Sat Oct 7 16:52:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0050750 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Leuven_2/0050750/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0050750 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-540 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: 65993716 53846056 12147660 1752460 0 50048224 -/+ buffers/cache: 3797832 62195884 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: ntraut Machine: tars-540 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:52:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: ntraut Machine: tars-540 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-6.0.0/0050750 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Leuven_2/0050750/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Leuven_2/0050750/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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/Leuven_2/0050750/session_1/anat_1/mprage.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998775, -0.0491878, -0.0054743) j_ras = (-0.0485166, 0.99494, -0.0879774) k_ras = (-0.009774, 0.0876038, 0.996107) writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 16:52:41 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998775, -0.0491878, -0.0054743) j_ras = (-0.0485166, 0.99494, -0.0879774) k_ras = (-0.009774, 0.0876038, 0.996107) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 16:52:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/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-540 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 16:52:52 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.1669 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1669/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1669/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, 5.00586e-09, 9.31323e-10) j_ras = (0, 0, -1) k_ras = (1.74623e-09, 1, 7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1669/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 16:52:54 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.1669/nu0.mnc ./tmp.mri_nu_correct.mni.1669/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1669/0/ -iterations 1000 -distance 50 [ntraut@tars-540:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/] [2017-10-07 16:52:55] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.1669/0/ ./tmp.mri_nu_correct.mni.1669/nu0.mnc ./tmp.mri_nu_correct.mni.1669/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 33 CV of field change: 0.000999611 mri_convert ./tmp.mri_nu_correct.mni.1669/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.1669/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.1669/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.00586e-09, 9.31323e-10) j_ras = (0, 0, -1) k_ras = (1.74623e-09, 1, 7.45058e-09) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sat Oct 7 16:53:59 CEST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Oct 7 16:53:59 CEST 2017 Ended at Sat Oct 7 16:54:29 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 16:54:31 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7266, pval=0.6675 >= 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-6.0.0/0050750/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/transforms/talairach_avi.log TalAviQA: 0.97723 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 16:54:31 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-6.0.0/0050750/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-540 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 16:54:31 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.2417 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2417/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.2417/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, 5.00586e-09, 9.31323e-10) j_ras = (0, 0, -1) k_ras = (1.74623e-09, 1, 7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.2417/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 16:54:34 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.2417/nu0.mnc ./tmp.mri_nu_correct.mni.2417/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2417/0/ [ntraut@tars-540:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/] [2017-10-07 16:54:34] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.2417/0/ ./tmp.mri_nu_correct.mni.2417/nu0.mnc ./tmp.mri_nu_correct.mni.2417/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 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 27 CV of field change: 0.000960639 -------------------------------------------------------- Iteration 2 Sat Oct 7 16:55:20 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.2417/nu1.mnc ./tmp.mri_nu_correct.mni.2417/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.2417/1/ [ntraut@tars-540:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/] [2017-10-07 16:55:20] 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.2417/1/ ./tmp.mri_nu_correct.mni.2417/nu1.mnc ./tmp.mri_nu_correct.mni.2417/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 16 CV of field change: 0.000954767 mri_binarize --i ./tmp.mri_nu_correct.mni.2417/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2417/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-6.0.0/0050750/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.2417/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2417/ones.mgz sysname Linux hostname tars-540 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.2417/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.2417/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.2417/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2417/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2417/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.2417/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2417/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2417/input.mean.dat sysname Linux hostname tars-540 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2417/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.2417/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2417/ones.mgz --i ./tmp.mri_nu_correct.mni.2417/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2417/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2417/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.2417/ones.mgz --i ./tmp.mri_nu_correct.mni.2417/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2417/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2417/output.mean.dat sysname Linux hostname tars-540 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2417/ones.mgz Loading ./tmp.mri_nu_correct.mni.2417/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.2417/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2417/nu2.mnc ./tmp.mri_nu_correct.mni.2417/nu2.mnc mul 1.06960097806968388267 Saving result to './tmp.mri_nu_correct.mni.2417/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.2417/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.2417/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.2417/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.00586e-09, 9.31323e-10) j_ras = (0, 0, -1) k_ras = (1.74623e-09, 1, 7.45058e-09) 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 ( 9, 139) to ( 3, 110) Sat Oct 7 16:56:37 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 16:56:38 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 1.12892 0.02962 -0.03454 -9.79909; -0.03565 1.05542 0.27351 -25.34316; 0.02626 -0.22579 1.00312 9.94508; 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 = 16 Starting OpenSpline(): npoints = 16 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 45 (45), valley at 27 (27) csf peak at 23, setting threshold to 37 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 45 (45), valley at 15 (15) csf peak at 23, setting threshold to 37 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 12 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 16:58:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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=11.0 skull bounding box = (51, 34, 17) --> (205, 255, 236) using (102, 108, 127) as brain centroid... mean wm in atlas = 108, using box (83,81,100) --> (120, 135,154) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 103 +- 6.1 after smoothing, mri peak at 103, scaling input intensities by 1.049 scaling channel 0 by 1.04854 initial log_p = -4.272 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.273814 @ (0.000, 0.000, 0.000) max log p = -4.206159 @ (-4.545, 4.545, -13.636) max log p = -4.108697 @ (2.273, -2.273, 6.818) max log p = -4.103994 @ (-1.136, 1.136, 1.136) max log p = -4.101005 @ (-0.568, 1.705, -1.705) max log p = -4.099584 @ (-0.284, -3.125, -0.852) Found translation: (-4.3, 2.0, -8.2): log p = -4.100 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.808, old_max_log_p =-4.100 (thresh=-4.1) 1.06375 0.00000 0.00000 -12.49382; 0.00000 1.11081 0.29764 -41.51353; 0.00000 -0.25882 0.96593 32.10440; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.808, old_max_log_p =-3.808 (thresh=-3.8) 1.06375 0.00000 0.00000 -12.49382; 0.00000 1.11081 0.29764 -41.51353; 0.00000 -0.25882 0.96593 32.10440; 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=-3.737, old_max_log_p =-3.808 (thresh=-3.8) 1.08303 -0.03891 -0.00809 -8.82328; 0.03159 1.06237 0.22074 -30.07398; 0.00000 -0.18896 1.00107 18.62321; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.737, old_max_log_p =-3.737 (thresh=-3.7) 1.08303 -0.03891 -0.00809 -8.82328; 0.03159 1.06237 0.22074 -30.07398; 0.00000 -0.18896 1.00107 18.62321; 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=-3.714, old_max_log_p =-3.737 (thresh=-3.7) 1.08078 -0.05110 -0.03641 -3.10704; 0.04936 1.05965 0.23694 -34.84317; 0.02607 -0.20760 0.99796 18.59357; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.711, old_max_log_p =-3.714 (thresh=-3.7) 1.07699 -0.05092 -0.03628 -2.65745; 0.04936 1.05965 0.23694 -34.84317; 0.02607 -0.20760 0.99796 18.59357; 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 1.07699 -0.05092 -0.03628 -2.65745; 0.04936 1.05965 0.23694 -34.84317; 0.02607 -0.20760 0.99796 18.59357; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.07699 -0.05092 -0.03628 -2.65745; 0.04936 1.05965 0.23694 -34.84317; 0.02607 -0.20760 0.99796 18.59357; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07699 -0.05092 -0.03628 -2.65745; 0.04936 1.05965 0.23694 -34.84317; 0.02607 -0.20760 0.99796 18.59357; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.711 (old=-4.272) transform before final EM align: 1.07699 -0.05092 -0.03628 -2.65745; 0.04936 1.05965 0.23694 -34.84317; 0.02607 -0.20760 0.99796 18.59357; 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 1.07699 -0.05092 -0.03628 -2.65745; 0.04936 1.05965 0.23694 -34.84317; 0.02607 -0.20760 0.99796 18.59357; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.07699 -0.05092 -0.03628 -2.65745; 0.04936 1.05965 0.23694 -34.84317; 0.02607 -0.20760 0.99796 18.59357; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.1 tol 0.000000 final transform: 1.07699 -0.05092 -0.03628 -2.65745; 0.04936 1.05965 0.23694 -34.84317; 0.02607 -0.20760 0.99796 18.59357; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1065.320046 mri_em_register stimesec 1.126828 mri_em_register ru_maxrss 609824 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157579 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 207 mri_em_register ru_nivcsw 4697 registration took 9 minutes and 18 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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=129 y=109 z=114 r=91 first estimation of the main basin volume: 3207206 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=148, y=103, z=72, Imax=255 CSF=16, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=9617178629 voxels, voxel volume =1.000 = 9617178629 mmm3 = 9617178.624 cm3 done. PostAnalyze...Basin Prior 38 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=115, z=106, r=10457 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=33 , nb = 45154 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=34 , nb = -1029843032 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=25 , nb = 1077470247 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=33 , nb = 1091671694 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=31 , nb = 1077005022 OTHER CSF_MIN=5, CSF_intensity=18, CSF_MAX=35 , nb = 1077613969 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 33, 26, 21, 43 after analyzing : 21, 26, 26, 30 RIGHT_CER before analyzing : 34, 26, 17, 56 after analyzing : 20, 26, 26, 33 LEFT_CER before analyzing : 25, 23, 22, 50 after analyzing : 23, 24, 25, 30 RIGHT_BRAIN before analyzing : 33, 26, 21, 43 after analyzing : 21, 26, 26, 30 LEFT_BRAIN before analyzing : 31, 25, 21, 42 after analyzing : 20, 25, 25, 29 OTHER before analyzing : 35, 43, 58, 86 after analyzing : 35, 53, 58, 61 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...71 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 71.892, std = 6.951 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.42, sigma = 3.51 after rotation: sse = 2.42, sigma = 3.51 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.42, its var is 2.85 before Erosion-Dilatation 0.00% 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...33 iterations mri_strip_skull: done peeling brain Brain Size = 1766724 voxels, voxel volume = 1.000 mm3 = 1766724 mmm3 = 1766.724 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 22.595564 mri_watershed stimesec 0.373943 mri_watershed ru_maxrss 835308 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 216166 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2832 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1352 mri_watershed ru_nivcsw 44 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Oct 7 17:08:31 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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=18.0 skull bounding box = (61, 50, 34) --> (195, 194, 199) using (106, 98, 117) as brain centroid... mean wm in atlas = 107, using box (90,80,97) --> (122, 115,137) to find MRI wm before smoothing, mri peak at 102 robust fit to distribution - 103 +- 5.8 after smoothing, mri peak at 103, scaling input intensities by 1.039 scaling channel 0 by 1.03883 initial log_p = -3.921 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.924537 @ (0.000, 0.000, 0.000) max log p = -3.857328 @ (-4.545, 4.545, -4.545) max log p = -3.743552 @ (2.273, 2.273, -2.273) max log p = -3.704609 @ (1.136, -1.136, 1.136) max log p = -3.700269 @ (0.568, 0.568, -1.705) max log p = -3.700269 @ (0.000, 0.000, 0.000) Found translation: (-0.6, 6.2, -7.4): log p = -3.700 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.458, old_max_log_p =-3.700 (thresh=-3.7) 1.07500 0.00000 0.00000 -10.11609; 0.00000 1.03837 0.27823 -29.48032; 0.00000 -0.25882 0.96593 33.21516; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.458, old_max_log_p =-3.458 (thresh=-3.5) 1.07500 0.00000 0.00000 -10.11609; 0.00000 1.03837 0.27823 -29.48032; 0.00000 -0.25882 0.96593 33.21516; 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=-3.306, old_max_log_p =-3.458 (thresh=-3.5) 1.05409 0.00000 0.00000 -9.32885; 0.00000 1.03333 0.21044 -19.86788; 0.00000 -0.19749 1.01888 16.82209; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.303, old_max_log_p =-3.306 (thresh=-3.3) 1.07385 0.00000 0.00000 -11.88008; 0.00000 1.03333 0.21044 -19.86788; 0.00000 -0.19749 1.01888 16.82209; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.303, old_max_log_p =-3.303 (thresh=-3.3) 1.07385 0.00000 0.00000 -11.88008; 0.00000 1.03333 0.21044 -19.86788; 0.00000 -0.19749 1.01888 16.82209; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.261, old_max_log_p =-3.303 (thresh=-3.3) 1.07496 0.01693 0.00345 -14.30310; -0.01761 1.03397 0.21921 -19.08953; 0.00014 -0.20573 1.01592 18.52161; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.255, old_max_log_p =-3.261 (thresh=-3.3) 1.07370 0.01691 0.00344 -14.13781; -0.01767 1.03760 0.21998 -19.57639; 0.00014 -0.20525 1.01354 18.72533; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.255, old_max_log_p =-3.255 (thresh=-3.3) 1.07370 0.01691 0.00344 -14.13781; -0.01767 1.03760 0.21998 -19.57639; 0.00014 -0.20525 1.01354 18.72533; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07370 0.01691 0.00344 -14.13781; -0.01767 1.03760 0.21998 -19.57639; 0.00014 -0.20525 1.01354 18.72533; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.07370 0.01691 0.00344 -14.13781; -0.01767 1.03760 0.21998 -19.57639; 0.00014 -0.20525 1.01354 18.72533; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07370 0.01691 0.00344 -14.13781; -0.01767 1.03760 0.21998 -19.57639; 0.00014 -0.20525 1.01354 18.72533; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.255 (old=-3.921) transform before final EM align: 1.07370 0.01691 0.00344 -14.13781; -0.01767 1.03760 0.21998 -19.57639; 0.00014 -0.20525 1.01354 18.72533; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07370 0.01691 0.00344 -14.13781; -0.01767 1.03760 0.21998 -19.57639; 0.00014 -0.20525 1.01354 18.72533; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.07370 0.01691 0.00344 -14.13781; -0.01767 1.03760 0.21998 -19.57639; 0.00014 -0.20525 1.01354 18.72533; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 3.8 tol 0.000000 final transform: 1.07370 0.01691 0.00344 -14.13781; -0.01767 1.03760 0.21998 -19.57639; 0.00014 -0.20525 1.01354 18.72533; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1151.805898 mri_em_register stimesec 1.956702 mri_em_register ru_maxrss 600984 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 159471 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 227 mri_em_register ru_nivcsw 9838 registration took 9 minutes and 53 seconds. #-------------------------------------- #@# CA Normalize Sat Oct 7 17:18:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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=18.0 skull bounding box = (61, 50, 34) --> (195, 194, 199) using (106, 98, 117) as brain centroid... mean wm in atlas = 107, using box (90,80,97) --> (122, 115,137) to find MRI wm before smoothing, mri peak at 102 robust fit to distribution - 103 +- 5.8 after smoothing, mri peak at 103, scaling input intensities by 1.039 scaling channel 0 by 1.03883 using 246344 sample points... INFO: compute sample coordinates transform 1.07370 0.01691 0.00344 -14.13781; -0.01767 1.03760 0.21998 -19.57639; 0.00014 -0.20525 1.01354 18.72533; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 50, 35) --> (190, 159, 194) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 1133 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 51, 33) --> (131, 158, 195) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 810 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 137, 62) --> (174, 178, 114) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 137, 59) --> (128, 175, 115) Right_Cerebellum_White_Matter: limiting intensities to 104.0 --> 132.0 0 of 7 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 124, 96) --> (145, 191, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 9 (0.0%) samples deleted using 1968 total control points for intensity normalization... bias field = 0.956 +- 0.046 11 of 1968 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 50, 35) --> (190, 159, 194) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 1404 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 51, 33) --> (131, 158, 195) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 1220 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 137, 62) --> (174, 178, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 77 (10.