0.739 0.145 0.034 27 2.6 caudalanteriorcingulate 5259 3525 9733 2.591 0.605 0.120 0.029 47 6.2 caudalmiddlefrontal 3483 2330 5258 2.074 0.615 0.141 0.048 46 6.5 cuneus 1061 677 1823 2.324 0.738 0.177 0.087 24 4.2 entorhinal 4864 3321 8796 2.374 0.631 0.137 0.048 65 9.7 fusiform 7016 4674 13325 2.378 0.658 0.134 0.036 89 10.3 inferiorparietal 5846 3973 13327 2.616 0.887 0.146 0.057 120 15.1 inferiortemporal 1407 954 2554 2.540 0.879 0.124 0.029 18 1.4 isthmuscingulate 8406 5619 14308 2.194 0.722 0.150 0.050 130 17.7 lateraloccipital 5351 3524 10861 2.710 0.821 0.147 0.054 86 12.5 lateralorbitofrontal 4672 3130 6916 1.966 0.589 0.150 0.055 78 10.5 lingual 2639 1905 5501 2.473 0.873 0.144 0.044 44 4.5 medialorbitofrontal 6508 4486 14276 2.627 0.705 0.125 0.033 71 8.7 middletemporal 1229 754 1992 2.295 0.668 0.100 0.037 13 2.0 parahippocampal 3140 2030 5537 2.457 0.658 0.141 0.046 40 6.3 paracentral 2046 1397 3939 2.523 0.589 0.114 0.027 18 2.2 parsopercularis 1104 721 1907 2.359 0.722 0.132 0.046 16 2.0 parsorbitalis 2927 1916 6047 2.689 0.744 0.123 0.032 30 3.7 parstriangularis 1790 1289 2059 1.840 0.494 0.162 0.054 24 4.1 pericalcarine 8053 5247 11744 2.064 0.630 0.127 0.037 86 11.9 postcentral 2430 1688 3879 2.271 0.634 0.145 0.041 32 3.9 posteriorcingulate 9482 6253 15899 2.428 0.680 0.123 0.038 92 15.1 precentral 6054 4090 11174 2.500 0.678 0.134 0.040 75 9.6 precuneus 1909 1320 3904 2.850 0.751 0.137 0.038 24 3.0 rostralanteriorcingulate 8092 5512 15743 2.569 0.666 0.148 0.049 122 15.7 rostralmiddlefrontal 16665 11194 33950 2.701 0.747 0.145 0.050 223 35.1 superiorfrontal 8937 5877 13322 2.121 0.543 0.134 0.044 105 15.7 superiorparietal 9036 6227 19576 2.626 0.784 0.123 0.035 95 13.1 superiortemporal 5420 3738 10524 2.511 0.632 0.131 0.038 73 8.3 supramarginal 910 552 1236 2.145 0.555 0.141 0.051 10 1.8 transversetemporal 3105 2153 6661 3.190 0.682 0.123 0.035 31 4.4 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 0050352 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365 Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 1542 1014 2786 2.549 0.572 0.125 0.026 18 1.6 caudalanteriorcingulate 5126 3420 8908 2.552 0.593 0.129 0.049 65 10.4 caudalmiddlefrontal 3021 1961 4084 1.971 0.522 0.138 0.041 42 4.9 cuneus 701 435 1756 3.006 0.836 0.162 0.076 19 2.2 entorhinal 4849 3201 9621 2.674 0.781 0.130 0.043 58 8.2 fusiform 8875 5746 17133 2.614 0.696 0.133 0.046 115 16.0 inferiorparietal 7063 4640 15203 2.663 0.803 0.143 0.067 143 21.1 inferiortemporal 1450 956 2652 2.481 0.792 0.135 0.039 18 2.1 isthmuscingulate 8041 5170 12610 2.195 0.705 0.149 0.056 134 18.4 lateraloccipital 5995 3862 10502 2.429 0.747 0.145 0.059 102 14.8 lateralorbitofrontal 4755 3235 7255 2.071 0.555 0.149 0.047 68 8.7 lingual 2512 1678 4773 2.448 0.939 0.138 0.054 40 5.5 medialorbitofrontal 7430 5066 17004 2.927 0.686 0.133 0.044 93 13.3 middletemporal 1239 770 2018 2.378 0.739 0.111 0.032 12 1.6 parahippocampal 2979 1920 4703 2.274 0.638 0.137 0.061 43 8.4 paracentral 2907 2000 5650 2.566 0.544 0.118 0.035 30 3.8 parsopercularis 1435 916 2556 2.655 0.766 0.147 0.059 27 3.5 parsorbitalis 2812 1882 5636 2.662 0.640 0.132 0.034 34 3.5 parstriangularis 2241 1554 2803 1.911 0.546 0.130 0.041 27 3.8 pericalcarine 7477 4868 10805 2.094 0.701 0.124 0.044 140 14.3 postcentral 2486 1700 4588 2.495 0.866 0.149 0.040 38 3.8 posteriorcingulate 9396 6125 14482 2.384 0.675 0.132 0.045 103 17.9 precentral 6753 4500 12606 2.505 0.681 0.131 0.039 80 10.4 precuneus 1525 1028 3561 3.105 0.885 0.131 0.040 21 2.5 rostralanteriorcingulate 9844 6566 19487 2.597 0.700 0.143 0.050 146 19.7 rostralmiddlefrontal 18652 12191 35936 2.671 0.777 0.141 0.056 299 44.0 superiorfrontal 7905 5343 13406 2.298 0.650 0.137 0.046 116 16.1 superiorparietal 8248 5407 15580 2.577 0.718 0.134 0.055 115 19.6 superiortemporal 5691 3740 10782 2.687 0.621 0.129 0.042 101 10.4 supramarginal 703 428 857 2.158 0.707 0.146 0.050 11 1.4 transversetemporal 3391 2322 6818 3.180 0.678 0.130 0.036 36 4.6 insula PIDs (2576 2579) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 11:49:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts pctsurfcon --s 0050352 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 11:49:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts pctsurfcon --s 0050352 --rh-only Waiting for PID 2645 of (2645 2656) to complete... Waiting for PID 2656 of (2645 2656) to complete... pctsurfcon --s 0050352 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts/pctsurfcon.log Sun Oct 8 11:49:40 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-6.0.0/0050352/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-928 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-6.0.0/0050352/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.wm.mgh --regheader 0050352 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 76153 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.wm.mgh Dim: 159921 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.gm.mgh --projfrac 0.3 --regheader 0050352 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 88661 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.gm.mgh Dim: 159921 