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 137, 59) --> (128, 175, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 65 (12.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 124, 96) --> (145, 191, 125) Brain_Stem: limiting intensities to 92.0 --> 132.0 43 of 86 (50.0%) samples deleted using 2852 total control points for intensity normalization... bias field = 1.005 +- 0.055 11 of 2770 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 50, 35) --> (190, 159, 194) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 1446 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 51, 33) --> (131, 158, 195) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 1326 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 137, 62) --> (174, 178, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 41 of 131 (31.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 137, 59) --> (128, 175, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 34 of 74 (45.9%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 124, 96) --> (145, 191, 125) Brain_Stem: limiting intensities to 89.0 --> 132.0 95 of 192 (49.5%) samples deleted using 3169 total control points for intensity normalization... bias field = 1.002 +- 0.048 1 of 2920 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 45 seconds. #-------------------------------------- #@# CA Reg Sat Oct 7 17:20:10 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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) = 1.18 (predicted orig area = 6.8) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.817, neg=0, invalid=762 0001: dt=164.684632, rms=0.751 (8.048%), neg=0, invalid=762 0002: dt=168.907216, rms=0.735 (2.117%), neg=0, invalid=762 0003: dt=177.852632, rms=0.729 (0.883%), neg=0, invalid=762 0004: dt=167.529412, rms=0.725 (0.581%), neg=0, invalid=762 0005: dt=295.936000, rms=0.721 (0.536%), neg=0, invalid=762 0006: dt=129.472000, rms=0.718 (0.412%), neg=0, invalid=762 0007: dt=369.920000, rms=0.715 (0.404%), neg=0, invalid=762 0008: dt=110.976000, rms=0.713 (0.279%), neg=0, invalid=762 0009: dt=1183.744000, rms=0.709 (0.624%), neg=0, invalid=762 0010: dt=110.976000, rms=0.705 (0.490%), neg=0, invalid=762 0011: dt=443.904000, rms=0.704 (0.168%), neg=0, invalid=762 0012: dt=443.904000, rms=0.704 (-1.213%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.704, neg=0, invalid=762 0013: dt=129.472000, rms=0.702 (0.308%), neg=0, invalid=762 0014: dt=517.888000, rms=0.701 (0.201%), neg=0, invalid=762 0015: dt=517.888000, rms=0.700 (0.090%), neg=0, invalid=762 0016: dt=517.888000, rms=0.700 (-0.675%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.702, neg=0, invalid=762 0017: dt=161.807910, rms=0.685 (2.465%), neg=0, invalid=762 0018: dt=85.595628, rms=0.673 (1.701%), neg=0, invalid=762 0019: dt=123.917448, rms=0.666 (1.163%), neg=0, invalid=762 0020: dt=73.228605, rms=0.660 (0.862%), neg=0, invalid=762 0021: dt=171.807487, rms=0.655 (0.793%), neg=0, invalid=762 0022: dt=62.208000, rms=0.650 (0.714%), neg=0, invalid=762 0023: dt=145.152000, rms=0.647 (0.528%), neg=0, invalid=762 0024: dt=83.067847, rms=0.644 (0.386%), neg=0, invalid=762 0025: dt=92.044944, rms=0.642 (0.264%), neg=0, invalid=762 0026: dt=103.680000, rms=0.640 (0.317%), neg=0, invalid=762 0027: dt=72.727273, rms=0.639 (0.230%), neg=0, invalid=762 0028: dt=72.727273, rms=0.637 (0.212%), neg=0, invalid=762 0029: dt=72.727273, rms=0.636 (0.302%), neg=0, invalid=762 0030: dt=72.727273, rms=0.633 (0.453%), neg=0, invalid=762 0031: dt=72.727273, rms=0.630 (0.471%), neg=0, invalid=762 0032: dt=72.727273, rms=0.626 (0.542%), neg=0, invalid=762 0033: dt=72.727273, rms=0.623 (0.482%), neg=0, invalid=762 0034: dt=72.727273, rms=0.620 (0.487%), neg=0, invalid=762 0035: dt=72.727273, rms=0.618 (0.410%), neg=0, invalid=762 0036: dt=72.727273, rms=0.615 (0.356%), neg=0, invalid=762 0037: dt=72.727273, rms=0.614 (0.315%), neg=0, invalid=762 0038: dt=72.727273, rms=0.612 (0.258%), neg=0, invalid=762 0039: dt=72.727273, rms=0.610 (0.246%), neg=0, invalid=762 0040: dt=72.727273, rms=0.609 (0.189%), neg=0, invalid=762 0041: dt=72.727273, rms=0.608 (0.173%), neg=0, invalid=762 0042: dt=72.727273, rms=0.607 (0.141%), neg=0, invalid=762 0043: dt=72.727273, rms=0.606 (0.160%), neg=0, invalid=762 0044: dt=72.727273, rms=0.606 (0.144%), neg=0, invalid=762 0045: dt=72.727273, rms=0.605 (0.137%), neg=0, invalid=762 0046: dt=72.727273, rms=0.604 (0.107%), neg=0, invalid=762 0047: dt=72.727273, rms=0.603 (0.108%), neg=0, invalid=762 0048: dt=72.727273, rms=0.603 (0.094%), neg=0, invalid=762 0049: dt=103.680000, rms=0.603 (0.017%), neg=0, invalid=762 0050: dt=103.680000, rms=0.603 (0.022%), neg=0, invalid=762 0051: dt=103.680000, rms=0.603 (0.020%), neg=0, invalid=762 0052: dt=103.680000, rms=0.602 (0.019%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.603, neg=0, invalid=762 0053: dt=36.288000, rms=0.602 (0.183%), neg=0, invalid=762 0054: dt=62.208000, rms=0.602 (0.046%), neg=0, invalid=762 0055: dt=62.208000, rms=0.601 (0.013%), neg=0, invalid=762 0056: dt=62.208000, rms=0.601 (-0.023%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.626, neg=0, invalid=762 0057: dt=0.000000, rms=0.626 (0.085%), neg=0, invalid=762 0058: dt=0.000000, rms=0.626 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.626, neg=0, invalid=762 0059: dt=0.175000, rms=0.626 (0.085%), neg=0, invalid=762 0060: dt=0.043750, rms=0.626 (-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=0.698, neg=0, invalid=762 0061: dt=5.627551, rms=0.674 (3.473%), neg=0, invalid=762 0062: dt=3.456000, rms=0.673 (0.207%), neg=0, invalid=762 0063: dt=3.456000, rms=0.673 (-0.066%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.673, neg=0, invalid=762 0064: dt=0.000000, rms=0.673 (0.058%), neg=0, invalid=762 0065: dt=0.000000, rms=0.673 (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=0.732, neg=0, invalid=762 0066: dt=1.280000, rms=0.728 (0.512%), neg=0, invalid=762 0067: dt=2.208633, rms=0.722 (0.859%), neg=0, invalid=762 0068: dt=0.256000, rms=0.722 (0.013%), neg=0, invalid=762 0069: dt=0.256000, rms=0.722 (0.013%), neg=0, invalid=762 0070: dt=0.256000, rms=0.722 (0.006%), neg=0, invalid=762 0071: dt=0.256000, rms=0.722 (0.000%), neg=0, invalid=762 0072: dt=1.948718, rms=0.720 (0.276%), neg=0, invalid=762 0073: dt=0.000000, rms=0.720 (0.000%), neg=0, invalid=762 0074: dt=0.100000, rms=0.720 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.720, neg=0, invalid=762 0075: dt=0.448000, rms=0.719 (0.087%), neg=0, invalid=762 0076: dt=0.768000, rms=0.719 (0.025%), neg=0, invalid=762 0077: dt=0.768000, rms=0.719 (0.022%), neg=0, invalid=762 0078: dt=0.768000, rms=0.719 (-0.002%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.685, neg=0, invalid=762 0079: dt=0.876173, rms=0.665 (2.866%), neg=0, invalid=762 0080: dt=0.080000, rms=0.664 (0.143%), neg=0, invalid=762 0081: dt=0.080000, rms=0.664 (-0.083%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0082: dt=0.028000, rms=0.664 (0.080%), neg=0, invalid=762 0083: dt=0.004000, rms=0.664 (0.001%), neg=0, invalid=762 0084: dt=0.004000, rms=0.664 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.18336 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.32 x + 0.0 (451 voxels, overlap=0.004) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (451 voxels, peak = 6), gca=8.0 gca peak = 0.15565 (16) mri peak = 0.14253 ( 8) Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (638 voxels, overlap=0.267) Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (638 voxels, peak = 7), gca=7.0 gca peak = 0.26829 (96) mri peak = 0.08369 (93) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (949 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (949 voxels, peak = 92), gca=91.7 gca peak = 0.20183 (93) mri peak = 0.06096 (94) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (740 voxels, overlap=0.923) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (740 voxels, peak = 92), gca=91.6 gca peak = 0.21683 (55) mri peak = 0.07718 (60) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (698 voxels, overlap=0.998) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (698 voxels, peak = 53), gca=53.1 gca peak = 0.30730 (58) mri peak = 0.08960 (57) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (787 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (787 voxels, peak = 56), gca=56.0 gca peak = 0.11430 (101) mri peak = 0.07622 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (59649 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (59649 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.07303 (108) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (62615 voxels, overlap=0.587) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (62615 voxels, peak = 109), gca=108.6 gca peak = 0.14995 (59) mri peak = 0.06940 (41) Left_Cerebral_Cortex (3): linear fit = 0.74 x + 0.0 (27264 voxels, overlap=0.068) Left_Cerebral_Cortex (3): linear fit = 0.74 x + 0.0 (27264 voxels, peak = 43), gca=43.4 gca peak = 0.15082 (58) mri peak = 0.05601 (42) Right_Cerebral_Cortex (42): linear fit = 0.76 x + 0.0 (27275 voxels, overlap=0.222) Right_Cerebral_Cortex (42): linear fit = 0.76 x + 0.0 (27275 voxels, peak = 44), gca=44.4 gca peak = 0.14161 (67) mri peak = 0.10047 (66) Right_Caudate (50): linear fit = 0.98 x + 0.0 (823 voxels, overlap=0.896) Right_Caudate (50): linear fit = 0.98 x + 0.0 (823 voxels, peak = 65), gca=65.3 gca peak = 0.15243 (71) mri peak = 0.09537 (72) Left_Caudate (11): linear fit = 0.94 x + 0.0 (1095 voxels, overlap=0.811) Left_Caudate (11): linear fit = 0.94 x + 0.0 (1095 voxels, peak = 67), gca=67.1 gca peak = 0.13336 (57) mri peak = 0.03864 (51) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (29887 voxels, overlap=0.680) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (29887 voxels, peak = 51), gca=51.0 gca peak = 0.13252 (56) mri peak = 0.03393 (49) Right_Cerebellum_Cortex (47): linear fit = 0.88 x + 0.0 (28352 voxels, overlap=0.329) Right_Cerebellum_Cortex (47): linear fit = 0.88 x + 0.0 (28352 voxels, peak = 49), gca=49.0 gca peak = 0.18181 (84) mri peak = 0.06255 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (8615 voxels, overlap=0.730) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (8615 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.06073 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7368 voxels, overlap=0.872) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7368 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.07062 (65) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (460 voxels, overlap=0.998) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (460 voxels, peak = 60), gca=59.6 gca peak = 0.39313 (56) mri peak = 0.07307 (59) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (526 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (526 voxels, peak = 59), gca=58.5 gca peak = 0.14181 (85) mri peak = 0.04639 (87) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5616 voxels, overlap=0.763) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5616 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.05363 (86) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4668 voxels, overlap=0.929) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4668 voxels, peak = 87), gca=86.7 gca peak = 0.13399 (79) mri peak = 0.04617 (72) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2358 voxels, overlap=0.864) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2358 voxels, peak = 83), gca=82.6 gca peak = 0.14159 (79) mri peak = 0.05602 (72) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2430 voxels, overlap=0.923) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2430 voxels, peak = 77), gca=77.0 gca peak = 0.10025 (80) mri peak = 0.06503 (85) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13034 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13034 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.05710 (102) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1423 voxels, overlap=0.512) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1423 voxels, peak = 98), gca=98.5 gca peak = 0.12801 (89) mri peak = 0.05647 (98) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1604 voxels, overlap=0.610) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1604 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 1.00000 (48) gca peak = 0.15061 (21) mri peak = 0.08719 (11) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (428 voxels, overlap=0.108) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (428 voxels, peak = 10), gca=10.0 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) 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 0.92 x + 0.0 estimating mean wm scale to be 1.06 x + 0.0 estimating mean csf scale to be 0.42 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=0.721, neg=0, invalid=762 0085: dt=129.472000, rms=0.716 (0.626%), neg=0, invalid=762 0086: dt=221.952000, rms=0.713 (0.407%), neg=0, invalid=762 0087: dt=110.976000, rms=0.712 (0.158%), neg=0, invalid=762 0088: dt=129.472000, rms=0.711 (0.155%), neg=0, invalid=762 0089: dt=221.952000, rms=0.710 (0.123%), neg=0, invalid=762 0090: dt=129.472000, rms=0.709 (0.129%), neg=0, invalid=762 0091: dt=129.472000, rms=0.709 (0.068%), neg=0, invalid=762 0092: dt=129.472000, rms=0.708 (0.094%), neg=0, invalid=762 0093: dt=221.952000, rms=0.707 (0.068%), neg=0, invalid=762 0094: dt=129.472000, rms=0.707 (0.096%), neg=0, invalid=762 0095: dt=129.472000, rms=0.706 (0.041%), neg=0, invalid=762 0096: dt=129.472000, rms=0.706 (0.071%), neg=0, invalid=762 0097: dt=129.472000, rms=0.705 (0.088%), neg=0, invalid=762 0098: dt=129.472000, rms=0.705 (0.115%), neg=0, invalid=762 0099: dt=129.472000, rms=0.704 (0.121%), neg=0, invalid=762 0100: dt=129.472000, rms=0.703 (0.148%), neg=0, invalid=762 0101: dt=129.472000, rms=0.702 (0.125%), neg=0, invalid=762 0102: dt=129.472000, rms=0.701 (0.125%), neg=0, invalid=762 0103: dt=129.472000, rms=0.700 (0.108%), neg=0, invalid=762 0104: dt=129.472000, rms=0.699 (0.120%), neg=0, invalid=762 0105: dt=129.472000, rms=0.699 (0.104%), neg=0, invalid=762 0106: dt=129.472000, rms=0.698 (0.093%), neg=0, invalid=762 0107: dt=129.472000, rms=0.697 (0.077%), neg=0, invalid=762 0108: dt=129.472000, rms=0.697 (0.079%), neg=0, invalid=762 0109: dt=129.472000, rms=0.696 (0.074%), neg=0, invalid=762 0110: dt=129.472000, rms=0.696 (0.073%), neg=0, invalid=762 0111: dt=129.472000, rms=0.695 (0.065%), neg=0, invalid=762 0112: dt=129.472000, rms=0.695 (0.062%), neg=0, invalid=762 0113: dt=129.472000, rms=0.695 (0.062%), neg=0, invalid=762 0114: dt=129.472000, rms=0.694 (0.057%), neg=0, invalid=762 0115: dt=129.472000, rms=0.694 (0.052%), neg=0, invalid=762 0116: dt=129.472000, rms=0.693 (0.045%), neg=0, invalid=762 0117: dt=129.472000, rms=0.693 (0.049%), neg=0, invalid=762 0118: dt=129.472000, rms=0.693 (0.049%), neg=0, invalid=762 0119: dt=129.472000, rms=0.692 (0.048%), neg=0, invalid=762 0120: dt=129.472000, rms=0.692 (0.043%), neg=0, invalid=762 0121: dt=129.472000, rms=0.692 (0.045%), neg=0, invalid=762 0122: dt=129.472000, rms=0.691 (0.047%), neg=0, invalid=762 0123: dt=129.472000, rms=0.691 (0.048%), neg=0, invalid=762 0124: dt=129.472000, rms=0.691 (0.047%), neg=0, invalid=762 0125: dt=129.472000, rms=0.691 (0.046%), neg=0, invalid=762 0126: dt=129.472000, rms=0.690 (0.042%), neg=0, invalid=762 0127: dt=129.472000, rms=0.690 (0.041%), neg=0, invalid=762 0128: dt=129.472000, rms=0.690 (0.048%), neg=0, invalid=762 0129: dt=129.472000, rms=0.689 (0.047%), neg=0, invalid=762 0130: dt=129.472000, rms=0.689 (0.044%), neg=0, invalid=762 0131: dt=129.472000, rms=0.689 (0.036%), neg=0, invalid=762 0132: dt=129.472000, rms=0.689 (0.029%), neg=0, invalid=762 0133: dt=129.472000, rms=0.688 (0.031%), neg=0, invalid=762 0134: dt=129.472000, rms=0.688 (0.032%), neg=0, invalid=762 0135: dt=129.472000, rms=0.688 (0.034%), neg=0, invalid=762 0136: dt=129.472000, rms=0.688 (0.033%), neg=0, invalid=762 0137: dt=129.472000, rms=0.687 (0.030%), neg=0, invalid=762 0138: dt=129.472000, rms=0.687 (0.030%), neg=0, invalid=762 0139: dt=129.472000, rms=0.687 (0.022%), neg=0, invalid=762 0140: dt=129.472000, rms=0.687 (0.021%), neg=0, invalid=762 0141: dt=517.888000, rms=0.687 (0.021%), neg=0, invalid=762 0142: dt=27.744000, rms=0.687 (0.001%), neg=0, invalid=762 0143: dt=27.744000, rms=0.687 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.688, neg=0, invalid=762 0144: dt=369.920000, rms=0.686 (0.211%), neg=0, invalid=762 0145: dt=92.480000, rms=0.686 (0.045%), neg=0, invalid=762 0146: dt=92.480000, rms=0.686 (0.011%), neg=0, invalid=762 0147: dt=92.480000, rms=0.686 (0.018%), neg=0, invalid=762 0148: dt=92.480000, rms=0.685 (0.025%), neg=0, invalid=762 0149: dt=92.480000, rms=0.685 (0.031%), neg=0, invalid=762 0150: dt=92.480000, rms=0.685 (0.035%), neg=0, invalid=762 0151: dt=92.480000, rms=0.685 (0.038%), neg=0, invalid=762 0152: dt=92.480000, rms=0.684 (0.035%), neg=0, invalid=762 0153: dt=92.480000, rms=0.684 (0.031%), neg=0, invalid=762 0154: dt=92.480000, rms=0.684 (0.030%), neg=0, invalid=762 0155: dt=92.480000, rms=0.684 (0.031%), neg=0, invalid=762 0156: dt=92.480000, rms=0.684 (0.031%), neg=0, invalid=762 0157: dt=92.480000, rms=0.683 (0.027%), neg=0, invalid=762 0158: dt=92.480000, rms=0.683 (0.023%), neg=0, invalid=762 0159: dt=92.480000, rms=0.683 (0.023%), neg=0, invalid=762 0160: dt=517.888000, rms=0.683 (0.017%), neg=0, invalid=762 0161: dt=517.888000, rms=0.683 (-0.055%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.684, neg=0, invalid=762 0162: dt=145.152000, rms=0.677 (1.008%), neg=0, invalid=762 0163: dt=331.776000, rms=0.669 (1.309%), neg=0, invalid=762 0164: dt=61.886792, rms=0.663 (0.831%), neg=0, invalid=762 0165: dt=124.416000, rms=0.661 (0.347%), neg=0, invalid=762 0166: dt=66.254743, rms=0.659 (0.298%), neg=0, invalid=762 0167: dt=145.152000, rms=0.657 (0.307%), neg=0, invalid=762 0168: dt=36.288000, rms=0.655 (0.243%), neg=0, invalid=762 0169: dt=331.776000, rms=0.652 (0.462%), neg=0, invalid=762 0170: dt=36.288000, rms=0.650 (0.375%), neg=0, invalid=762 0171: dt=145.152000, rms=0.648 (0.216%), neg=0, invalid=762 0172: dt=36.288000, rms=0.647 (0.152%), neg=0, invalid=762 0173: dt=331.776000, rms=0.645 (0.286%), neg=0, invalid=762 0174: dt=36.288000, rms=0.644 (0.269%), neg=0, invalid=762 0175: dt=124.416000, rms=0.643 (0.154%), neg=0, invalid=762 0176: dt=62.208000, rms=0.642 (0.126%), neg=0, invalid=762 0177: dt=145.152000, rms=0.641 (0.170%), neg=0, invalid=762 0178: dt=62.208000, rms=0.640 (0.083%), neg=0, invalid=762 0179: dt=145.152000, rms=0.639 (0.148%), neg=0, invalid=762 0180: dt=36.288000, rms=0.639 (0.071%), neg=0, invalid=762 0181: dt=414.720000, rms=0.637 (0.217%), neg=0, invalid=762 0182: dt=36.288000, rms=0.636 (0.220%), neg=0, invalid=762 0183: dt=124.416000, rms=0.635 (0.115%), neg=0, invalid=762 0184: dt=36.288000, rms=0.635 (0.059%), neg=0, invalid=762 0185: dt=145.152000, rms=0.634 (0.088%), neg=0, invalid=762 0186: dt=62.208000, rms=0.634 (0.077%), neg=0, invalid=762 0187: dt=82.944000, rms=0.634 (0.057%), neg=0, invalid=762 0188: dt=103.680000, rms=0.633 (0.087%), neg=0, invalid=762 0189: dt=36.288000, rms=0.633 (0.047%), neg=0, invalid=762 0190: dt=36.288000, rms=0.633 (0.030%), neg=0, invalid=762 0191: dt=36.288000, rms=0.632 (0.046%), neg=0, invalid=762 0192: dt=36.288000, rms=0.632 (0.073%), neg=0, invalid=762 0193: dt=36.288000, rms=0.631 (0.098%), neg=0, invalid=762 0194: dt=36.288000, rms=0.630 (0.110%), neg=0, invalid=762 0195: dt=36.288000, rms=0.630 (0.125%), neg=0, invalid=762 0196: dt=36.288000, rms=0.629 (0.137%), neg=0, invalid=762 0197: dt=36.288000, rms=0.628 (0.136%), neg=0, invalid=762 0198: dt=36.288000, rms=0.627 (0.145%), neg=0, invalid=762 0199: dt=36.288000, rms=0.626 (0.148%), neg=0, invalid=762 0200: dt=36.288000, rms=0.625 (0.151%), neg=0, invalid=762 0201: dt=36.288000, rms=0.624 (0.145%), neg=0, invalid=762 0202: dt=36.288000, rms=0.623 (0.140%), neg=0, invalid=762 0203: dt=36.288000, rms=0.623 (0.130%), neg=0, invalid=762 0204: dt=36.288000, rms=0.622 (0.123%), neg=0, invalid=762 0205: dt=36.288000, rms=0.621 (0.123%), neg=0, invalid=762 0206: dt=36.288000, rms=0.620 (0.118%), neg=0, invalid=762 0207: dt=36.288000, rms=0.620 (0.113%), neg=0, invalid=762 0208: dt=36.288000, rms=0.619 (0.100%), neg=0, invalid=762 0209: dt=36.288000, rms=0.618 (0.098%), neg=0, invalid=762 0210: dt=36.288000, rms=0.618 (0.094%), neg=0, invalid=762 0211: dt=36.288000, rms=0.617 (0.099%), neg=0, invalid=762 0212: dt=36.288000, rms=0.617 (0.096%), neg=0, invalid=762 0213: dt=36.288000, rms=0.616 (0.087%), neg=0, invalid=762 0214: dt=36.288000, rms=0.616 (0.072%), neg=0, invalid=762 0215: dt=36.288000, rms=0.615 (0.073%), neg=0, invalid=762 0216: dt=36.288000, rms=0.615 (0.084%), neg=0, invalid=762 0217: dt=36.288000, rms=0.614 (0.079%), neg=0, invalid=762 0218: dt=36.288000, rms=0.614 (0.079%), neg=0, invalid=762 0219: dt=36.288000, rms=0.613 (0.072%), neg=0, invalid=762 0220: dt=36.288000, rms=0.613 (0.064%), neg=0, invalid=762 0221: dt=36.288000, rms=0.613 (0.060%), neg=0, invalid=762 0222: dt=36.288000, rms=0.612 (0.064%), neg=0, invalid=762 0223: dt=36.288000, rms=0.612 (0.065%), neg=0, invalid=762 0224: dt=36.288000, rms=0.611 (0.065%), neg=0, invalid=762 0225: dt=36.288000, rms=0.611 (0.064%), neg=0, invalid=762 0226: dt=36.288000, rms=0.611 (0.054%), neg=0, invalid=762 0227: dt=36.288000, rms=0.610 (0.051%), neg=0, invalid=762 0228: dt=36.288000, rms=0.610 (0.051%), neg=0, invalid=762 0229: dt=36.288000, rms=0.610 (0.057%), neg=0, invalid=762 0230: dt=36.288000, rms=0.609 (0.049%), neg=0, invalid=762 0231: dt=36.288000, rms=0.609 (0.048%), neg=0, invalid=762 0232: dt=36.288000, rms=0.609 (0.049%), neg=0, invalid=762 0233: dt=36.288000, rms=0.608 (0.049%), neg=0, invalid=762 0234: dt=36.288000, rms=0.608 (0.045%), neg=0, invalid=762 0235: dt=36.288000, rms=0.608 (0.047%), neg=0, invalid=762 0236: dt=36.288000, rms=0.608 (0.047%), neg=0, invalid=762 0237: dt=36.288000, rms=0.607 (0.045%), neg=0, invalid=762 0238: dt=36.288000, rms=0.607 (0.044%), neg=0, invalid=762 0239: dt=36.288000, rms=0.607 (0.048%), neg=0, invalid=762 0240: dt=36.288000, rms=0.607 (0.042%), neg=0, invalid=762 0241: dt=36.288000, rms=0.606 (0.043%), neg=0, invalid=762 0242: dt=36.288000, rms=0.606 (0.040%), neg=0, invalid=762 0243: dt=36.288000, rms=0.606 (0.041%), neg=0, invalid=762 0244: dt=36.288000, rms=0.606 (0.036%), neg=0, invalid=762 0245: dt=36.288000, rms=0.605 (0.041%), neg=0, invalid=762 0246: dt=36.288000, rms=0.605 (0.003%), neg=0, invalid=762 0247: dt=36.288000, rms=0.605 (0.006%), neg=0, invalid=762 0248: dt=18.144000, rms=0.605 (0.000%), neg=0, invalid=762 0249: dt=2.268000, rms=0.605 (0.000%), neg=0, invalid=762 0250: dt=1.134000, rms=0.605 (0.001%), neg=0, invalid=762 0251: dt=0.141750, rms=0.605 (0.000%), neg=0, invalid=762 0252: dt=0.035437, rms=0.605 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.606, neg=0, invalid=762 0253: dt=145.152000, rms=0.603 (0.523%), neg=0, invalid=762 0254: dt=62.208000, rms=0.603 (0.082%), neg=0, invalid=762 0255: dt=124.416000, rms=0.602 (0.090%), neg=0, invalid=762 0256: dt=36.288000, rms=0.602 (0.059%), neg=0, invalid=762 0257: dt=497.664000, rms=0.601 (0.176%), neg=0, invalid=762 0258: dt=36.288000, rms=0.600 (0.097%), neg=0, invalid=762 0259: dt=103.680000, rms=0.600 (0.038%), neg=0, invalid=762 0260: dt=103.680000, rms=0.600 (0.022%), neg=0, invalid=762 0261: dt=103.680000, rms=0.599 (0.069%), neg=0, invalid=762 0262: dt=103.680000, rms=0.599 (0.072%), neg=0, invalid=762 0263: dt=103.680000, rms=0.598 (0.077%), neg=0, invalid=762 0264: dt=103.680000, rms=0.598 (0.090%), neg=0, invalid=762 0265: dt=103.680000, rms=0.597 (0.104%), neg=0, invalid=762 0266: dt=103.680000, rms=0.597 (0.095%), neg=0, invalid=762 0267: dt=103.680000, rms=0.596 (0.079%), neg=0, invalid=762 0268: dt=103.680000, rms=0.596 (0.080%), neg=0, invalid=762 0269: dt=103.680000, rms=0.595 (0.084%), neg=0, invalid=762 0270: dt=103.680000, rms=0.595 (0.084%), neg=0, invalid=762 0271: dt=103.680000, rms=0.594 (0.069%), neg=0, invalid=762 0272: dt=103.680000, rms=0.594 (0.067%), neg=0, invalid=762 0273: dt=103.680000, rms=0.593 (0.075%), neg=0, invalid=762 0274: dt=103.680000, rms=0.593 (0.077%), neg=0, invalid=762 0275: dt=103.680000, rms=0.593 (0.079%), neg=0, invalid=762 0276: dt=103.680000, rms=0.592 (0.075%), neg=0, invalid=762 0277: dt=103.680000, rms=0.592 (0.061%), neg=0, invalid=762 0278: dt=103.680000, rms=0.591 (0.057%), neg=0, invalid=762 0279: dt=103.680000, rms=0.591 (0.086%), neg=0, invalid=762 0280: dt=103.680000, rms=0.590 (0.062%), neg=0, invalid=762 0281: dt=103.680000, rms=0.590 (0.043%), neg=0, invalid=762 0282: dt=103.680000, rms=0.590 (0.073%), neg=0, invalid=762 0283: dt=103.680000, rms=0.589 (0.060%), neg=0, invalid=762 0284: dt=103.680000, rms=0.589 (0.044%), neg=0, invalid=762 0285: dt=103.680000, rms=0.589 (0.074%), neg=0, invalid=762 0286: dt=103.680000, rms=0.588 (0.051%), neg=0, invalid=762 0287: dt=103.680000, rms=0.588 (0.053%), neg=0, invalid=762 0288: dt=103.680000, rms=0.588 (0.058%), neg=0, invalid=762 0289: dt=103.680000, rms=0.588 (0.051%), neg=0, invalid=762 0290: dt=103.680000, rms=0.587 (0.054%), neg=0, invalid=762 0291: dt=103.680000, rms=0.587 (0.041%), neg=0, invalid=762 0292: dt=103.680000, rms=0.587 (0.032%), neg=0, invalid=762 0293: dt=103.680000, rms=0.586 (0.070%), neg=0, invalid=762 0294: dt=103.680000, rms=0.586 (0.042%), neg=0, invalid=762 0295: dt=103.680000, rms=0.586 (0.031%), neg=0, invalid=762 0296: dt=103.680000, rms=0.586 (0.040%), neg=0, invalid=762 0297: dt=103.680000, rms=0.585 (0.049%), neg=0, invalid=762 0298: dt=103.680000, rms=0.585 (0.037%), neg=0, invalid=762 0299: dt=103.680000, rms=0.585 (0.033%), neg=0, invalid=762 0300: dt=103.680000, rms=0.585 (0.048%), neg=0, invalid=762 0301: dt=103.680000, rms=0.585 (0.025%), neg=0, invalid=762 0302: dt=103.680000, rms=0.584 (0.032%), neg=0, invalid=762 0303: dt=103.680000, rms=0.584 (0.046%), neg=0, invalid=762 0304: dt=103.680000, rms=0.584 (0.027%), neg=0, invalid=762 0305: dt=103.680000, rms=0.584 (0.037%), neg=0, invalid=762 0306: dt=103.680000, rms=0.584 (0.032%), neg=0, invalid=762 0307: dt=103.680000, rms=0.583 (0.023%), neg=0, invalid=762 0308: dt=103.680000, rms=0.583 (0.035%), neg=0, invalid=762 0309: dt=103.680000, rms=0.583 (0.040%), neg=0, invalid=762 0310: dt=103.680000, rms=0.583 (0.023%), neg=0, invalid=762 0311: dt=103.680000, rms=0.583 (0.026%), neg=0, invalid=762 0312: dt=103.680000, rms=0.583 (0.027%), neg=0, invalid=762 0313: dt=103.680000, rms=0.582 (0.025%), neg=0, invalid=762 0314: dt=103.680000, rms=0.582 (0.036%), neg=0, invalid=762 0315: dt=103.680000, rms=0.582 (0.031%), neg=0, invalid=762 0316: dt=103.680000, rms=0.582 (0.020%), neg=0, invalid=762 0317: dt=103.680000, rms=0.582 (0.031%), neg=0, invalid=762 0318: dt=103.680000, rms=0.582 (0.015%), neg=0, invalid=762 0319: dt=103.680000, rms=0.582 (0.017%), neg=0, invalid=762 0320: dt=103.680000, rms=0.581 (0.033%), neg=0, invalid=762 0321: dt=103.680000, rms=0.581 (0.021%), neg=0, invalid=762 0322: dt=103.680000, rms=0.581 (0.026%), neg=0, invalid=762 0323: dt=103.680000, rms=0.581 (0.016%), neg=0, invalid=762 0324: dt=103.680000, rms=0.581 (0.001%), neg=0, invalid=762 0325: dt=62.208000, rms=0.581 (0.032%), neg=0, invalid=762 0326: dt=0.007594, rms=0.581 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.590, neg=0, invalid=762 0327: dt=25.600000, rms=0.588 (0.351%), neg=0, invalid=762 0328: dt=44.800000, rms=0.587 (0.213%), neg=0, invalid=762 0329: dt=44.800000, rms=0.584 (0.367%), neg=0, invalid=762 0330: dt=67.111111, rms=0.582 (0.346%), neg=0, invalid=762 0331: dt=11.200000, rms=0.581 (0.225%), neg=0, invalid=762 0332: dt=8.000000, rms=0.580 (0.124%), neg=0, invalid=762 0333: dt=0.700000, rms=0.580 (0.012%), neg=0, invalid=762 0334: dt=0.350000, rms=0.580 (0.006%), neg=0, invalid=762 0335: dt=0.175000, rms=0.580 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.582, neg=0, invalid=762 0336: dt=53.384615, rms=0.576 (0.902%), neg=0, invalid=762 0337: dt=32.000000, rms=0.574 (0.411%), neg=0, invalid=762 0338: dt=32.000000, rms=0.573 (0.216%), neg=0, invalid=762 0339: dt=38.400000, rms=0.571 (0.222%), neg=0, invalid=762 0340: dt=25.600000, rms=0.570 (0.179%), neg=0, invalid=762 0341: dt=38.400000, rms=0.569 (0.203%), neg=0, invalid=762 0342: dt=11.200000, rms=0.569 (0.107%), neg=0, invalid=762 0343: dt=153.600000, rms=0.566 (0.422%), neg=0, invalid=762 0344: dt=20.235294, rms=0.564 (0.348%), neg=0, invalid=762 0345: dt=25.600000, rms=0.564 (0.101%), neg=0, invalid=762 0346: dt=38.400000, rms=0.563 (0.126%), neg=0, invalid=762 0347: dt=11.200000, rms=0.563 (0.081%), neg=0, invalid=762 0348: dt=153.600000, rms=0.561 (0.244%), neg=0, invalid=762 0349: dt=11.200000, rms=0.560 (0.228%), neg=0, invalid=762 0350: dt=32.000000, rms=0.559 (0.108%), neg=0, invalid=762 0351: dt=11.200000, rms=0.559 (0.060%), neg=0, invalid=762 0352: dt=128.000000, rms=0.558 (0.161%), neg=0, invalid=762 0353: dt=20.506122, rms=0.557 (0.184%), neg=0, invalid=762 0354: dt=32.000000, rms=0.557 (0.060%), neg=0, invalid=762 0355: dt=32.000000, rms=0.556 (0.092%), neg=0, invalid=762 0356: dt=11.200000, rms=0.556 (0.037%), neg=0, invalid=762 0357: dt=11.200000, rms=0.556 (0.024%), neg=0, invalid=762 0358: dt=11.200000, rms=0.556 (0.044%), neg=0, invalid=762 0359: dt=11.200000, rms=0.555 (0.057%), neg=0, invalid=762 0360: dt=11.200000, rms=0.555 (0.074%), neg=0, invalid=762 0361: dt=11.200000, rms=0.554 (0.093%), neg=0, invalid=762 0362: dt=11.200000, rms=0.554 (0.095%), neg=0, invalid=762 0363: dt=11.200000, rms=0.553 (0.111%), neg=0, invalid=762 0364: dt=11.200000, rms=0.553 (0.115%), neg=0, invalid=762 0365: dt=11.200000, rms=0.552 (0.117%), neg=0, invalid=762 0366: dt=11.200000, rms=0.551 (0.123%), neg=0, invalid=762 0367: dt=11.200000, rms=0.551 (0.127%), neg=0, invalid=762 0368: dt=11.200000, rms=0.550 (0.125%), neg=0, invalid=762 0369: dt=11.200000, rms=0.549 (0.121%), neg=0, invalid=762 0370: dt=11.200000, rms=0.549 (0.125%), neg=0, invalid=762 0371: dt=11.200000, rms=0.548 (0.124%), neg=0, invalid=762 0372: dt=11.200000, rms=0.547 (0.122%), neg=0, invalid=762 0373: dt=11.200000, rms=0.547 (0.113%), neg=0, invalid=762 0374: dt=11.200000, rms=0.547 (0.011%), neg=0, invalid=762 0375: dt=11.200000, rms=0.546 (0.020%), neg=0, invalid=762 0376: dt=5.600000, rms=0.546 (0.002%), neg=0, invalid=762 0377: dt=2.400000, rms=0.546 (0.002%), neg=0, invalid=762 0378: dt=0.150000, rms=0.546 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.565, neg=0, invalid=762 0379: dt=0.000000, rms=0.564 (0.154%), neg=0, invalid=762 0380: dt=0.000000, rms=0.564 (0.000%), neg=0, invalid=762 0381: dt=0.150000, rms=0.564 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.565, neg=0, invalid=762 0382: dt=0.000000, rms=0.564 (0.154%), neg=0, invalid=762 0383: dt=0.000000, rms=0.564 (0.000%), neg=0, invalid=762 0384: dt=0.150000, rms=0.564 (-0.015%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.600, neg=0, invalid=762 0385: dt=1.280000, rms=0.597 (0.494%), neg=0, invalid=762 0386: dt=0.000000, rms=0.597 (-0.002%), neg=0, invalid=762 0387: dt=0.100000, rms=0.597 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=762 0388: dt=0.448000, rms=0.596 (0.184%), neg=0, invalid=762 0389: dt=0.192000, rms=0.596 (0.007%), neg=0, invalid=762 0390: dt=0.192000, rms=0.596 (-0.003%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.553, neg=0, invalid=762 0391: dt=0.320000, rms=0.540 (2.329%), neg=0, invalid=762 0392: dt=0.384000, rms=0.533 (1.230%), neg=0, invalid=762 0393: dt=0.320000, rms=0.531 (0.425%), neg=0, invalid=762 0394: dt=0.320000, rms=0.529 (0.265%), neg=0, invalid=762 0395: dt=0.320000, rms=0.529 (0.187%), neg=0, invalid=762 0396: dt=0.320000, rms=0.528 (0.139%), neg=0, invalid=762 0397: dt=0.320000, rms=0.527 (0.109%), neg=0, invalid=762 0398: dt=0.320000, rms=0.527 (0.092%), neg=0, invalid=762 0399: dt=0.320000, rms=0.526 (0.067%), neg=0, invalid=762 0400: dt=0.320000, rms=0.526 (0.063%), neg=0, invalid=762 0401: dt=0.320000, rms=0.526 (0.052%), neg=0, invalid=762 0402: dt=0.320000, rms=0.526 (0.042%), neg=0, invalid=762 0403: dt=0.320000, rms=0.525 (0.039%), neg=0, invalid=762 0404: dt=0.320000, rms=0.525 (0.069%), neg=0, invalid=762 0405: dt=0.320000, rms=0.525 (0.024%), neg=0, invalid=762 0406: dt=0.320000, rms=0.525 (0.046%), neg=0, invalid=762 0407: dt=0.320000, rms=0.524 (0.018%), neg=0, invalid=762 0408: dt=0.320000, rms=0.524 (0.038%), neg=0, invalid=762 0409: dt=0.320000, rms=0.524 (0.012%), neg=0, invalid=762 0410: dt=0.320000, rms=0.524 (0.016%), neg=0, invalid=762 0411: dt=0.320000, rms=0.524 (0.013%), neg=0, invalid=762 0412: dt=0.112000, rms=0.524 (0.004%), neg=0, invalid=762 0413: dt=0.112000, rms=0.524 (0.006%), neg=0, invalid=762 0414: dt=0.112000, rms=0.524 (0.014%), neg=0, invalid=762 0415: dt=0.112000, rms=0.524 (0.006%), neg=0, invalid=762 0416: dt=0.112000, rms=0.524 (0.012%), neg=0, invalid=762 0417: dt=0.112000, rms=0.524 (0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.525, neg=0, invalid=762 0418: dt=0.112000, rms=0.523 (0.421%), neg=0, invalid=762 0419: dt=0.197917, rms=0.521 (0.324%), neg=0, invalid=762 0420: dt=0.112000, rms=0.520 (0.113%), neg=0, invalid=762 0421: dt=0.112000, rms=0.520 (0.083%), neg=0, invalid=762 0422: dt=0.112000, rms=0.519 (0.066%), neg=0, invalid=762 0423: dt=0.112000, rms=0.519 (0.047%), neg=0, invalid=762 0424: dt=0.112000, rms=0.519 (0.042%), neg=0, invalid=762 0425: dt=0.112000, rms=0.519 (0.060%), neg=0, invalid=762 0426: dt=0.112000, rms=0.518 (0.070%), neg=0, invalid=762 0427: dt=0.112000, rms=0.518 (0.061%), neg=0, invalid=762 0428: dt=0.112000, rms=0.518 (0.040%), neg=0, invalid=762 0429: dt=0.112000, rms=0.518 (0.007%), neg=0, invalid=762 0430: dt=0.112000, rms=0.518 (-0.022%), neg=0, invalid=762 0431: dt=0.000000, rms=0.518 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.516, neg=0, invalid=762 0432: dt=0.000000, rms=0.515 (0.183%), neg=0, invalid=762 0433: dt=0.000000, rms=0.515 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.516, neg=0, invalid=762 0434: dt=295.936000, rms=0.515 (0.212%), neg=0, invalid=762 0435: dt=110.976000, rms=0.515 (0.020%), neg=0, invalid=762 0436: dt=110.976000, rms=0.515 (0.011%), neg=0, invalid=762 0437: dt=110.976000, rms=0.515 (0.006%), neg=0, invalid=762 0438: dt=110.976000, rms=0.515 (0.024%), neg=0, invalid=762 0439: dt=110.976000, rms=0.515 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.516, neg=0, invalid=762 0440: dt=31.104000, rms=0.515 (0.223%), neg=0, invalid=762 0441: dt=36.288000, rms=0.515 (0.022%), neg=0, invalid=762 0442: dt=36.288000, rms=0.515 (0.011%), neg=0, invalid=762 0443: dt=36.288000, rms=0.515 (-0.018%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.516, neg=0, invalid=762 0444: dt=124.416000, rms=0.513 (0.509%), neg=0, invalid=762 0445: dt=36.288000, rms=0.512 (0.096%), neg=0, invalid=762 0446: dt=36.288000, rms=0.512 (0.045%), neg=0, invalid=762 0447: dt=36.288000, rms=0.512 (0.065%), neg=0, invalid=762 0448: dt=36.288000, rms=0.511 (0.080%), neg=0, invalid=762 0449: dt=36.288000, rms=0.511 (0.092%), neg=0, invalid=762 0450: dt=36.288000, rms=0.510 (0.099%), neg=0, invalid=762 0451: dt=36.288000, rms=0.510 (0.090%), neg=0, invalid=762 0452: dt=36.288000, rms=0.510 (0.072%), neg=0, invalid=762 0453: dt=36.288000, rms=0.510 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0454: dt=38.400000, rms=0.507 (0.670%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0455: dt=66.105263, rms=0.505 (0.398%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0456: dt=25.600000, rms=0.504 (0.314%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0457: dt=38.400000, rms=0.503 (0.178%), neg=0, invalid=762 0458: dt=38.400000, rms=0.502 (0.151%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0459: dt=38.400000, rms=0.500 (0.341%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0460: dt=38.400000, rms=0.500 (0.173%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=1, neg = 0 0461: dt=38.400000, rms=0.498 (0.334%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0462: dt=38.400000, rms=0.497 (0.158%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 4 iterations, nbhd size=0, neg = 0 0463: dt=38.400000, rms=0.496 (0.256%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0464: dt=38.400000, rms=0.495 (0.178%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 11 iterations, nbhd size=1, neg = 0 0465: dt=38.400000, rms=0.494 (0.243%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0466: dt=38.400000, rms=0.493 (0.211%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0467: dt=38.400000, rms=0.492 (0.147%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 11 iterations, nbhd size=1, neg = 0 0468: dt=38.400000, rms=0.491 (0.199%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0469: dt=38.400000, rms=0.490 (0.195%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0470: dt=38.400000, rms=0.489 (0.153%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0471: dt=38.400000, rms=0.489 (0.059%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 11 iterations, nbhd size=1, neg = 0 0472: dt=38.400000, rms=0.488 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0473: dt=38.400000, rms=0.488 (0.078%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 0474: dt=38.400000, rms=0.487 (0.138%), neg=0, invalid=762 0475: dt=38.400000, rms=0.487 (-0.095%), neg=0, invalid=762 0476: dt=11.200000, rms=0.487 (0.043%), neg=0, invalid=762 0477: dt=25.600000, rms=0.487 (0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.488, neg=0, invalid=762 0478: dt=69.097345, rms=0.483 (0.940%), neg=0, invalid=762 0479: dt=11.200000, rms=0.483 (0.157%), neg=0, invalid=762 0480: dt=11.200000, rms=0.482 (0.066%), neg=0, invalid=762 0481: dt=11.200000, rms=0.482 (0.069%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0482: dt=11.200000, rms=0.482 (0.047%), neg=0, invalid=762 0483: dt=11.200000, rms=0.482 (0.061%), neg=0, invalid=762 0484: dt=11.200000, rms=0.481 (0.083%), neg=0, invalid=762 0485: dt=11.200000, rms=0.481 (0.088%), neg=0, invalid=762 0486: dt=11.200000, rms=0.480 (0.068%), neg=0, invalid=762 0487: dt=32.000000, rms=0.480 (0.032%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0488: dt=2.880000, rms=0.488 (0.242%), neg=0, invalid=762 0489: dt=1.008000, rms=0.488 (0.007%), neg=0, invalid=762 0490: dt=1.008000, rms=0.488 (0.001%), neg=0, invalid=762 0491: dt=1.008000, rms=0.488 (-0.013%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 0492: dt=6.933333, rms=0.488 (0.343%), neg=0, invalid=762 0493: dt=7.333333, rms=0.487 (0.052%), neg=0, invalid=762 0494: dt=7.333333, rms=0.487 (0.045%), neg=0, invalid=762 0495: dt=7.333333, rms=0.487 (0.001%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0496: dt=7.333333, rms=0.487 (-0.077%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 0497: dt=0.000000, rms=0.492 (0.208%), neg=0, invalid=762 0498: dt=0.000000, rms=0.492 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.493, neg=0, invalid=762 0499: dt=0.000000, rms=0.492 (0.208%), neg=0, invalid=762 0500: dt=0.000000, rms=0.492 (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=0.485, neg=0, invalid=762 iter 0, gcam->neg = 888 after 17 iterations, nbhd