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.w-g.pct.mgh --annot 0050352 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/lh.w-g.pct.mgh --annot 0050352 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-928 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/lh.w-g.pct.mgh Vertex Area is 0.673795 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 0050352 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts/pctsurfcon.log Sun Oct 8 11:49:40 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-6.0.0/0050352/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-928 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-6.0.0/0050352/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.wm.mgh --regheader 0050352 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 76979 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.wm.mgh Dim: 165183 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.gm.mgh --projfrac 0.3 --regheader 0050352 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 90051 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.gm.mgh Dim: 165183 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.w-g.pct.mgh --annot 0050352 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.w-g.pct.mgh --annot 0050352 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-928 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.w-g.pct.mgh Vertex Area is 0.661551 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 (2645 2656) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 11:49:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 3168 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 4008 voxels changed to hypointensity... 7379 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 11:50:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352 mri_aparc2aseg --s 0050352 --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 11:50:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352 mri_aparc2aseg --s 0050352 --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 11:50:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352 mri_aparc2aseg --s 0050352 --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 2839 of (2839 2842 2845) to complete... Waiting for PID 2842 of (2839 2842 2845) to complete... Waiting for PID 2845 of (2839 2842 2845) to complete... mri_aparc2aseg --s 0050352 --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 0050352 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.80 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 66 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 29 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 63 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 89 rescaling Left_Caudate from 75 --> 73 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 35 rescaling Fourth_Ventricle from 22 --> 14 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 61 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 50 rescaling Left_Accumbens_area from 62 --> 66 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 68 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 65 rescaling Right_Thalamus_Proper from 85 --> 85 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 93 rescaling Right_Hippocampus from 53 --> 64 rescaling Right_Amygdala from 55 --> 77 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 87 rescaling Fifth_Ventricle from 40 --> 42 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 558621 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 159 changed. pass 2: 14 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc+aseg.mgz mri_aparc2aseg --s 0050352 --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 0050352 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.80 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 66 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 29 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 63 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 89 rescaling Left_Caudate from 75 --> 73 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 35 rescaling Fourth_Ventricle from 22 --> 14 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 61 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 50 rescaling Left_Accumbens_area from 62 --> 66 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 68 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 65 rescaling Right_Thalamus_Proper from 85 --> 85 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 93 rescaling Right_Hippocampus from 53 --> 64 rescaling Right_Amygdala from 55 --> 77 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 87 rescaling Fifth_Ventricle from 40 --> 42 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 558598 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 159 changed. pass 2: 14 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0050352 --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 0050352 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.80 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 66 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 29 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 