size=1, neg = 0 0501: dt=2.282389, rms=0.448 (7.572%), neg=0, invalid=762 0502: dt=0.096000, rms=0.448 (0.080%), neg=0, invalid=762 0503: dt=0.096000, rms=0.448 (-0.077%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.449, neg=0, invalid=762 0504: dt=0.080000, rms=0.448 (0.315%), neg=0, invalid=762 0505: dt=0.001750, rms=0.448 (-0.001%), neg=0, invalid=762 0506: dt=0.001750, rms=0.448 (0.000%), neg=0, invalid=762 0507: dt=0.001750, rms=0.448 (-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=0.432, neg=0, invalid=762 0508: dt=0.000000, rms=0.432 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.432, neg=0, invalid=762 0509: dt=32.368000, rms=0.432 (0.003%), neg=0, invalid=762 0510: dt=27.744000, rms=0.432 (0.001%), neg=0, invalid=762 0511: dt=27.744000, rms=0.432 (0.000%), neg=0, invalid=762 0512: dt=27.744000, rms=0.432 (-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=0.432, neg=0, invalid=762 0513: dt=0.000000, rms=0.432 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.432, neg=0, invalid=762 0514: dt=82.944000, rms=0.432 (0.037%), neg=0, invalid=762 0515: dt=124.416000, rms=0.432 (0.048%), neg=0, invalid=762 0516: dt=31.104000, rms=0.431 (0.007%), neg=0, invalid=762 0517: dt=31.104000, rms=0.431 (0.005%), neg=0, invalid=762 0518: dt=31.104000, rms=0.431 (0.008%), neg=0, invalid=762 0519: dt=31.104000, rms=0.431 (0.012%), neg=0, invalid=762 0520: dt=31.104000, rms=0.431 (0.014%), neg=0, invalid=762 0521: dt=31.104000, rms=0.431 (0.014%), neg=0, invalid=762 0522: dt=31.104000, rms=0.431 (0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.432, neg=0, invalid=762 0523: dt=11.200000, rms=0.432 (0.051%), neg=0, invalid=762 0524: dt=8.000000, rms=0.432 (0.011%), neg=0, invalid=762 0525: dt=8.000000, rms=0.432 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.432, neg=0, invalid=762 0526: dt=87.646910, rms=0.429 (0.623%), neg=0, invalid=762 0527: dt=25.600000, rms=0.428 (0.221%), neg=0, invalid=762 0528: dt=25.600000, rms=0.428 (0.087%), neg=0, invalid=762 0529: dt=25.600000, rms=0.427 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0530: dt=25.600000, rms=0.427 (0.155%), neg=0, invalid=762 0531: dt=25.600000, rms=0.426 (0.170%), neg=0, invalid=762 0532: dt=25.600000, rms=0.425 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0533: dt=25.600000, rms=0.424 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0534: dt=25.600000, rms=0.424 (0.149%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0535: dt=25.600000, rms=0.423 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0536: dt=25.600000, rms=0.423 (0.091%), neg=0, invalid=762 0537: dt=44.800000, rms=0.423 (0.025%), neg=0, invalid=762 0538: dt=44.800000, rms=0.423 (-0.007%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.427, neg=0, invalid=762 0539: dt=2.304000, rms=0.427 (0.015%), neg=0, invalid=762 0540: dt=0.576000, rms=0.427 (0.001%), neg=0, invalid=762 0541: dt=0.576000, rms=0.427 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.427, neg=0, invalid=762 0542: dt=8.258065, rms=0.427 (0.078%), neg=0, invalid=762 0543: dt=11.750000, rms=0.426 (0.060%), neg=0, invalid=762 0544: dt=11.750000, rms=0.426 (0.076%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0545: dt=11.750000, rms=0.426 (0.106%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 11 iterations, nbhd size=1, neg = 0 0546: dt=11.750000, rms=0.425 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0547: dt=11.750000, rms=0.424 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0548: dt=11.750000, rms=0.423 (0.236%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 5 iterations, nbhd size=0, neg = 0 0549: dt=11.750000, rms=0.422 (0.189%), neg=0, invalid=762 iter 0, gcam->neg = 29 after 5 iterations, nbhd size=0, neg = 0 0550: dt=11.750000, rms=0.422 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 14 iterations, nbhd size=1, neg = 0 0551: dt=11.750000, rms=0.422 (-0.062%), neg=0, invalid=762 0552: dt=0.001688, rms=0.422 (0.000%), neg=0, invalid=762 0553: dt=0.000000, rms=0.422 (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=0.429, neg=0, invalid=762 0554: dt=0.000000, rms=0.429 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=762 0555: dt=0.000000, rms=0.429 (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=0.417, neg=0, invalid=762 iter 0, gcam->neg = 977 after 16 iterations, nbhd size=1, neg = 0 0556: dt=1.498062, rms=0.406 (2.762%), neg=0, invalid=762 0557: dt=0.000013, rms=0.406 (0.000%), neg=0, invalid=762 0558: dt=0.000013, rms=0.406 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=762 0559: dt=0.064000, rms=0.405 (0.031%), neg=0, invalid=762 0560: dt=0.020000, rms=0.405 (0.002%), neg=0, invalid=762 0561: dt=0.020000, rms=0.405 (-0.001%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 26 minutes and 19 seconds. mri_ca_register utimesec 9524.458062 mri_ca_register stimesec 9.812508 mri_ca_register ru_maxrss 1335004 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 3743978 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 62736 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 4241 mri_ca_register ru_nivcsw 41527 FSRUNTIME@ mri_ca_register 2.4385 hours 2 threads #-------------------------------------- #@# SubCort Seg Sat Oct 7 19:46:28 CEST 2017 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname tars-540 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-6.0.0/0050750/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 2 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.79 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 = 0.13940 ( 3) Left_Lateral_Ventricle (4): linear fit = 0.09 x + 0.0 (1070 voxels, overlap=0.007) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1070 voxels, peak = 2), gca=8.0 gca peak = 0.17677 (13) mri peak = 0.10599 ( 3) Right_Lateral_Ventricle (43): linear fit = 0.08 x + 0.0 (1231 voxels, overlap=0.008) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1231 voxels, peak = 1), gca=5.2 gca peak = 0.28129 (95) mri peak = 0.09184 (93) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (778 voxels, overlap=1.017) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (778 voxels, peak = 92), gca=91.7 gca peak = 0.16930 (96) mri peak = 0.10729 (95) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (784 voxels, overlap=0.870) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (784 voxels, peak = 95), gca=94.6 gca peak = 0.24553 (55) mri peak = 0.08864 (57) Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (954 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (954 voxels, peak = 52), gca=52.0 gca peak = 0.30264 (59) mri peak = 0.09237 (57) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (940 voxels, overlap=1.009) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (940 voxels, peak = 55), gca=55.2 gca peak = 0.07580 (103) mri peak = 0.07926 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (42162 voxels, overlap=0.643) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (42162 voxels, peak = 107), gca=106.6 gca peak = 0.07714 (104) mri peak = 0.07918 (108) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (44235 voxels, overlap=0.567) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (44235 voxels, peak = 109), gca=108.7 gca peak = 0.09712 (58) mri peak = 0.06356 (41) Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (37728 voxels, overlap=0.278) Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (37728 voxels, peak = 43), gca=43.2 gca peak = 0.11620 (58) mri peak = 0.05599 (42) Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (36741 voxels, overlap=0.261) Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (36741 voxels, peak = 44), gca=43.8 gca peak = 0.30970 (66) mri peak = 0.09476 (66) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1298 voxels, overlap=1.008) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1298 voxels, peak = 65), gca=65.0 gca peak = 0.15280 (69) mri peak = 0.10427 (69) Left_Caudate (11): linear fit = 0.93 x + 0.0 (1168 voxels, overlap=0.590) Left_Caudate (11): linear fit = 0.93 x + 0.0 (1168 voxels, peak = 64), gca=63.8 gca peak = 0.13902 (56) mri peak = 0.04432 (51) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (24367 voxels, overlap=0.925) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (24367 voxels, peak = 53), gca=52.9 gca peak = 0.14777 (55) mri peak = 0.04553 (51) Right_Cerebellum_Cortex (47): linear fit = 0.89 x + 0.0 (22879 voxels, overlap=0.774) Right_Cerebellum_Cortex (47): linear fit = 0.89 x + 0.0 (22879 voxels, peak = 49), gca=49.2 gca peak = 0.16765 (84) mri peak = 0.07477 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6678 voxels, overlap=0.729) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6678 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.06981 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (6038 voxels, overlap=0.862) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (6038 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.08199 (61) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (662 voxels, overlap=1.032) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (662 voxels, peak = 60), gca=59.6 gca peak = 0.33601 (57) mri peak = 0.06929 (56) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (690 voxels, overlap=1.032) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (690 voxels, peak = 60), gca=59.6 gca peak = 0.11131 (90) mri peak = 0.06840 (87) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4553 voxels, overlap=0.974) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4553 voxels, peak = 91), gca=91.3 gca peak = 0.11793 (83) mri peak = 0.06103 (87) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4555 voxels, overlap=0.979) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4555 voxels, peak = 87), gca=86.7 gca peak = 0.08324 (81) mri peak = 0.05634 (72) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2674 voxels, overlap=0.925) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2674 voxels, peak = 79), gca=79.0 gca peak = 0.10360 (77) mri peak = 0.05700 (71) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2424 voxels, overlap=0.856) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2424 voxels, peak = 74), gca=74.3 gca peak = 0.08424 (78) mri peak = 0.06534 (85) Brain_Stem (16): linear fit = 1.12 x + 0.0 (12561 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.12 x + 0.0 (12561 voxels, peak = 88), gca=87.8 gca peak = 0.12631 (89) mri peak = 0.05698 (96) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1574 voxels, overlap=0.550) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1574 voxels, peak = 100), gca=100.1 gca peak = 0.14500 (87) mri peak = 0.05138 (98) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1661 voxels, overlap=0.514) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1661 voxels, peak = 99), gca=98.7 gca peak = 0.14975 (24) mri peak = 0.11155 ( 7) gca peak = 0.19357 (14) mri peak = 0.11908 ( 5) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (156 voxels, overlap=0.058) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (156 voxels, peak = 4), gca=4.0 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.91 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.30837 ( 7) mri peak = 0.13940 ( 3) Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (1070 voxels, overlap=0.923) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1070 voxels, peak = 2), gca=2.8 gca peak = 0.30173 ( 5) mri peak = 0.10599 ( 3) Right_Lateral_Ventricle (43): linear fit = 0.63 x + 0.0 (1231 voxels, overlap=0.871) Right_Lateral_Ventricle (43): linear fit = 0.63 x + 0.0 (1231 voxels, peak = 3), gca=3.2 gca peak = 0.26756 (90) mri peak = 0.09184 (93) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (778 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (778 voxels, peak = 90), gca=89.6 gca peak = 0.18436 (95) mri peak = 0.10729 (95) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (784 voxels, overlap=1.002) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (784 voxels, peak = 95), gca=94.5 gca peak = 0.27737 (52) mri peak = 0.08864 (57) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (954 voxels, overlap=1.006) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (954 voxels, peak = 52), gca=52.0 gca peak = 0.26463 (55) mri peak = 0.09237 (57) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (940 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (940 voxels, peak = 55), gca=55.0 gca peak = 0.07501 (106) mri peak = 0.07926 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42162 voxels, overlap=0.793) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42162 voxels, peak = 106), gca=106.0 gca peak = 0.07788 (109) mri peak = 0.07918 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (44235 voxels, overlap=0.761) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (44235 voxels, peak = 109), gca=109.0 gca peak = 0.13076 (43) mri peak = 0.06356 (41) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (37728 voxels, overlap=0.944) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (37728 voxels, peak = 45), gca=44.5 gca peak = 0.15264 (44) mri peak = 0.05599 (42) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (36741 voxels, overlap=0.955) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (36741 voxels, peak = 46), gca=45.5 gca peak = 0.31027 (65) mri peak = 0.09476 (66) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1298 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1298 voxels, peak = 65), gca=65.0 gca peak = 0.13777 (72) mri peak = 0.10427 (69) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1168 voxels, overlap=0.990) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1168 voxels, peak = 72), gca=72.0 gca peak = 0.14779 (52) mri peak = 0.04432 (51) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (24367 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (24367 voxels, peak = 50), gca=50.2 gca peak = 0.16597 (49) mri peak = 0.04553 (51) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (22879 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (22879 voxels, peak = 49), gca=49.0 gca peak = 0.15948 (90) mri peak = 0.07477 (88) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (6678 voxels, overlap=0.960) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (6678 voxels, peak = 89), gca=88.7 gca peak = 0.15042 (90) mri peak = 0.06981 (88) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (6038 voxels, overlap=0.988) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (6038 voxels, peak = 88), gca=87.8 gca peak = 0.31733 (61) mri peak = 0.08199 (61) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (662 voxels, overlap=1.015) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (662 voxels, peak = 62), gca=61.9 gca peak = 0.32226 (60) mri peak = 0.06929 (56) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (690 voxels, overlap=1.014) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (690 voxels, peak = 62), gca=61.5 gca peak = 0.10566 (90) mri peak = 0.06840 (87) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4553 voxels, overlap=0.991) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4553 voxels, peak = 91), gca=91.3 gca peak = 0.09554 (90) mri peak = 0.06103 (87) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4555 voxels, overlap=0.993) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4555 voxels, peak = 90), gca=90.0 gca peak = 0.08313 (79) mri peak = 0.05634 (72) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2674 voxels, overlap=0.923) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2674 voxels, peak = 78), gca=77.8 gca peak = 0.09182 (72) mri peak = 0.05700 (71) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2424 voxels, overlap=0.920) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2424 voxels, peak = 71), gca=70.9 gca peak = 0.07952 (88) mri peak = 0.06534 (85) Brain_Stem (16): linear fit = 0.99 x + 0.0 (12561 voxels, overlap=0.825) Brain_Stem (16): linear fit = 0.99 x + 0.0 (12561 voxels, peak = 87), gca=86.7 gca peak = 0.10013 (100) mri peak = 0.05698 (96) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1574 voxels, overlap=0.870) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1574 voxels, peak = 100), gca=100.5 gca peak = 0.15404 (97) mri peak = 0.05138 (98) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1661 voxels, overlap=0.941) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1661 voxels, peak = 97), gca=97.5 gca peak = 0.33708 (10) mri peak = 0.11155 ( 7) gca peak = 0.45928 ( 6) mri peak = 0.11908 ( 5) Fourth_Ventricle (15): linear fit = 0.73 x + 0.0 (156 voxels, overlap=0.422) Fourth_Ventricle (15): linear fit = 0.73 x + 0.0 (156 voxels, peak = 4), gca=4.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17854 (25) gca peak Left_Thalamus = 0.64095 (88) gca peak Third_Ventricle = 0.33708 (10) gca peak CSF = 0.26605 (13) gca peak Left_Accumbens_area = 0.54646 (57) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.67383 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24804 (22) gca peak Right_Accumbens_area = 0.45106 (64) gca peak Right_vessel = 0.71728 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65560 (13) gca peak WM_hypointensities = 0.06831 (79) gca peak non_WM_hypointensities = 0.09816 (45) gca peak Optic_Chiasm = 0.59400 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.59 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 61927 voxels changed in iteration 0 of unlikely voxel relabeling 110 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 24624 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels) 333 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 76303 changed. image ll: -2.143, PF=0.500 pass 2: 23456 changed. image ll: -2.142, PF=0.500 pass 3: 8681 changed. pass 4: 3618 changed. 37100 voxels changed in iteration 0 of unlikely voxel relabeling 374 voxels changed in iteration 1 of unlikely voxel relabeling 27 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5962 voxels changed in iteration 0 of unlikely voxel relabeling 85 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4967 voxels changed in iteration 0 of unlikely voxel relabeling 45 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4509 voxels changed in iteration 0 of unlikely voxel relabeling 43 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3769.489950 mri_ca_label stimesec 1.423783 mri_ca_label ru_maxrss 2102892 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 697281 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 62728 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 288 mri_ca_label ru_nivcsw 5184 auto-labeling took 62 minutes and 5 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/transforms/cc_up.lta 0050750 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-6.0.0/0050750/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/norm.mgz 23542 voxels in left wm, 54242 in right wm, xrange [122, 130] searching rotation angles z=[-6 8], y=[-9 5] searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.0 global minimum found at slice 127.0, rotations (-1.64, 0.28) final transformation (x=127.0, yr=-1.644, zr=0.276): 0.99958 -0.00482 -0.02869 4.51957; 0.00481 0.99999 -0.00014 27.40418; 0.02869 0.00000 0.99959 20.39857; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 100 104 eigenvectors: 0.00055 0.00039 1.00000; -0.10824 -0.99412 0.00045; 0.99412 -0.10824 -0.00050; error in mid anterior detected - correcting... writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/aseg.auto.mgz... corpus callosum segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Sat Oct 7 20:49:16 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Oct 7 20:49:16 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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... 1400 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 45 (45), valley at 16 (16) csf peak at 23, setting threshold to 37 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 46 (46), valley at 17 (17) csf peak at 24, setting threshold to 38 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 52 seconds. #-------------------------------------------- #@# Mask BFS Sat Oct 7 20:52:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1722888 voxels in mask (pct= 10.27) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Oct 7 20:52:11 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 (106.0): 106.2 +- 4.8 [79.0 --> 125.0] GM (67.0) : 66.1 +- 9.6 [30.0 --> 95.0] setting bottom of white matter range to 75.7 setting top of gray matter range to 85.3 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... 3632 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3643 filled 1067 bright non-wm voxels segmented. 2066 diagonally connected voxels added... white matter segmentation took 1.3 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 0.44 minutes reading wm segmentation from wm.seg.mgz... 35 voxels added to wm to prevent paths from MTL structures to cortex 3357 additional wm voxels added 0 additional wm voxels added SEG EDIT: 53805 voxels turned on, 36449 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 98 new 98 115,126,128 old 98 new 98 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 11 found - 11 modified | TOTAL: 11 pass 2 (xy+): 0 found - 11 modified | TOTAL: 11 pass 1 (xy-): 18 found - 18 modified | TOTAL: 29 pass 2 (xy-): 0 found - 18 modified | TOTAL: 29 pass 1 (yz+): 20 found - 20 modified | TOTAL: 49 pass 2 (yz+): 0 found - 20 modified | TOTAL: 49 pass 1 (yz-): 26 found - 26 modified | TOTAL: 75 pass 2 (yz-): 0 found - 26 modified | TOTAL: 75 pass 1 (xz+): 27 found - 27 modified | TOTAL: 102 pass 2 (xz+): 0 found - 27 modified | TOTAL: 102 pass 1 (xz-): 15 found - 15 modified | TOTAL: 117 pass 2 (xz-): 0 found - 15 modified | TOTAL: 117 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 16 found - 16 modified | TOTAL: 24 pass 2 (+++): 0 found - 16 modified | TOTAL: 24 pass 1 (+++): 17 found - 17 modified | TOTAL: 41 pass 2 (+++): 0 found - 17 modified | TOTAL: 41 pass 1 (+++): 19 found - 19 modified | TOTAL: 60 pass 2 (+++): 0 found - 19 modified | TOTAL: 60 Iteration Number : 1 pass 1 (++): 99 found - 99 modified | TOTAL: 99 pass 2 (++): 0 found - 99 modified | TOTAL: 99 pass 1 (+-): 100 found - 100 modified | TOTAL: 199 pass 2 (+-): 0 found - 100 modified | TOTAL: 199 pass 1 (--): 74 found - 74 modified | TOTAL: 273 pass 2 (--): 1 found - 75 modified | TOTAL: 274 pass 3 (--): 0 found - 75 modified | TOTAL: 274 pass 1 (-+): 90 found - 90 modified | TOTAL: 364 pass 2 (-+): 0 found - 90 modified | TOTAL: 364 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 5 found - 5 modified | TOTAL: 8 pass 2 (xy-): 0 found - 5 modified | TOTAL: 8 pass 1 (yz+): 3 found - 3 modified | TOTAL: 11 pass 2 (yz+): 0 found - 3 modified | TOTAL: 11 pass 1 (yz-): 5 found - 5 modified | TOTAL: 16 pass 2 (yz-): 0 found - 5 modified | TOTAL: 16 pass 1 (xz+): 3 found - 3 modified | TOTAL: 19 pass 2 (xz+): 0 found - 3 modified | TOTAL: 19 pass 1 (xz-): 2 found - 2 modified | TOTAL: 21 pass 2 (xz-): 0 found - 2 modified | TOTAL: 21 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 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 1 found - 1 modified | TOTAL: 3 pass 2 (+-): 0 found - 1 modified | TOTAL: 3 pass 1 (--): 0 found - 0 modified | TOTAL: 3 pass 1 (-+): 2 found - 2 modified | TOTAL: 5 pass 2 (-+): 0 found - 2 modified | TOTAL: 5 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 567 (out of 577790: 0.098133) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Oct 7 20:53:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.07370 0.01691 0.00344 -14.13783; -0.01767 1.03760 0.21998 -19.57637; 0.00014 -0.20525 1.01354 18.72534; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.07370 0.01691 0.00344 -14.13783; -0.01767 1.03760 0.21998 -19.57637; 0.00014 -0.20525 1.01354 18.72534; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1399 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) no need to search using seed (126, 122, 151), TAL = (2.0, 23.0, 6.0) talairach voxel to voxel transform 0.93111 -0.01515 0.00012 12.86493; 0.01523 0.92384 -0.20057 22.05638; 0.00295 0.18709 0.94602 -14.01035; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 122, 151) --> (2.0, 23.0, 6.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (2.00, 23.00, 6.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 23.00, 6.00) SRC: (111.60, 106.12, 151.98) search lh wm seed point around talairach space (-16.00, 23.00, 6.00), SRC: (145.12, 106.67, 152.09) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sat Oct 7 20:54:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 2 found - 2 modified | TOTAL: 4 pass 2 (xz-): 0 found - 2 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 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 : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 10 (out of 279827: 0.003574) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 2633 vertices, 2815 faces slice 50: 10555 vertices, 10897 faces slice 60: 21730 vertices, 22135 faces slice 70: 33340 vertices, 33748 faces slice 80: 45458 vertices, 45878 faces slice 90: 57202 vertices, 57616 faces slice 100: 69863 vertices, 70320 faces slice 110: 81500 vertices, 81917 faces slice 120: 92740 vertices, 93191 faces slice 130: 103887 vertices, 104312 faces slice 140: 113791 vertices, 114149 faces slice 150: 121857 vertices, 122184 faces slice 160: 129453 vertices, 129787 faces slice 170: 135793 vertices, 136073 faces slice 180: 140894 vertices, 141134 faces slice 190: 144400 vertices, 144581 faces slice 200: 145306 vertices, 145380 faces slice 210: 145306 vertices, 145380 faces slice 220: 145306 vertices, 145380 faces slice 230: 145306 vertices, 145380 faces slice 240: 145306 vertices, 145380 faces slice 250: 145306 vertices, 145380 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... 145306 voxel in cpt #1: X=-74 [v=145306,e=436140,f=290760] located at (-26.545834, -23.816422, 21.178843) For the whole surface: X=-74 [v=145306,e=436140,f=290760] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat Oct 7 20:54:41 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 4 found - 4 modified | TOTAL: 4 pass 2 (yz+): 0 found - 4 modified | TOTAL: 4 pass 1 (yz-): 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 : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 276063: 0.001449) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 910 vertices, 994 faces slice 50: 6845 vertices, 7169 faces slice 60: 16711 vertices, 17111 faces slice 70: 28266 vertices, 28672 faces slice 80: 40256 vertices, 40629 faces slice 90: 52343 vertices, 52711 faces slice 100: 63732 vertices, 64136 faces slice 110: 76149 vertices, 76588 faces slice 120: 87623 vertices, 88013 faces slice 130: 98951 vertices, 99386 faces slice 140: 110267 vertices, 110682 faces slice 150: 118976 vertices, 119275 faces slice 160: 126195 vertices, 126500 faces slice 170: 133396 vertices, 133670 faces slice 180: 139226 vertices, 139458 faces slice 190: 143524 vertices, 143716 faces slice 200: 144894 vertices, 144958 faces slice 210: 144894 vertices, 144958 faces slice 220: 144894 vertices, 144958 faces slice 230: 144894 vertices, 144958 faces slice 240: 144894 vertices, 144958 faces slice 250: 144894 vertices, 144958 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... 144894 voxel in cpt #1: X=-64 [v=144894,e=434874,f=289916] located at (27.677950, -19.839296, 21.416201) For the whole surface: X=-64 [v=144894,e=434874,f=289916] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Oct 7 20:54:46 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sat Oct 7 20:54:46 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 20919 of (20919 20922) to complete... Waiting for PID 20922 of (20919 20922) 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 (20919 20922) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sat Oct 7 20:54:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sat Oct 7 20:54:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 20966 of (20966 20969) to complete... Waiting for PID 20969 of (20966 20969) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.5 mm, total surface area = 77174 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.157 (target=0.015) step 005: RMS=0.121 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.051 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.041 (target=0.015) step 050: RMS=0.040 (target=0.015) step 055: RMS=0.040 (target=0.015) step 060: RMS=0.039 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 42.011613 mris_inflate stimesec 0.106983 mris_inflate ru_maxrss 211940 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30438 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10224 mris_inflate ru_oublock 10240 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3492 mris_inflate ru_nivcsw 3298 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 47.5 mm, total surface area = 75948 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.159 (target=0.015) step 005: RMS=0.120 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.054 (target=0.015) step 035: RMS=0.050 (target=0.015) step 040: RMS=0.047 (target=0.015) step 045: RMS=0.045 (target=0.015) step 050: RMS=0.044 (target=0.015) step 055: RMS=0.043 (target=0.015) step 060: RMS=0.042 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 42.103599 mris_inflate stimesec 0.098984 mris_inflate ru_maxrss 211800 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30402 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10200 mris_inflate ru_oublock 10216 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2224 mris_inflate ru_nivcsw 4017 PIDs (20966 20969) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sat Oct 7 20:55:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sat Oct 7 20:55:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 21037 of (21037 21041) to complete... Waiting for PID 21041 of (21037 21041) 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 0.95 +- 0.56 (0.00-->6.67) (max @ vno 58114 --> 58115) face area 0.03 +- 0.03 (-0.11-->0.75) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.309... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.140, avgs=0 005/300: dt: 0.9000, rms radial error=175.882, avgs=0 010/300: dt: 0.9000, rms radial error=175.326, avgs=0 015/300: dt: 0.9000, rms radial error=174.594, avgs=0 020/300: dt: 0.9000, rms radial error=173.762, avgs=0 025/300: dt: 0.9000, rms radial error=172.872, avgs=0 030/300: dt: 0.9000, rms radial error=171.950, avgs=0 035/300: dt: 0.9000, rms radial error=171.012, avgs=0 040/300: dt: 0.9000, rms radial error=170.066, avgs=0 045/300: dt: 0.9000, rms radial error=169.119, avgs=0 050/300: dt: 0.9000, rms radial error=168.176, avgs=0 055/300: dt: 0.9000, rms radial error=167.236, avgs=0 060/300: dt: 0.9000, rms radial error=166.300, avgs=0 065/300: dt: 0.9000, rms radial error=165.367, avgs=0 070/300: dt: 0.9000, rms radial error=164.440, avgs=0 075/300: dt: 0.9000, rms radial error=163.516, avgs=0 080/300: dt: 0.9000, rms radial error=162.599, avgs=0 085/300: dt: 0.9000, rms radial error=161.686, avgs=0 090/300: dt: 0.9000, rms radial error=160.779, avgs=0 095/300: dt: 0.9000, rms radial error=159.876, avgs=0 100/300: dt: 0.9000, rms radial error=158.979, avgs=0 105/300: dt: 0.9000, rms radial error=158.086, avgs=0 110/300: dt: 0.9000, rms radial error=157.198, avgs=0 115/300: dt: 0.9000, rms radial error=156.315, avgs=0 120/300: dt: 0.9000, rms radial error=155.436, avgs=0 125/300: dt: 0.9000, rms radial error=154.563, avgs=0 130/300: dt: 0.9000, rms radial error=153.694, avgs=0 135/300: dt: 0.9000, rms radial error=152.830, avgs=0 140/300: dt: 0.9000, rms radial error=151.970, avgs=0 145/300: dt: 0.9000, rms radial error=151.116, avgs=0 150/300: dt: 0.9000, rms radial error=150.266, avgs=0 155/300: dt: 0.9000, rms radial error=149.420, avgs=0 160/300: dt: 0.9000, rms radial error=148.580, avgs=0 165/300: dt: 0.9000, rms radial error=147.744, avgs=0 170/300: dt: 0.9000, rms radial error=146.912, avgs=0 175/300: dt: 0.9000, rms radial error=146.085, avgs=0 180/300: dt: 0.9000, rms radial error=145.262, avgs=0 185/300: dt: 0.9000, rms radial error=144.444, avgs=0 190/300: dt: 0.9000, rms radial error=143.631, avgs=0 195/300: dt: 0.9000, rms radial error=142.822, avgs=0 200/300: dt: 0.9000, rms radial error=142.017, avgs=0 205/300: dt: 0.9000, rms radial error=141.217, avgs=0 210/300: dt: 0.9000, rms radial error=140.421, avgs=0 215/300: dt: 0.9000, rms radial error=139.630, avgs=0 220/300: dt: 0.9000, rms radial error=138.843, avgs=0 225/300: dt: 0.9000, rms radial error=138.060, avgs=0 230/300: dt: 0.9000, rms radial error=137.282, avgs=0 235/300: dt: 0.9000, rms radial error=136.508, avgs=0 240/300: dt: 0.9000, rms radial error=135.738, avgs=0 245/300: dt: 0.9000, rms radial error=134.973, avgs=0 250/300: dt: 0.9000, rms radial error=134.212, avgs=0 255/300: dt: 0.9000, rms radial error=133.456, avgs=0 260/300: dt: 0.9000, rms radial error=132.703, avgs=0 265/300: dt: 0.9000, rms radial error=131.955, avgs=0 270/300: dt: 0.9000, rms radial error=131.211, avgs=0 275/300: dt: 0.9000, rms radial error=130.471, avgs=0 280/300: dt: 0.9000, rms radial error=129.735, avgs=0 285/300: dt: 0.9000, rms radial error=129.003, avgs=0 290/300: dt: 0.9000, rms radial error=128.276, avgs=0 295/300: dt: 0.9000, rms radial error=127.552, avgs=0 300/300: dt: 0.9000, rms radial error=126.833, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17050.65 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 2887.70 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00031 epoch 3 (K=160.0), pass 1, starting sse = 300.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/12 = 0.00830 epoch 4 (K=640.0), pass 1, starting sse = 21.68 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.24/17 = 0.01429 final distance error %25.97 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 275.022190 mris_sphere stimesec 0.170974 mris_sphere ru_maxrss 212140 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 30485 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10264 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 9058 mris_sphere ru_nivcsw 20374 FSRUNTIME@ mris_sphere 0.0750 hours 1 threads mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.57 (0.00-->7.40) (max @ vno 55082 --> 56147) face area 0.03 +- 0.03 (-0.09-->0.79) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.315... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.939, avgs=0 005/300: dt: 0.9000, rms radial error=175.680, avgs=0 010/300: dt: 0.9000, rms radial error=175.124, avgs=0 015/300: dt: 0.9000, rms radial error=174.394, avgs=0 020/300: dt: 0.9000, rms radial error=173.567, avgs=0 025/300: dt: 0.9000, rms radial error=172.683, avgs=0 030/300: dt: 0.9000, rms radial error=171.768, avgs=0 035/300: dt: 0.9000, rms radial error=170.836, avgs=0 040/300: dt: 0.9000, rms radial error=169.897, avgs=0 045/300: dt: 0.9000, rms radial error=168.955, avgs=0 050/300: dt: 0.9000, rms radial error=168.015, avgs=0 055/300: dt: 0.9000, rms radial error=167.077, avgs=0 060/300: dt: 0.9000, rms radial error=166.143, avgs=0 065/300: dt: 0.9000, rms radial error=165.214, avgs=0 070/300: dt: 0.9000, rms radial error=164.289, avgs=0 075/300: dt: 0.9000, rms radial error=163.368, avgs=0 080/300: dt: 0.9000, rms radial error=162.453, avgs=0 085/300: dt: 0.9000, rms radial error=161.542, avgs=0 090/300: dt: 0.9000, rms radial error=160.637, avgs=0 095/300: dt: 0.9000, rms radial error=159.737, avgs=0 100/300: dt: 0.9000, rms radial error=158.842, avgs=0 105/300: dt: 0.9000, rms radial error=157.952, avgs=0 110/300: dt: 0.9000, rms radial error=157.067, avgs=0 115/300: dt: 0.9000, rms radial error=156.187, avgs=0 120/300: dt: 0.9000, rms radial error=155.311, avgs=0 125/300: dt: 0.9000, rms radial error=154.441, avgs=0 130/300: dt: 0.9000, rms radial error=153.575, avgs=0 135/300: dt: 0.9000, rms radial error=152.714, avgs=0 140/300: dt: 0.9000, rms radial error=151.857, avgs=0 145/300: dt: 0.9000, rms radial error=151.006, avgs=0 150/300: dt: 0.9000, rms radial error=150.159, avgs=0 155/300: dt: 0.9000, rms radial error=149.317, avgs=0 160/300: dt: 0.9000, rms radial error=148.479, avgs=0 165/300: dt: 0.9000, rms radial error=147.646, avgs=0 170/300: dt: 0.9000, rms radial error=146.818, avgs=0 175/300: dt: 0.9000, rms radial error=145.994, avgs=0 180/300: dt: 0.9000, rms radial error=145.174, avgs=0 185/300: dt: 0.9000, rms radial error=144.359, avgs=0 190/300: dt: 0.9000, rms radial error=143.548, avgs=0 195/300: dt: 0.9000, rms radial error=142.741, avgs=0 200/300: dt: 0.9000, rms radial error=141.939, avgs=0 205/300: dt: 0.9000, rms radial error=141.142, avgs=0 210/300: dt: 0.9000, rms radial error=140.348, avgs=0 215/300: dt: 0.9000, rms radial error=139.559, avgs=0 220/300: dt: 0.9000, rms radial error=138.775, avgs=0 225/300: dt: 0.9000, rms radial error=137.994, avgs=0 230/300: dt: 0.9000, rms radial error=137.218, avgs=0 235/300: dt: 0.9000, rms radial error=136.447, avgs=0 240/300: dt: 0.9000, rms radial error=135.680, avgs=0 245/300: dt: 0.9000, rms radial error=134.917, avgs=0 250/300: dt: 0.9000, rms radial error=134.158, avgs=0 255/300: dt: 0.9000, rms radial error=133.403, avgs=0 260/300: dt: 0.9000, rms radial error=132.653, avgs=0 265/300: dt: 0.9000, rms radial error=131.907, avgs=0 270/300: dt: 0.9000, rms radial error=131.165, avgs=0 275/300: dt: 0.9000, rms radial error=130.427, avgs=0 280/300: dt: 0.9000, rms radial error=129.694, avgs=0 285/300: dt: 0.9000, rms radial error=128.964, avgs=0 290/300: dt: 0.9000, rms radial error=128.238, avgs=0 295/300: dt: 0.9000, rms radial error=127.517, avgs=0 300/300: dt: 0.9000, rms radial error=126.799, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16910.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 2 (K=40.0), pass 1, starting sse = 2824.96 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00022 epoch 3 (K=160.0), pass 1, starting sse = 291.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/11 = 0.00933 epoch 4 (K=640.0), pass 1, starting sse = 19.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.19/15 = 0.01292 final distance error %25.63 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 261.709214 mris_sphere stimesec 0.173973 mris_sphere ru_maxrss 211988 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 30446 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10240 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8998 mris_sphere ru_nivcsw 20512 FSRUNTIME@ mris_sphere 0.0727 hours 1 threads PIDs (21037 21041) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sat Oct 7 21:00:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat Oct 7 21:00:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat Oct 7 21:00:06 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050750 lh #@# Fix Topology rh Sat Oct 7 21:00:06 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050750 rh Waiting for PID 21264 of (21264 21267) to complete... Waiting for PID 21267 of (21264 21267) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050750 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=-74 (nv=145306, nf=290760, ne=436140, g=38) 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 10 iterations marking ambiguous vertices... 