63 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 89 rescaling Left_Caudate from 75 --> 73 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 35 rescaling Fourth_Ventricle from 22 --> 14 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 61 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 50 rescaling Left_Accumbens_area from 62 --> 66 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 68 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 65 rescaling Right_Thalamus_Proper from 85 --> 85 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 93 rescaling Right_Hippocampus from 53 --> 64 rescaling Right_Amygdala from 55 --> 77 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 87 rescaling Fifth_Ventricle from 40 --> 42 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 558598 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 159 changed. pass 2: 14 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (2839 2842 2845) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 11:57:31 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 11:57:31 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-6.0.0/0050352/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-928 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-6.0.0/0050352/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-928 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 11:57:31 CEST 2017 Ended at Sun Oct 8 11:57:38 CEST 2017 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 11:57:38 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352 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 0050352 $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 0050352 sysname Linux hostname tars-928 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1712602 mm^3 (det: 1.137512 ) Computing euler number orig.nofix lheno = -294, rheno = -354 orig.nofix lhholes = 148, rhholes = 178 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 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 11:59:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352 mri_aparc2aseg --s 0050352 --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 0050352 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-6.0.0/0050352/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 9038 vertices from left hemi Ripped 8147 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-6.0.0/0050352/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 1119622 Used brute-force search on 711 voxels Fixing Parahip LH WM Found 6 clusters 0 k 2.000000 1 k 4.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1561.000000 Fixing Parahip RH WM Found 8 clusters 0 k 1.000000 1 k 1.000000 2 k 2.000000 3 k 2.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1734.000000 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 0050352 --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 0050352 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-928 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1712602 mm^3 (det: 1.137512 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 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-6.0.0/0050352/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 12:08:55 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 3670 of (3670 3675 3682 3687 3694) to complete... Waiting for PID 3675 of (3670 3675 3682 3687 3694) to complete... Waiting for PID 3682 of (3670 3675 3682 3687 3694) to complete... Waiting for PID 3687 of (3670 3675 3682 3687 3694) to complete... Waiting for PID 3694 of (3670 3675 3682 3687 3694) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 429 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4558 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 632 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8541 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 263 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4340 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 450 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6433 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 1000 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6784 mri_label2label: Done PIDs (3670 3675 3682 3687 3694) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 3755 of (3755 3761 3767 3772) to complete... Waiting for PID 3761 of (3755 3761 3767 3772) to complete... Waiting for PID 3767 of (3755 3761 3767 3772) to complete... Waiting for PID 3772 of (3755 3761 3767 3772) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 465 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4535 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 4184 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 17773 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 609 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4790 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 1134 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4556 mri_label2label: Done PIDs (3755 3761 3767 3772) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 3814 of (3814 3820 3826 3832 3838) to complete... Waiting for PID 3820 of (3814 3820 3826 3832 3838) to complete... Waiting for