5054 ambiguous faces found in tessellation segmenting defects... 42 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 42 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.6836 (-4.8418) -vertex loglikelihood: -6.5785 (-3.2892) -normal dot loglikelihood: -3.6107 (-3.6107) -quad curv loglikelihood: -6.3693 (-3.1846) Total Loglikelihood : -26.2420 CORRECTING DEFECT 0 (vertices=73, convex hull=103, v0=97) After retessellation of defect 0 (v0=97), euler #=-39 (142206,425292,283047) : difference with theory (-39) = 0 CORRECTING DEFECT 1 (vertices=142, convex hull=112, v0=4257) After retessellation of defect 1 (v0=4257), euler #=-38 (142241,425447,283168) : difference with theory (-38) = 0 CORRECTING DEFECT 2 (vertices=82, convex hull=78, v0=5136) After retessellation of defect 2 (v0=5136), euler #=-37 (142264,425549,283248) : difference with theory (-37) = 0 CORRECTING DEFECT 3 (vertices=41, convex hull=80, v0=6023) After retessellation of defect 3 (v0=6023), euler #=-36 (142284,425643,283323) : difference with theory (-36) = 0 CORRECTING DEFECT 4 (vertices=193, convex hull=64, v0=10191) After retessellation of defect 4 (v0=10191), euler #=-35 (142299,425713,283379) : difference with theory (-35) = 0 CORRECTING DEFECT 5 (vertices=31, convex hull=58, v0=15824) After retessellation of defect 5 (v0=15824), euler #=-34 (142313,425778,283431) : difference with theory (-34) = 0 CORRECTING DEFECT 6 (vertices=126, convex hull=94, v0=18879) After retessellation of defect 6 (v0=18879), euler #=-33 (142338,425892,283521) : difference with theory (-33) = 0 CORRECTING DEFECT 7 (vertices=33, convex hull=76, v0=19452) After retessellation of defect 7 (v0=19452), euler #=-32 (142362,425994,283600) : difference with theory (-32) = 0 CORRECTING DEFECT 8 (vertices=70, convex hull=104, v0=32961) After retessellation of defect 8 (v0=32961), euler #=-31 (142390,426121,283700) : difference with theory (-31) = 0 CORRECTING DEFECT 9 (vertices=12, convex hull=26, v0=37782) After retessellation of defect 9 (v0=37782), euler #=-30 (142391,426133,283712) : difference with theory (-30) = 0 CORRECTING DEFECT 10 (vertices=38, convex hull=54, v0=41020) After retessellation of defect 10 (v0=41020), euler #=-29 (142400,426182,283753) : difference with theory (-29) = 0 CORRECTING DEFECT 11 (vertices=20, convex hull=51, v0=46843) After retessellation of defect 11 (v0=46843), euler #=-28 (142412,426239,283799) : difference with theory (-28) = 0 CORRECTING DEFECT 12 (vertices=97, convex hull=128, v0=50525) After retessellation of defect 12 (v0=50525), euler #=-27 (142468,426469,283974) : difference with theory (-27) = 0 CORRECTING DEFECT 13 (vertices=18, convex hull=20, v0=59679) After retessellation of defect 13 (v0=59679), euler #=-26 (142470,426478,283982) : difference with theory (-26) = 0 CORRECTING DEFECT 14 (vertices=39, convex hull=53, v0=60920) After retessellation of defect 14 (v0=60920), euler #=-25 (142487,426551,284039) : difference with theory (-25) = 0 CORRECTING DEFECT 15 (vertices=66, convex hull=89, v0=65716) After retessellation of defect 15 (v0=65716), euler #=-24 (142509,426651,284118) : difference with theory (-24) = 0 CORRECTING DEFECT 16 (vertices=40, convex hull=70, v0=67209) After retessellation of defect 16 (v0=67209), euler #=-23 (142529,426740,284188) : difference with theory (-23) = 0 CORRECTING DEFECT 17 (vertices=7, convex hull=21, v0=70637) After retessellation of defect 17 (v0=70637), euler #=-22 (142530,426748,284196) : difference with theory (-22) = 0 CORRECTING DEFECT 18 (vertices=39, convex hull=85, v0=81530) After retessellation of defect 18 (v0=81530), euler #=-21 (142547,426836,284268) : difference with theory (-21) = 0 CORRECTING DEFECT 19 (vertices=94, convex hull=106, v0=82641) After retessellation of defect 19 (v0=82641), euler #=-20 (142587,427001,284394) : difference with theory (-20) = 0 CORRECTING DEFECT 20 (vertices=20, convex hull=51, v0=94477) After retessellation of defect 20 (v0=94477), euler #=-19 (142596,427048,284433) : difference with theory (-19) = 0 CORRECTING DEFECT 21 (vertices=106, convex hull=119, v0=103834) After retessellation of defect 21 (v0=103834), euler #=-18 (142629,427197,284550) : difference with theory (-18) = 0 CORRECTING DEFECT 22 (vertices=39, convex hull=31, v0=105603) After retessellation of defect 22 (v0=105603), euler #=-17 (142635,427225,284573) : difference with theory (-17) = 0 CORRECTING DEFECT 23 (vertices=6, convex hull=30, v0=107887) After retessellation of defect 23 (v0=107887), euler #=-16 (142638,427242,284588) : difference with theory (-16) = 0 CORRECTING DEFECT 24 (vertices=5, convex hull=28, v0=109974) After retessellation of defect 24 (v0=109974), euler #=-15 (142640,427254,284599) : difference with theory (-15) = 0 CORRECTING DEFECT 25 (vertices=125, convex hull=59, v0=110871) After retessellation of defect 25 (v0=110871), euler #=-14 (142649,427305,284642) : difference with theory (-14) = 0 CORRECTING DEFECT 26 (vertices=133, convex hull=100, v0=111995) After retessellation of defect 26 (v0=111995), euler #=-13 (142679,427441,284749) : difference with theory (-13) = 0 CORRECTING DEFECT 27 (vertices=659, convex hull=301, v0=112630) After retessellation of defect 27 (v0=112630), euler #=-12 (142768,427860,285080) : difference with theory (-12) = 0 CORRECTING DEFECT 28 (vertices=21, convex hull=26, v0=114375) After retessellation of defect 28 (v0=114375), euler #=-11 (142774,427885,285100) : difference with theory (-11) = 0 CORRECTING DEFECT 29 (vertices=6, convex hull=34, v0=117917) After retessellation of defect 29 (v0=117917), euler #=-10 (142775,427900,285115) : difference with theory (-10) = 0 CORRECTING DEFECT 30 (vertices=187, convex hull=124, v0=127727) After retessellation of defect 30 (v0=127727), euler #=-9 (142823,428110,285278) : difference with theory (-9) = 0 CORRECTING DEFECT 31 (vertices=29, convex hull=71, v0=128786) After retessellation of defect 31 (v0=128786), euler #=-8 (142836,428180,285336) : difference with theory (-8) = 0 CORRECTING DEFECT 32 (vertices=58, convex hull=76, v0=129683) After retessellation of defect 32 (v0=129683), euler #=-7 (142864,428294,285423) : difference with theory (-7) = 0 CORRECTING DEFECT 33 (vertices=57, convex hull=89, v0=130009) After retessellation of defect 33 (v0=130009), euler #=-6 (142877,428372,285489) : difference with theory (-6) = 0 CORRECTING DEFECT 34 (vertices=54, convex hull=78, v0=130911) After retessellation of defect 34 (v0=130911), euler #=-5 (142894,428456,285557) : difference with theory (-5) = 0 CORRECTING DEFECT 35 (vertices=121, convex hull=112, v0=133625) After retessellation of defect 35 (v0=133625), euler #=-4 (142935,428633,285694) : difference with theory (-4) = 0 CORRECTING DEFECT 36 (vertices=41, convex hull=80, v0=136330) After retessellation of defect 36 (v0=136330), euler #=-3 (142961,428745,285781) : difference with theory (-3) = 0 CORRECTING DEFECT 37 (vertices=41, convex hull=88, v0=138075) After retessellation of defect 37 (v0=138075), euler #=-2 (142985,428853,285866) : difference with theory (-2) = 0 CORRECTING DEFECT 38 (vertices=27, convex hull=50, v0=140558) After retessellation of defect 38 (v0=140558), euler #=-1 (142996,428907,285910) : difference with theory (-1) = 0 CORRECTING DEFECT 39 (vertices=8, convex hull=28, v0=142181) After retessellation of defect 39 (v0=142181), euler #=0 (142997,428919,285922) : difference with theory (0) = 0 CORRECTING DEFECT 40 (vertices=99, convex hull=116, v0=142878) After retessellation of defect 40 (v0=142878), euler #=1 (143020,429045,286026) : difference with theory (1) = 0 CORRECTING DEFECT 41 (vertices=25, convex hull=27, v0=144860) After retessellation of defect 41 (v0=144860), euler #=2 (143025,429069,286046) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.07-->10.92) (max @ vno 118438 --> 125560) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.07-->10.92) (max @ vno 118438 --> 125560) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 150 mutations (35.7%), 270 crossovers (64.3%), 185 vertices were eliminated building final representation... 2281 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=143025, nf=286046, ne=429069, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 25.8 minutes 0 defective edges removing intersecting faces 000: 336 intersecting 001: 21 intersecting mris_fix_topology utimesec 1549.117498 mris_fix_topology stimesec 0.395939 mris_fix_topology ru_maxrss 448776 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 57321 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 10224 mris_fix_topology ru_oublock 13712 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 584 mris_fix_topology ru_nivcsw 4306 FSRUNTIME@ mris_fix_topology lh 0.4301 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050750 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=-64 (nv=144894, nf=289916, ne=434874, g=33) 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 10 iterations marking ambiguous vertices... 4611 ambiguous faces found in tessellation segmenting defects... 44 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 40 into 39 43 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5933 (-4.7966) -vertex loglikelihood: -6.6080 (-3.3040) -normal dot loglikelihood: -3.6639 (-3.6639) -quad curv loglikelihood: -6.5499 (-3.2749) Total Loglikelihood : -26.4150 CORRECTING DEFECT 0 (vertices=25, convex hull=24, v0=0) After retessellation of defect 0 (v0=0), euler #=-40 (142055,425005,282910) : difference with theory (-40) = 0 CORRECTING DEFECT 1 (vertices=191, convex hull=76, v0=11075) After retessellation of defect 1 (v0=11075), euler #=-39 (142077,425099,282983) : difference with theory (-39) = 0 CORRECTING DEFECT 2 (vertices=62, convex hull=64, v0=32958) After retessellation of defect 2 (v0=32958), euler #=-38 (142101,425201,283062) : difference with theory (-38) = 0 CORRECTING DEFECT 3 (vertices=22, convex hull=42, v0=45373) After retessellation of defect 3 (v0=45373), euler #=-37 (142113,425252,283102) : difference with theory (-37) = 0 CORRECTING DEFECT 4 (vertices=21, convex hull=31, v0=56142) After retessellation of defect 4 (v0=56142), euler #=-36 (142116,425272,283120) : difference with theory (-36) = 0 CORRECTING DEFECT 5 (vertices=48, convex hull=71, v0=61268) After retessellation of defect 5 (v0=61268), euler #=-35 (142142,425380,283203) : difference with theory (-35) = 0 CORRECTING DEFECT 6 (vertices=111, convex hull=89, v0=62172) After retessellation of defect 6 (v0=62172), euler #=-34 (142176,425521,283311) : difference with theory (-34) = 0 CORRECTING DEFECT 7 (vertices=61, convex hull=77, v0=62849) After retessellation of defect 7 (v0=62849), euler #=-33 (142203,425629,283393) : difference with theory (-33) = 0 CORRECTING DEFECT 8 (vertices=15, convex hull=22, v0=63299) After retessellation of defect 8 (v0=63299), euler #=-32 (142205,425641,283404) : difference with theory (-32) = 0 CORRECTING DEFECT 9 (vertices=67, convex hull=79, v0=73404) After retessellation of defect 9 (v0=73404), euler #=-31 (142233,425755,283491) : difference with theory (-31) = 0 CORRECTING DEFECT 10 (vertices=31, convex hull=77, v0=79095) After retessellation of defect 10 (v0=79095), euler #=-30 (142251,425840,283559) : difference with theory (-30) = 0 CORRECTING DEFECT 11 (vertices=151, convex hull=57, v0=92955) After retessellation of defect 11 (v0=92955), euler #=-29 (142272,425925,283624) : difference with theory (-29) = 0 CORRECTING DEFECT 12 (vertices=40, convex hull=67, v0=93278) After retessellation of defect 12 (v0=93278), euler #=-28 (142295,426020,283697) : difference with theory (-28) = 0 CORRECTING DEFECT 13 (vertices=19, convex hull=34, v0=94462) After retessellation of defect 13 (v0=94462), euler #=-27 (142296,426036,283713) : difference with theory (-27) = 0 CORRECTING DEFECT 14 (vertices=192, convex hull=116, v0=97374) After retessellation of defect 14 (v0=97374), euler #=-26 (142349,426245,283870) : difference with theory (-26) = 0 CORRECTING DEFECT 15 (vertices=6, convex hull=37, v0=97501) After retessellation of defect 15 (v0=97501), euler #=-25 (142351,426260,283884) : difference with theory (-25) = 0 CORRECTING DEFECT 16 (vertices=121, convex hull=49, v0=97772) After retessellation of defect 16 (v0=97772), euler #=-24 (142365,426321,283932) : difference with theory (-24) = 0 CORRECTING DEFECT 17 (vertices=48, convex hull=70, v0=99966) After retessellation of defect 17 (v0=99966), euler #=-23 (142394,426438,284021) : difference with theory (-23) = 0 CORRECTING DEFECT 18 (vertices=69, convex hull=50, v0=104337) After retessellation of defect 18 (v0=104337), euler #=-22 (142408,426503,284073) : difference with theory (-22) = 0 CORRECTING DEFECT 19 (vertices=199, convex hull=177, v0=104484) After retessellation of defect 19 (v0=104484), euler #=-22 (142487,426835,284326) : difference with theory (-21) = 1 CORRECTING DEFECT 20 (vertices=7, convex hull=28, v0=105154) After retessellation of defect 20 (v0=105154), euler #=-21 (142490,426853,284342) : difference with theory (-20) = 1 CORRECTING DEFECT 21 (vertices=93, convex hull=43, v0=106568) After retessellation of defect 21 (v0=106568), euler #=-20 (142498,426894,284376) : difference with theory (-19) = 1 CORRECTING DEFECT 22 (vertices=41, convex hull=77, v0=110827) After retessellation of defect 22 (v0=110827), euler #=-19 (142519,426989,284451) : difference with theory (-18) = 1 CORRECTING DEFECT 23 (vertices=30, convex hull=33, v0=111096) After retessellation of defect 23 (v0=111096), euler #=-18 (142520,427005,284467) : difference with theory (-17) = 1 CORRECTING DEFECT 24 (vertices=29, convex hull=26, v0=111284) After retessellation of defect 24 (v0=111284), euler #=-17 (142523,427020,284480) : difference with theory (-16) = 1 CORRECTING DEFECT 25 (vertices=304, convex hull=115, v0=112171) After retessellation of defect 25 (v0=112171), euler #=-16 (142579,427237,284642) : difference with theory (-15) = 1 CORRECTING DEFECT 26 (vertices=44, convex hull=39, v0=113259) After retessellation of defect 26 (v0=113259), euler #=-15 (142587,427275,284673) : difference with theory (-14) = 1 CORRECTING DEFECT 27 (vertices=32, convex hull=31, v0=113314) After retessellation of defect 27 (v0=113314), euler #=-14 (142591,427300,284695) : difference with theory (-13) = 1 CORRECTING DEFECT 28 (vertices=13, convex hull=28, v0=116550) After retessellation of defect 28 (v0=116550), euler #=-13 (142595,427322,284714) : difference with theory (-12) = 1 CORRECTING DEFECT 29 (vertices=221, convex hull=213, v0=121131) After retessellation of defect 29 (v0=121131), euler #=-12 (142678,427687,284997) : difference with theory (-11) = 1 CORRECTING DEFECT 30 (vertices=42, convex hull=61, v0=123213) After retessellation of defect 30 (v0=123213), euler #=-11 (142707,427798,285080) : difference with theory (-10) = 1 CORRECTING DEFECT 31 (vertices=5, convex hull=20, v0=126247) After retessellation of defect 31 (v0=126247), euler #=-10 (142707,427803,285086) : difference with theory (-9) = 1 CORRECTING DEFECT 32 (vertices=7, convex hull=21, v0=126960) After retessellation of defect 32 (v0=126960), euler #=-9 (142708,427811,285094) : difference with theory (-8) = 1 CORRECTING DEFECT 33 (vertices=33, convex hull=74, v0=128680) After retessellation of defect 33 (v0=128680), euler #=-8 (142728,427906,285170) : difference with theory (-7) = 1 CORRECTING DEFECT 34 (vertices=52, convex hull=79, v0=129921) After retessellation of defect 34 (v0=129921), euler #=-7 (142747,427999,285245) : difference with theory (-6) = 1 CORRECTING DEFECT 35 (vertices=34, convex hull=67, v0=131992) After retessellation of defect 35 (v0=131992), euler #=-6 (142759,428064,285299) : difference with theory (-5) = 1 CORRECTING DEFECT 36 (vertices=166, convex hull=133, v0=134047) After retessellation of defect 36 (v0=134047), euler #=-5 (142795,428231,285431) : difference with theory (-4) = 1 CORRECTING DEFECT 37 (vertices=7, convex hull=41, v0=136242) After retessellation of defect 37 (v0=136242), euler #=-4 (142798,428252,285450) : difference with theory (-3) = 1 CORRECTING DEFECT 38 (vertices=29, convex hull=51, v0=136387) After retessellation of defect 38 (v0=136387), euler #=-3 (142812,428313,285498) : difference with theory (-2) = 1 CORRECTING DEFECT 39 (vertices=56, convex hull=98, v0=137864) After retessellation of defect 39 (v0=137864), euler #=-1 (142834,428426,285591) : difference with theory (-1) = 0 CORRECTING DEFECT 40 (vertices=35, convex hull=55, v0=141582) After retessellation of defect 40 (v0=141582), euler #=0 (142844,428478,285634) : difference with theory (0) = 0 CORRECTING DEFECT 41 (vertices=30, convex hull=72, v0=142050) After retessellation of defect 41 (v0=142050), euler #=1 (142860,428550,285691) : difference with theory (1) = 0 CORRECTING DEFECT 42 (vertices=29, convex hull=61, v0=143930) After retessellation of defect 42 (v0=143930), euler #=2 (142876,428622,285748) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.02-->9.49) (max @ vno 132144 --> 136510) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.02-->9.49) (max @ vno 132144 --> 136510) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 145 mutations (34.6%), 274 crossovers (65.4%), 57 vertices were eliminated building final representation... 2018 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=142876, nf=285748, ne=428622, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 19.5 minutes 0 defective edges removing intersecting faces 000: 192 intersecting 001: 2 intersecting mris_fix_topology utimesec 1171.144958 mris_fix_topology stimesec 0.170974 mris_fix_topology ru_maxrss 446892 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 56467 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 20400 mris_fix_topology ru_oublock 13656 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 628 mris_fix_topology ru_nivcsw 3289 FSRUNTIME@ mris_fix_topology rh 0.3252 hours 1 threads PIDs (21264 21267) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 143025 - 429069 + 286046 = 2 --> 0 holes F =2V-4: 286046 = 286050-4 (0) 2E=3F: 858138 = 858138 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 142876 - 428622 + 285748 = 2 --> 0 holes F =2V-4: 285748 = 285752-4 (0) 2E=3F: 857244 = 857244 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 31 intersecting 001: 3 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 31 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Oct 7 21:26:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050750 lh #-------------------------------------------- #@# Make White Surf rh Sat Oct 7 21:26:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050750 rh Waiting for PID 23169 of (23169 23172) to complete... Waiting for PID 23172 of (23169 23172) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050750 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-6.0.0/0050750/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... 17276 bright wm thresholded. 1249 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.orig... computing class statistics... border white: 265437 voxels (1.58%) border gray 306999 voxels (1.83%) WM (96.0): 96.5 +- 9.6 [70.0 --> 110.0] GM (63.0) : 62.7 +- 11.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 44.4 (was 70) setting MAX_BORDER_WHITE to 112.6 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 32.7 (was 40) setting MAX_GRAY to 93.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 44.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 21.1 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.05-->4.04) (max @ vno 117688 --> 118438) face area 0.28 +- 0.12 (0.00-->3.29) mean absolute distance = 0.61 +- 0.71 3863 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=103+-7.8, GM=56+-7.8 mean inside = 90.9, mean outside = 67.