PID 3826 of (3814 3820 3826 3832 3838) to complete... Waiting for PID 3832 of (3814 3820 3826 3832 3838) to complete... Waiting for PID 3838 of (3814 3820 3826 3832 3838) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 1579 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6220 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 3361 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11475 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 565 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2583 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 603 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1893 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 549 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1748 mri_label2label: Done PIDs (3814 3820 3826 3832 3838) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 3919 of (3919 3925 3931 3937 3943) to complete... Waiting for PID 3925 of (3919 3925 3931 3937 3943) to complete... Waiting for PID 3931 of (3919 3925 3931 3937 3943) to complete... Waiting for PID 3937 of (3919 3925 3931 3937 3943) to complete... Waiting for PID 3943 of (3919 3925 3931 3937 3943) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 104 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1118 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 179 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2271 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1616 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 188 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2184 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 365 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2684 mri_label2label: Done PIDs (3919 3925 3931 3937 3943) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 3988 of (3988 3994 4000 4005) to complete... Waiting for PID 3994 of (3988 3994 4000 4005) to complete... Waiting for PID 4000 of (3988 3994 4000 4005) to complete... Waiting for PID 4005 of (3988 3994 4000 4005) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 90 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1639 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 1882 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8917 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 163 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2075 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 527 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1678 mri_label2label: Done PIDs (3988 3994 4000 4005) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 4052 of (4052 4058 4064 4069 4074) to complete... Waiting for PID 4058 of (4052 4058 4064 4069 4074) to complete... Waiting for PID 4064 of (4052 4058 4064 4069 4074) to complete... Waiting for PID 4069 of (4052 4058 4064 4069 4074) to complete... Waiting for PID 4074 of (4052 4058 4064 4069 4074) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 1170 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4575 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 1483 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4817 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 644 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 262 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 732 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921 Number of reverse mapping hits = 264 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 714 mri_label2label: Done PIDs (4052 4058 4064 4069 4074) completed and logs appended. mris_label2annot --s 0050352 --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-6.0.0/0050352/label cmdline mris_label2annot --s 0050352 --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-928 machine x86_64 user ntraut subject 0050352 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-6.0.0/0050352/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 110687 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.BA_exvivo.annot mris_label2annot --s 0050352 --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-6.0.0/0050352/label cmdline mris_label2annot --s 0050352 --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-928 machine x86_64 user ntraut subject 0050352 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-6.0.0/0050352/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 131466 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 282813 Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 1264 762 2039 2.137 0.690 0.140 0.046 16 2.2 BA1_exvivo 4066 2764 6269 2.202 0.598 0.133 0.038 46 6.5 BA2_exvivo 1185 811 1341 1.896 0.575 0.141 0.038 13 1.8 BA3a_exvivo 2625 1746 3897 1.899 0.706 0.125 0.036 28 3.8 BA3b_exvivo 2093 1292 3153 2.281 0.709 0.137 0.045 26 4.3 BA4a_exvivo 1515 1056 2241 2.232 0.677 0.132 0.038 12 2.5 BA4p_exvivo 13908 9155 24122 2.471 0.692 0.136 0.048 169 28.3 BA6_exvivo 2336 1562 4233 2.432 0.586 0.111 0.027 20 2.7 BA44_exvivo 3687 2465 7665 2.579 0.732 0.132 0.038 45 6.0 BA45_exvivo 3460 2497 4797 1.865 0.568 0.170 0.063 62 9.3 V1_exvivo 8815 5767 13023 2.027 0.647 0.149 0.053 138 19.1 V2_exvivo 2297 1555 4609 2.492 0.767 0.144 0.042 34 4.0 MT_exvivo 929 549 1365 2.249 0.681 0.153 0.073 18 3.3 perirhinal_exvivo 1054 744 2325 2.670 0.821 0.164 0.073 21 3.6 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050352 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 282813 Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 803 454 1195 2.064 0.669 0.143 0.048 11 1.6 BA1_exvivo 1570 1039 2454 2.229 0.559 0.124 0.039 17 2.6 BA2_exvivo 1036 703 1028 1.855 0.510 0.146 0.040 12 1.7 BA3a_exvivo 1640 1114 1795 1.578 0.348 0.110 0.028 11 1.9 BA3b_exvivo 2004 1270 2973 2.227 0.720 0.138 0.049 24 4.4 BA4a_exvivo 1150 835 1635 2.193 0.658 0.136 0.037 9 1.9 BA4p_exvivo 7478 4950 12444 2.388 0.692 0.140 0.050 85 16.6 BA6_exvivo 1403 947 2439 2.326 0.543 0.123 0.035 15 2.1 BA44_exvivo 1584 1014 3841 2.812 0.739 0.126 0.037 19 2.2 BA45_exvivo 3740 2654 5176 1.882 0.575 0.168 0.064 66 10.2 V1_exvivo 4349 2917 6614 2.028 0.654 0.159 0.056 78 9.8 V2_exvivo 577 389 1083 2.470 0.700 0.133 0.038 8 0.9 MT_exvivo 485 307 711 2.241 0.701 0.158 0.083 9 1.9 perirhinal_exvivo 636 410 1250 2.459 0.742 0.179 0.092 16 2.9 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 12:12:21 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 4207 of (4207 4213 4219 4225 4231) to complete... Waiting for PID 4213 of (4207 4213 4219 4225 4231) to complete... Waiting for PID 4219 of (4207 4213 4219 4225 4231) to complete... Waiting for PID 4225 of (4207 4213 4219 4225 4231) to complete... Waiting for PID 4231 of (4207 4213 4219 4225 4231) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 501 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4463 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 690 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7377 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 326 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4306 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 585 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5107 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 1317 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 7064 mri_label2label: Done PIDs (4207 4213 4219 4225 4231) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 4284 of (4284 4290 4296 4302) to complete... Waiting for PID 4290 of (4284 4290 4296 4302) to complete... Waiting for PID 4296 of (4284 4290 4296 4302) to complete... Waiting for PID 4302 of (4284 4290 4296 4302) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 588 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 5061 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 3560 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 15816 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 1684 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8596 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 1882 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 7237 mri_label2label: Done PIDs (4284 4290 4296 4302) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 4358 of (4358 4364 4370 4375 4382) to complete... Waiting for PID 4364 of (4358 4364 4370 4375 4382) to complete... Waiting for PID 4370 of (4358 4364 4370 4375 4382) to complete... Waiting for PID 4375 of (4358 4364 4370 4375 4382) to complete... Waiting for PID 4382 of (4358 4364 4370 4375 4382) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 1904 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6631 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 3270 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11286 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 615 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2547 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 295 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1333 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 190 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 942 mri_label2label: Done PIDs (4358 4364 4370 4375 4382) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 4434 of (4434 4440 4446 4452 4458) to complete... Waiting for PID 4440 of (4434 4440 4446 4452 4458) to complete... Waiting for PID 4446 of (4434 4440 4446 4452 4458) to complete... Waiting for PID 4452 of (4434 4440 4446 4452 4458) to complete... Waiting for PID 4458 of (4434 4440 4446 4452 4458) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 126 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1002 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 147 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2835 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1797 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 282 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2465 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 271 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1659 mri_label2label: Done PIDs (4434 4440 4446 4452 4458) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 4504 of (4504 4510 4516 4521) to complete... Waiting for PID 4510 of (4504 4510 4516 4521) to complete... Waiting for PID 4516 of (4504 4510 4516 4521) to complete... Waiting for PID 4521 of (4504 4510 4516 4521) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 279 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1768 