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=72.1, 47 (47) missing vertices, mean dist 0.3 [0.4 (%33.4)->0.7 (%66.6))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.13-->4.28) (max @ vno 118425 --> 118438) face area 0.28 +- 0.13 (0.00-->3.07) mean absolute distance = 0.25 +- 0.47 1930 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5271825.0, rms=13.138 001: dt: 0.5000, sse=3005785.2, rms=9.489 (27.779%) 002: dt: 0.5000, sse=2013719.1, rms=7.324 (22.815%) 003: dt: 0.5000, sse=1508228.5, rms=5.917 (19.212%) 004: dt: 0.5000, sse=1277168.9, rms=5.148 (12.994%) 005: dt: 0.5000, sse=1174616.0, rms=4.759 (7.560%) 006: dt: 0.5000, sse=1131625.9, rms=4.588 (3.581%) 007: dt: 0.5000, sse=1108851.1, rms=4.491 (2.120%) rms = 4.44, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=1098067.9, rms=4.443 (1.064%) 009: dt: 0.2500, sse=795530.4, rms=2.852 (35.812%) 010: dt: 0.2500, sse=730558.0, rms=2.382 (16.484%) 011: dt: 0.2500, sse=713016.9, rms=2.235 (6.176%) 012: dt: 0.2500, sse=702743.1, rms=2.135 (4.459%) rms = 2.09, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=696518.9, rms=2.086 (2.306%) 014: dt: 0.1250, sse=673976.6, rms=1.862 (10.730%) rms = 1.83, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=670945.9, rms=1.834 (1.532%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=74.6, 46 (3) missing vertices, mean dist -0.1 [0.3 (%69.3)->0.2 (%30.7))] %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.93 +- 0.25 (0.08-->4.35) (max @ vno 118425 --> 118438) face area 0.36 +- 0.17 (0.00-->4.17) mean absolute distance = 0.21 +- 0.38 2178 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1229511.0, rms=4.259 016: dt: 0.5000, sse=1060756.0, rms=3.457 (18.830%) rms = 4.16, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=877236.9, rms=2.276 (34.160%) 018: dt: 0.2500, sse=829630.3, rms=1.849 (18.749%) 019: dt: 0.2500, sse=812019.8, rms=1.664 (10.014%) rms = 1.64, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=809809.9, rms=1.643 (1.274%) 021: dt: 0.1250, sse=798838.6, rms=1.507 (8.265%) rms = 1.50, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=797913.9, rms=1.496 (0.718%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=76.5, 42 (2) missing vertices, mean dist -0.1 [0.2 (%64.5)->0.2 (%35.5))] %83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.92 +- 0.25 (0.14-->4.35) (max @ vno 118425 --> 118438) face area 0.36 +- 0.17 (0.00-->4.21) mean absolute distance = 0.21 +- 0.34 2466 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=939422.2, rms=2.762 rms = 3.43, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=823934.1, rms=1.825 (33.919%) 024: dt: 0.2500, sse=788027.9, rms=1.422 (22.101%) rms = 1.40, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=787901.2, rms=1.404 (1.246%) 026: dt: 0.1250, sse=779684.1, rms=1.313 (6.453%) rms = 1.31, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=779613.6, rms=1.314 (-0.040%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=77.4, 39 (1) missing vertices, mean dist -0.0 [0.2 (%55.1)->0.2 (%44.9))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=809463.2, rms=1.747 rms = 2.52, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=761423.1, rms=1.138 (34.856%) 029: dt: 0.2500, sse=751407.6, rms=0.976 (14.230%) rms = 0.97, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=749454.6, rms=0.973 (0.297%) rms = 0.96, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=747903.9, rms=0.956 (1.776%) positioning took 0.5 minutes generating cortex label... 6 non-cortical segments detected only using segment with 7737 vertices erasing segment 0 (vno[0] = 46564) erasing segment 2 (vno[0] = 105308) erasing segment 3 (vno[0] = 109291) erasing segment 4 (vno[0] = 112899) erasing segment 5 (vno[0] = 116145) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.area vertex spacing 0.92 +- 0.26 (0.05-->4.28) (max @ vno 118425 --> 118438) face area 0.35 +- 0.16 (0.00-->4.03) refinement took 5.3 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050750 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-6.0.0/0050750/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... 17276 bright wm thresholded. 1249 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.orig... computing class statistics... border white: 265437 voxels (1.58%) border gray 306999 voxels (1.83%) WM (96.0): 96.5 +- 9.6 [70.0 --> 110.0] GM (63.0) : 62.7 +- 11.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.4 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 31.7 (was 40) setting MAX_GRAY to 92.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 43.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.1 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.30) (max @ vno 130905 --> 135482) face area 0.28 +- 0.12 (0.00-->2.47) mean absolute distance = 0.63 +- 0.72 3664 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-7.0, GM=55+-9.6 mean inside = 90.9, mean outside = 67.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=71.9, 66 (66) missing vertices, mean dist 0.4 [0.4 (%33.2)->0.7 (%66.8))] %80 local maxima, %15 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 0.93 +- 0.26 (0.14-->3.79) (max @ vno 130905 --> 135482) face area 0.28 +- 0.13 (0.00-->2.89) mean absolute distance = 0.25 +- 0.46 1792 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5437863.0, rms=13.354 001: dt: 0.5000, sse=3160110.5, rms=9.776 (26.795%) 002: dt: 0.5000, sse=2122772.5, rms=7.592 (22.335%) 003: dt: 0.5000, sse=1566823.0, rms=6.105 (19.591%) 004: dt: 0.5000, sse=1300604.0, rms=5.242 (14.144%) 005: dt: 0.5000, sse=1174655.9, rms=4.776 (8.891%) 006: dt: 0.5000, sse=1123815.0, rms=4.572 (4.261%) 007: dt: 0.5000, sse=1097647.1, rms=4.459 (2.468%) rms = 4.41, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=1086866.9, rms=4.410 (1.109%) 009: dt: 0.2500, sse=787550.8, rms=2.830 (35.823%) 010: dt: 0.2500, sse=722971.9, rms=2.362 (16.549%) 011: dt: 0.2500, sse=706203.1, rms=2.220 (5.986%) 012: dt: 0.2500, sse=695499.6, rms=2.127 (4.194%) rms = 2.08, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=691120.6, rms=2.083 (2.058%) 014: dt: 0.1250, sse=669167.0, rms=1.872 (10.164%) rms = 1.85, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=666902.3, rms=1.847 (1.322%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=74.4, 75 (7) missing vertices, mean dist -0.1 [0.3 (%69.2)->0.2 (%30.8))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.93 +- 0.25 (0.10-->3.68) (max @ vno 130905 --> 135482) face area 0.36 +- 0.17 (0.00-->3.56) mean absolute distance = 0.21 +- 0.37 2429 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1237341.6, rms=4.274 016: dt: 0.5000, sse=1063422.2, rms=3.458 (19.084%) rms = 4.14, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=880677.6, rms=2.282 (34.009%) 018: dt: 0.2500, sse=832537.7, rms=1.849 (18.970%) 019: dt: 0.2500, sse=814467.4, rms=1.668 (9.781%) rms = 1.65, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=814086.2, rms=1.647 (1.306%) 021: dt: 0.1250, sse=801645.6, rms=1.514 (8.034%) rms = 1.50, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=801109.9, rms=1.504 (0.660%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=76.3, 68 (5) missing vertices, mean dist -0.1 [0.2 (%64.7)->0.2 (%35.3))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.92 +- 0.25 (0.07-->3.66) (max @ vno 130905 --> 135482) face area 0.36 +- 0.16 (0.00-->3.41) mean absolute distance = 0.21 +- 0.32 2805 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=935604.3, rms=2.739 rms = 3.38, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=822372.9, rms=1.825 (33.375%) 024: dt: 0.2500, sse=789042.7, rms=1.418 (22.275%) rms = 1.41, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=785546.5, rms=1.407 (0.800%) 026: dt: 0.1250, sse=778368.8, rms=1.316 (6.419%) rms = 1.32, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=778594.1, rms=1.320 (-0.239%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=77.1, 70 (4) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=802229.0, rms=1.699 rms = 2.43, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=758485.6, rms=1.131 (33.457%) 029: dt: 0.2500, sse=750351.8, rms=0.982 (13.146%) rms = 0.98, time step reduction 2 of 3 to 0.125... rms = 0.98, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=748955.0, rms=0.976 (0.572%) positioning took 0.5 minutes generating cortex label... 5 non-cortical segments detected only using segment with 7953 vertices erasing segment 0 (vno[0] = 41902) erasing segment 2 (vno[0] = 105129) erasing segment 3 (vno[0] = 108396) erasing segment 4 (vno[0] = 112326) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.area vertex spacing 0.92 +- 0.25 (0.02-->3.61) (max @ vno 130905 --> 135482) face area 0.35 +- 0.16 (0.00-->3.26) refinement took 5.4 minutes PIDs (23169 23172) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sat Oct 7 21:31:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sat Oct 7 21:31:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 23398 of (23398 23401) to complete... Waiting for PID 23401 of (23398 23401) 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 (23398 23401) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sat Oct 7 21:31:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sat Oct 7 21:31:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 23446 of (23446 23449) to complete... Waiting for PID 23449 of (23446 23449) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 48.5 mm, total surface area = 90922 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.183 (target=0.015) step 005: RMS=0.128 (target=0.015) step 010: RMS=0.095 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.8 minutes mris_inflate utimesec 45.561073 mris_inflate stimesec 0.099984 mris_inflate ru_maxrss 208744 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30277 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11200 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2105 mris_inflate ru_nivcsw 3370 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 47.7 mm, total surface area = 90106 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.187 (target=0.015) step 005: RMS=0.129 (target=0.015) step 010: RMS=0.098 (target=0.015) step 015: RMS=0.080 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.041 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.029 (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 45.581070 mris_inflate stimesec 0.114982 mris_inflate ru_maxrss 208952 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30839 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10056 mris_inflate ru_oublock 11192 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2365 mris_inflate ru_nivcsw 3429 PIDs (23446 23449) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sat Oct 7 21:32:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Sat Oct 7 21:32:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 23551 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... Waiting for PID 23554 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... Waiting for PID 23557 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... Waiting for PID 23560 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... Waiting for PID 23563 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... Waiting for PID 23566 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... Waiting for PID 23569 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... Waiting for PID 23572 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... Waiting for PID 23575 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... Waiting for PID 23578 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... Waiting for PID 23582 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... Waiting for PID 23585 of (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = -36.485*4pi (-458.489) --> 37 handles ICI = 189.7, FI = 1867.5, variation=30660.762 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 188 vertices thresholded to be in k1 ~ [-1.06 0.23], k2 ~ [-0.28 0.18] total integrated curvature = 0.515*4pi (6.471) --> 0 handles ICI = 1.5, FI = 8.8, variation=153.998 150 vertices thresholded to be in [-0.06 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 109 vertices thresholded to be in [-0.29 0.11] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.021 done. mris_curvature -w rh.white.preaparc total integrated curvature = 22.888*4pi (287.618) --> -22 handles ICI = 195.8, FI = 1859.2, variation=29566.691 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 171 vertices thresholded to be in k1 ~ [-0.42 0.88], k2 ~ [-0.23 0.13] total integrated curvature = 0.397*4pi (4.986) --> 1 handles ICI = 1.4, FI = 9.3, variation=159.895 145 vertices thresholded to be in [-0.05 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 112 vertices thresholded to be in [-0.19 0.17] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.022 done. PIDs (23551 23554 23557 23560 23563 23566 23569 23572 23575 23578 23582 23585) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sat Oct 7 21:33:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050750 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 [ 0050750/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 [ 277 ] Gb_filter = 0 WARN: S lookup min: -0.720491 WARN: S explicit min: 0.000000 vertex = 1408 #----------------------------------------- #@# Curvature Stats rh Sat Oct 7 21:33:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050750 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 [ 0050750/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 [ 304 ] Gb_filter = 0 WARN: S lookup min: -0.767007 WARN: S explicit min: 0.000000 vertex = 420 #-------------------------------------------- #@# Sphere lh Sat Oct 7 21:33:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sat Oct 7 21:33:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 23724 of (23724 23727) to complete... Waiting for PID 23727 of (23724 23727) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0.284... 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 %20.31 pass 1: epoch 2 of 3 starting distance error %20.25 unfolding complete - removing small folds... starting distance error %20.13 removing remaining folds... final distance error %20.16 MRISunfold() return, current seed 1234 -01: dt=0.0000, 82 negative triangles 285: dt=0.9900, 82 negative triangles 286: dt=0.9900, 30 negative triangles 287: dt=0.9900, 21 negative triangles 288: dt=0.9900, 12 negative triangles 289: dt=0.9900, 8 negative triangles 290: dt=0.9900, 4 negative triangles 291: dt=0.9900, 2 negative triangles 292: dt=0.9900, 1 negative triangles 293: dt=0.9900, 1 negative triangles 294: dt=0.9900, 1 negative triangles 295: dt=0.9900, 2 negative triangles 296: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.15 hours mris_sphere utimesec 4351.074536 mris_sphere stimesec 1.432782 mris_sphere ru_maxrss 294032 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 51744 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10088 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 151197 mris_sphere ru_nivcsw 322877 FSRUNTIME@ mris_sphere 1.1460 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0.288... 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 %20.50 pass 1: epoch 2 of 3 starting distance error %20.43 unfolding complete - removing small folds... starting distance error %20.24 removing remaining folds... final distance error %20.27 MRISunfold() return, current seed 1234 -01: dt=0.0000, 90 negative triangles 254: dt=0.9900, 90 negative triangles 255: dt=0.9900, 48 negative triangles 256: dt=0.9900, 32 negative triangles 257: dt=0.9900, 25 negative triangles 258: dt=0.9900, 18 negative triangles 259: dt=0.9900, 23 negative triangles 260: dt=0.9900, 20 negative triangles 261: dt=0.9900, 13 negative triangles 262: dt=0.9900, 17 negative triangles 263: dt=0.9900, 13 negative triangles 264: dt=0.9900, 11 negative triangles 265: dt=0.9900, 10 negative triangles 266: dt=0.9900, 13 negative triangles 267: dt=0.9900, 9 negative triangles 268: dt=0.9900, 4 negative triangles 269: dt=0.9900, 8 negative triangles 270: dt=0.9900, 3 negative triangles 271: dt=0.9900, 1 negative triangles 272: dt=0.9900, 2 negative triangles 273: dt=0.9900, 3 negative triangles 274: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.06 hours mris_sphere utimesec 3809.138922 mris_sphere stimesec 1.646749 mris_sphere ru_maxrss 296092 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 51761 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10088 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 154426 mris_sphere ru_nivcsw 318715 FSRUNTIME@ mris_sphere 1.0577 hours 1 threads PIDs (23724 23727) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sat Oct 7 22:42:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Sat Oct 7 22:42:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 27278 of (27278 27281) to complete... Waiting for PID 27281 of (27278 27281) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 = 5.709 curvature mean = 0.040, std = 0.821 curvature mean = 0.008, std = 0.857 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 330321.3, tmin=1.0954 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 223654.4, tmin=2.1959 d=16.00 min @ (0.00, 0.00, 4.00) sse = 217280.4, tmin=3.3052 d=8.00 min @ (0.00, 0.00, -2.00) sse = 211870.0, tmin=4.4438 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 210909.9, tmin=5.5979 d=2.00 min @ (0.00, -0.50, 0.50) sse = 210595.0, tmin=6.7412 d=1.00 min @ (0.25, 0.25, 0.00) sse = 210485.1, tmin=7.8902 d=0.50 min @ (0.12, 0.12, -0.12) sse = 210442.3, tmin=9.0485 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 9.05 min curvature mean = 0.023, std = 0.836 curvature mean = 0.004, std = 0.945 curvature mean = 0.023, std = 0.847 curvature mean = 0.002, std = 0.978 curvature mean = 0.022, std = 0.850 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.024, std = 0.274 curvature mean = 0.044, std = 0.248 curvature mean = 0.055, std = 0.354 curvature mean = 0.042, std = 0.304 curvature mean = 0.041, std = 0.550 curvature mean = 0.041, std = 0.329 curvature mean = 0.024, std = 0.697 curvature mean = 0.041, std = 0.341 curvature mean = 0.009, std = 0.809 MRISregister() return, current seed 0 -01: dt=0.0000, 35 negative triangles 116: dt=0.9900, 35 negative triangles expanding nbhd size to 1 117: dt=0.9900, 43 negative triangles 118: dt=0.9900, 28 negative triangles 119: dt=0.9900, 37 negative triangles 120: dt=0.9900, 28 negative triangles 121: dt=0.9900, 38 negative triangles 122: dt=0.9900, 22 negative triangles 123: dt=0.9900, 27 negative triangles 124: dt=0.9900, 21 negative triangles 125: dt=0.9900, 21 negative triangles 126: dt=0.9900, 14 negative triangles 127: dt=0.9900, 14 negative triangles 128: dt=0.9900, 12 negative triangles 129: dt=0.9900, 17 negative triangles 130: dt=0.9900, 16 negative triangles 131: dt=0.9900, 12 negative triangles 132: dt=0.9900, 12 negative triangles 133: dt=0.9900, 11 negative triangles 134: dt=0.9900, 6 negative triangles 135: dt=0.9900, 6 negative triangles 136: dt=0.9900, 6 negative triangles 137: dt=0.9900, 7 negative triangles 138: dt=0.9900, 6 negative triangles 139: dt=0.9900, 7 negative triangles 140: dt=0.9900, 6 negative triangles 141: dt=0.9900, 6 negative triangles 142: dt=0.9900, 4 negative triangles 143: dt=0.9900, 4 negative triangles 144: dt=0.9900, 2 negative triangles 145: dt=0.9900, 3 negative triangles 146: dt=0.9900, 2 