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 2018 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 8977 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 251 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1263 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 396 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1574 mri_label2label: Done PIDs (4504 4510 4516 4521) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 4579 of (4579 4585 4591 4596 4602) to complete... Waiting for PID 4585 of (4579 4585 4591 4596 4602) to complete... Waiting for PID 4591 of (4579 4585 4591 4596 4602) to complete... Waiting for PID 4596 of (4579 4585 4591 4596 4602) to complete... Waiting for PID 4602 of (4579 4585 4591 4596 4602) 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 1188 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4420 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 1581 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5018 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 95 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 363 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 195 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 889 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 0050352 --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 = 0050352 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-6.0.0/0050352/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183 Number of reverse mapping hits = 79 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 370 mri_label2label: Done PIDs (4579 4585 4591 4596 4602) completed and logs appended. mris_label2annot --s 0050352 --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-6.0.0/0050352/label cmdline mris_label2annot --s 0050352 --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-928 machine x86_64 user ntraut subject 0050352 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-6.0.0/0050352/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 115506 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.BA_exvivo.annot mris_label2annot --s 0050352 --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-6.0.0/0050352/label cmdline mris_label2annot --s 0050352 --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-928 machine x86_64 user ntraut subject 0050352 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-6.0.0/0050352/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 137244 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 289365 Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 1113 655 1936 2.206 0.833 0.149 0.062 17 2.7 BA1_exvivo 3341 2188 5246 2.300 0.605 0.135 0.044 40 6.5 BA2_exvivo 1215 867 1244 1.971 0.495 0.142 0.037 12 1.7 BA3a_exvivo 2286 1513 2760 1.659 0.569 0.112 0.051 82 5.7 BA3b_exvivo 2018 1228 3158 2.363 0.654 0.127 0.059 25 5.1 BA4a_exvivo 1587 1070 2117 2.243 0.660 0.132 0.046 15 2.8 BA4p_exvivo 12072 7760 20645 2.501 0.779 0.138 0.052 158 28.2 BA6_exvivo 4478 2988 8571 2.621 0.572 0.118 0.034 46 5.8 BA44_exvivo 5432 3676 10839 2.634 0.653 0.139 0.041 76 8.3 BA45_exvivo 4068 2739 5413 1.875 0.549 0.141 0.049 61 8.0 V1_exvivo 8541 5588 12255 2.060 0.615 0.150 0.050 134 17.7 V2_exvivo 2316 1556 4345 2.513 0.723 0.141 0.042 32 3.4 MT_exvivo 789 485 1866 2.910 0.952 0.159 0.070 15 2.8 perirhinal_exvivo 421 279 808 2.436 0.677 0.157 0.073 9 1.4 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 0050352 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 289365 Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 ) lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371 rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338 lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115 rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702 SubCortGMVol 65474.000 SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406 SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413 BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226 BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042 BrainSegVolNotVent 1346802.000 CerebellumVol 159751.000 VentChorVol 19992.000 3rd4th5thCSF 5338.000 CSFVol 2234.000, OptChiasmVol 252.000 MaskVol 1787646.000 747 464 1190 1.948 0.739 0.152 0.058 11 1.8 BA1_exvivo 1766 1123 2907 2.394 0.631 0.116 0.038 16 2.6 BA2_exvivo 1101 778 1048 1.941 0.489 0.143 0.036 11 1.6 BA3a_exvivo 1768 1211 1826 1.522 0.386 0.096 0.022 10 1.5 BA3b_exvivo 1256 782 2056 2.289 0.710 0.140 0.070 20 3.9 BA4a_exvivo 1395 937 1948 2.362 0.654 0.132 0.049 13 2.7 BA4p_exvivo 7774 4988 12516 2.373 0.769 0.143 0.054 105 19.3 BA6_exvivo 1094 750 2301 2.670 0.552 0.114 0.034 11 1.4 BA44_exvivo 1445 956 3617 2.784 0.654 0.151 0.049 24 2.7 BA45_exvivo 3840 2590 5064 1.874 0.546 0.139 0.049 57 7.5 V1_exvivo 4616 3027 6524 1.985 0.594 0.151 0.050 69 9.2 V2_exvivo 340 225 783 2.675 0.725 0.156 0.047 6 0.6 MT_exvivo 486 294 1063 2.891 0.950 0.161 0.075 10 1.8 perirhinal_exvivo 311 198 629 2.409 0.929 0.188 0.095 10 1.4 entorhinal_exvivo Started at Sat Oct 7 23:40:21 CEST 2017 Ended at Sun Oct 8 12:15:48 CEST 2017 #@#%# recon-all-run-time-hours 12.591 recon-all -s 0050352 finished without error at Sun Oct 8 12:15:48 CEST 2017