negative triangles 147: dt=0.9900, 2 negative triangles 148: dt=0.9900, 2 negative triangles 149: dt=0.9900, 1 negative triangles 150: dt=0.9900, 1 negative triangles 151: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.35 hours mris_register utimesec 4955.095710 mris_register stimesec 3.135523 mris_register ru_maxrss 262984 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 36450 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 10064 mris_register ru_oublock 10160 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 362195 mris_register ru_nivcsw 218161 FSRUNTIME@ mris_register 1.3537 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 = 5.736 curvature mean = 0.036, std = 0.813 curvature mean = 0.007, std = 0.863 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 368960.4, tmin=1.0955 d=32.00 min @ (-8.00, -8.00, 8.00) sse = 237942.6, tmin=2.1968 d=16.00 min @ (0.00, 4.00, 0.00) sse = 223147.4, tmin=3.3101 d=8.00 min @ (-2.00, -2.00, -2.00) sse = 212211.3, tmin=4.4488 d=4.00 min @ (1.00, 0.00, 1.00) sse = 208355.6, tmin=5.6056 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 208353.4, tmin=6.7551 d=1.00 min @ (0.25, 0.00, 0.00) sse = 208158.5, tmin=7.9061 d=0.50 min @ (-0.12, -0.12, 0.00) sse = 208116.4, tmin=9.0598 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 9.06 min curvature mean = 0.018, std = 0.828 curvature mean = 0.003, std = 0.949 curvature mean = 0.016, std = 0.839 curvature mean = 0.001, std = 0.980 curvature mean = 0.015, std = 0.841 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.024, std = 0.281 curvature mean = 0.041, std = 0.242 curvature mean = 0.052, std = 0.356 curvature mean = 0.036, std = 0.299 curvature mean = 0.039, std = 0.545 curvature mean = 0.036, std = 0.324 curvature mean = 0.023, std = 0.692 curvature mean = 0.036, std = 0.336 curvature mean = 0.007, std = 0.804 MRISregister() return, current seed 0 -01: dt=0.0000, 115 negative triangles 119: dt=0.9900, 115 negative triangles 120: dt=0.9405, 143 negative triangles expanding nbhd size to 1 121: dt=0.9900, 144 negative triangles 122: dt=0.9900, 112 negative triangles 123: dt=0.9900, 112 negative triangles 124: dt=0.9900, 104 negative triangles 125: dt=0.9900, 100 negative triangles 126: dt=0.9900, 94 negative triangles 127: dt=0.9900, 91 negative triangles 128: dt=0.9900, 87 negative triangles 129: dt=0.9900, 78 negative triangles 130: dt=0.9900, 66 negative triangles 131: dt=0.9900, 57 negative triangles 132: dt=0.9900, 60 negative triangles 133: dt=0.9900, 57 negative triangles 134: dt=0.9900, 58 negative triangles 135: dt=0.9900, 55 negative triangles 136: dt=0.9900, 54 negative triangles 137: dt=0.9900, 57 negative triangles 138: dt=0.9900, 58 negative triangles 139: dt=0.9900, 56 negative triangles 140: dt=0.9900, 61 negative triangles 141: dt=0.9900, 60 negative triangles 142: dt=0.9900, 55 negative triangles 143: dt=0.9900, 59 negative triangles 144: dt=0.9900, 57 negative triangles 145: dt=0.9900, 56 negative triangles 146: dt=0.9405, 57 negative triangles 147: dt=0.9405, 56 negative triangles 148: dt=0.9405, 54 negative triangles 149: dt=0.9405, 56 negative triangles 150: dt=0.9405, 55 negative triangles 151: dt=0.9405, 52 negative triangles 152: dt=0.9405, 51 negative triangles 153: dt=0.9405, 52 negative triangles 154: dt=0.9405, 51 negative triangles 155: dt=0.9405, 49 negative triangles 156: dt=0.9405, 50 negative triangles 157: dt=0.9405, 52 negative triangles 158: dt=0.9405, 48 negative triangles 159: dt=0.9405, 50 negative triangles 160: dt=0.9405, 47 negative triangles 161: dt=0.9405, 48 negative triangles 162: dt=0.9405, 49 negative triangles 163: dt=0.9405, 48 negative triangles 164: dt=0.9405, 47 negative triangles 165: dt=0.9405, 47 negative triangles 166: dt=0.9405, 49 negative triangles 167: dt=0.9405, 49 negative triangles 168: dt=0.9405, 45 negative triangles 169: dt=0.9405, 48 negative triangles 170: dt=0.9405, 43 negative triangles 171: dt=0.9405, 42 negative triangles 172: dt=0.9405, 43 negative triangles 173: dt=0.9405, 38 negative triangles 174: dt=0.9405, 40 negative triangles 175: dt=0.9405, 40 negative triangles 176: dt=0.9405, 41 negative triangles 177: dt=0.9405, 40 negative triangles 178: dt=0.9405, 40 negative triangles 179: dt=0.9405, 40 negative triangles 180: dt=0.9405, 38 negative triangles 181: dt=0.9405, 38 negative triangles 182: dt=0.9405, 35 negative triangles 183: dt=0.9405, 33 negative triangles 184: dt=0.9405, 33 negative triangles 185: dt=0.9405, 30 negative triangles 186: dt=0.9405, 31 negative triangles 187: dt=0.9405, 33 negative triangles 188: dt=0.9405, 31 negative triangles 189: dt=0.9405, 32 negative triangles 190: dt=0.9405, 36 negative triangles 191: dt=0.9405, 32 negative triangles 192: dt=0.9405, 34 negative triangles 193: dt=0.9405, 32 negative triangles 194: dt=0.9405, 25 negative triangles 195: dt=0.9405, 23 negative triangles 196: dt=0.9405, 24 negative triangles 197: dt=0.9405, 21 negative triangles 198: dt=0.9405, 20 negative triangles 199: dt=0.9405, 21 negative triangles 200: dt=0.9405, 21 negative triangles 201: dt=0.9405, 20 negative triangles 202: dt=0.9405, 20 negative triangles 203: dt=0.9405, 20 negative triangles 204: dt=0.9405, 16 negative triangles 205: dt=0.9405, 14 negative triangles 206: dt=0.9405, 13 negative triangles 207: dt=0.9405, 12 negative triangles 208: dt=0.9405, 12 negative triangles 209: dt=0.9405, 10 negative triangles 210: dt=0.9405, 10 negative triangles 211: dt=0.9405, 10 negative triangles 212: dt=0.9405, 7 negative triangles 213: dt=0.9405, 8 negative triangles 214: dt=0.9405, 7 negative triangles 215: dt=0.9405, 7 negative triangles 216: dt=0.9405, 7 negative triangles 217: dt=0.9405, 5 negative triangles 218: dt=0.9405, 6 negative triangles 219: dt=0.9405, 5 negative triangles 220: dt=0.9405, 5 negative triangles 221: dt=0.9405, 5 negative triangles 222: dt=0.9405, 4 negative triangles 223: dt=0.9405, 4 negative triangles 224: dt=0.9405, 2 negative triangles 225: dt=0.9405, 3 negative triangles 226: dt=0.9405, 1 negative triangles 227: dt=0.9405, 3 negative triangles 228: dt=0.9405, 3 negative triangles 229: dt=0.9405, 1 negative triangles 230: dt=0.9405, 1 negative triangles 231: dt=0.9405, 3 negative triangles 232: dt=0.9405, 2 negative triangles 233: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.32 hours mris_register utimesec 4735.961024 mris_register stimesec 3.210511 mris_register ru_maxrss 263844 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 38027 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10168 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 338257 mris_register ru_nivcsw 224801 FSRUNTIME@ mris_register 1.3161 hours 1 threads PIDs (27278 27281) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 00:03:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 00:03:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 31054 of (31054 31057) to complete... Waiting for PID 31057 of (31054 31057) 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 (31054 31057) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 00:03:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Sun Oct 8 00:03:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 31099 of (31099 31102) to complete... Waiting for PID 31102 of (31099 31102) 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 (31099 31102) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 00:03:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050750 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Sun Oct 8 00:03:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050750 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 31146 of (31146 31149) to complete... Waiting for PID 31149 of (31146 31149) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050750 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... 954 labels changed using aseg relabeling using gibbs priors... 000: 3281 changed, 143025 examined... 001: 738 changed, 13555 examined... 002: 197 changed, 4072 examined... 003: 77 changed, 1204 examined... 004: 25 changed, 458 examined... 005: 11 changed, 155 examined... 006: 3 changed, 56 examined... 007: 1 changed, 18 examined... 008: 1 changed, 8 examined... 009: 1 changed, 9 examined... 010: 0 changed, 5 examined... 217 labels changed using aseg 000: 104 total segments, 64 labels (225 vertices) changed 001: 42 total segments, 4 labels (13 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 7 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1714 vertices marked for relabeling... 1714 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 0050750 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... 1180 labels changed using aseg relabeling using gibbs priors... 000: 2982 changed, 142876 examined... 001: 666 changed, 12786 examined... 002: 147 changed, 3833 examined... 003: 43 changed, 881 examined... 004: 11 changed, 274 examined... 005: 5 changed, 74 examined... 006: 1 changed, 31 examined... 007: 0 changed, 7 examined... 196 labels changed using aseg 000: 107 total segments, 69 labels (309 vertices) changed 001: 41 total segments, 3 labels (3 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1057 vertices marked for relabeling... 1057 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 16 seconds. PIDs (31146 31149) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 00:04:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050750 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 00:04:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050750 rh Waiting for PID 31198 of (31198 31201) to complete... Waiting for PID 31201 of (31198 31201) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050750 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-6.0.0/0050750/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... 17276 bright wm thresholded. 1249 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.orig... computing class statistics... border white: 265437 voxels (1.58%) border gray 306999 voxels (1.83%) WM (96.0): 96.5 +- 9.6 [70.0 --> 110.0] GM (63.0) : 62.7 +- 11.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 44.4 (was 70) setting MAX_BORDER_WHITE to 112.6 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 32.7 (was 40) setting MAX_GRAY to 93.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 44.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 21.1 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-7.8, GM=56+-7.8 mean inside = 90.9, mean outside = 67.4 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.92 +- 0.26 (0.05-->4.28) (max @ vno 118425 --> 118438) face area 0.35 +- 0.16 (0.00-->4.00) mean absolute distance = 0.40 +- 0.67 1837 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 202 points - only 0.00% unknown deleting segment 1 with 13 points - only 0.00% unknown deleting segment 2 with 364 points - only 0.00% unknown deleting segment 3 with 30 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 6 with 27 points - only 0.00% unknown deleting segment 7 with 29 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 281 points - only 0.00% unknown deleting segment 11 with 15 points - only 0.00% unknown deleting segment 12 with 75 points - only 0.00% unknown deleting segment 13 with 38 points - only 0.00% unknown deleting segment 14 with 8 points - only 0.00% unknown deleting segment 15 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown deleting segment 17 with 11 points - only 0.00% unknown deleting segment 18 with 47 points - only 0.00% unknown deleting segment 19 with 7 points - only 0.00% unknown deleting segment 20 with 62 points - only 0.00% unknown deleting segment 21 with 12 points - only 0.00% unknown deleting segment 22 with 45 points - only 0.00% unknown mean border=71.7, 37 (37) missing vertices, mean dist 0.2 [0.5 (%16.0)->0.4 (%84.0))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.94 +- 0.26 (0.12-->4.37) (max @ vno 118425 --> 118438) face area 0.35 +- 0.17 (0.00-->3.88) mean absolute distance = 0.25 +- 0.49 1920 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2276356.5, rms=7.533 001: dt: 0.5000, sse=1332293.6, rms=4.711 (37.465%) 002: dt: 0.5000, sse=1195662.0, rms=4.169 (11.514%) rms = 4.33, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=954201.5, rms=2.900 (30.429%) 004: dt: 0.2500, sse=874596.5, rms=2.338 (19.372%) 005: dt: 0.2500, sse=843550.9, rms=2.076 (11.235%) 006: dt: 0.2500, sse=836433.5, rms=2.004 (3.429%) 007: dt: 0.2500, sse=831209.9, rms=1.936 (3.396%) rms = 1.91, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=827306.4, rms=1.909 (1.390%) 009: dt: 0.1250, sse=817247.7, rms=1.802 (5.619%) rms = 1.79, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=815937.3, rms=1.786 (0.879%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 179 points - only 0.00% unknown deleting segment 1 with 10 points - only 0.00% unknown deleting segment 2 with 335 points - only 0.00% unknown deleting segment 3 with 27 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 17 points - only 0.00% unknown deleting segment 6 with 20 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 18 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown deleting segment 13 with 7 points - only 0.00% unknown deleting segment 14 with 137 points - only 0.00% unknown deleting segment 15 with 59 points - only 0.00% unknown deleting segment 16 with 34 points - only 0.00% unknown deleting segment 17 with 8 points - only 0.00% unknown deleting segment 18 with 7 points - only 0.00% unknown deleting segment 19 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 20 with 3 points - only 0.00% unknown deleting segment 21 with 10 points - only 0.00% unknown deleting segment 22 with 31 points - only 0.00% unknown deleting segment 23 with 10 points - only 0.00% unknown deleting segment 24 with 47 points - only 0.00% unknown mean border=74.4, 45 (8) missing vertices, mean dist -0.1 [0.3 (%70.1)->0.2 (%29.9))] %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.93 +- 0.26 (0.09-->4.36) (max @ vno 118425 --> 118438) face area 0.37 +- 0.17 (0.00-->4.11) mean absolute distance = 0.21 +- 0.39 2277 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1236846.5, rms=4.173 011: dt: 0.5000, sse=1057101.0, rms=3.296 (21.017%) rms = 4.04, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=885031.8, rms=2.135 (35.216%) 013: dt: 0.2500, sse=839933.7, rms=1.709 (19.958%) 014: dt: 0.2500, sse=825702.2, rms=1.550 (9.301%) rms = 1.54, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=824591.9, rms=1.541 (0.621%) 016: dt: 0.1250, sse=814833.5, rms=1.414 (8.187%) rms = 1.41, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=814388.2, rms=1.408 (0.451%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 177 points - only 0.00% unknown deleting segment 1 with 373 points - only 0.00% unknown deleting segment 2 with 28 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 19 points - only 0.00% unknown deleting segment 5 with 20 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 24 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 166 points - only 0.00% unknown deleting segment 12 with 14 points - only 0.00% unknown deleting segment 13 with 37 points - only 0.00% unknown deleting segment 14 with 64 points - only 0.00% unknown deleting segment 15 with 8 points - only 0.00% unknown deleting segment 16 with 10 points - only 0.00% unknown deleting segment 17 with 7 points - only 0.00% unknown deleting segment 18 with 37 points - only 0.00% unknown deleting segment 19 with 40 points - only 0.00% unknown deleting segment 20 with 7 points - only 0.00% unknown deleting segment 21 with 54 points - only 0.00% unknown mean border=76.3, 49 (4) missing vertices, mean dist -0.1 [0.2 (%64.9)->0.2 (%35.1))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.93 +- 0.26 (0.06-->4.33) (max @ vno 118425 --> 118438) face area 0.36 +- 0.17 (0.00-->4.06) mean absolute distance = 0.21 +- 0.34 2615 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=954038.4, rms=2.751 rms = 3.41, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=835214.4, rms=1.787 (35.031%) 019: dt: 0.2500, sse=798126.9, rms=1.357 (24.067%) rms = 1.34, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=796150.6, rms=1.336 (1.554%) 021: dt: 0.1250, sse=789338.7, rms=1.243 (6.970%) rms = 1.25, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=789301.6, rms=1.247 (-0.294%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 177 points - only 0.00% unknown deleting segment 1 with 373 points - only 0.00% unknown deleting segment 2 with 27 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 25 points - only 0.00% unknown deleting segment 5 with 21 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 5 points - only 0.00% unknown deleting segment 8 with 29 points - only 0.00% unknown deleting segment 9 with 180 points - only 0.00% unknown deleting segment 10 with 18 points - only 0.00% unknown deleting segment 11 with 37 points - only 0.00% unknown deleting segment 12 with 65 points - only 0.00% unknown deleting segment 13 with 12 points - only 0.00% unknown deleting segment 14 with 10 points - only 0.00% unknown deleting segment 15 with 7 points - only 0.00% unknown deleting segment 16 with 31 points - only 0.00% unknown deleting segment 17 with 39 points - only 0.00% unknown deleting segment 18 with 10 points - only 0.00% unknown deleting segment 19 with 58 points - only 0.00% unknown mean border=77.3, 46 (4) missing vertices, mean dist -0.0 [0.2 (%55.2)->0.2 (%44.8))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=820790.8, rms=1.719 rms = 2.51, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=772662.1, rms=1.093 (36.446%) 024: dt: 0.2500, sse=763731.9, rms=0.933 (14.628%) rms = 0.94, time step reduction 2 of 3 to 0.125... rms = 0.93, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=762624.0, rms=0.925 (0.784%) positioning took 0.5 minutes generating cortex label... 7 non-cortical segments detected only using segment with 7719 vertices erasing segment 1 (vno[0] = 94367) erasing segment 2 (vno[0] = 104189) erasing segment 3 (vno[0] = 105308) erasing segment 4 (vno[0] = 109291) erasing segment 5 (vno[0] = 112899) erasing segment 6 (vno[0] = 116145) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.area vertex spacing 0.92 +- 0.26 (0.05-->4.28) (max @ vno 118425 --> 118438) face area 0.36 +- 0.17 (0.00-->3.98) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 5 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=43.3, 47 (47) missing vertices, mean dist 1.5 [0.0 (%0.0)->2.6 (%100.0))] % 8 local maxima, %49 large gradients and %39 min vals, 1174 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=33256030.0, rms=34.506 001: dt: 0.0500, sse=28926212.0, rms=32.127 (6.894%) 002: dt: 0.0500, sse=25782710.0, rms=30.283 (5.740%) 003: dt: 0.0500, sse=23353306.0, rms=28.777 (4.973%) 004: dt: 0.0500, sse=21382914.0, rms=27.495 (4.455%) 005: dt: 0.0500, sse=19724586.0, rms=26.368 (4.100%) 006: dt: 0.0500, sse=18290992.0, rms=25.353 (3.850%) 007: dt: 0.0500, sse=17026548.0, rms=24.422 (3.670%) 008: dt: 0.0500, sse=15896522.0, rms=23.560 (3.532%) 009: dt: 0.0500, sse=14875295.0, rms=22.752 (3.429%) 010: dt: 0.0500, sse=13945160.0, rms=21.990 (3.347%) positioning took 1.0 minutes mean border=43.2, 37 (20) missing vertices, mean dist 1.3 [0.0 (%0.0)->2.1 (%100.0))] % 8 local maxima, %49 large gradients and %38 min vals, 1083 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=14540261.0, rms=22.484 011: dt: 0.0500, sse=13686722.0, rms=21.778 (3.142%) 012: dt: 0.0500, sse=12902471.0, rms=21.108 (3.076%) 013: dt: 0.0500, sse=12179133.0, rms=20.470 (3.020%) 014: dt: 0.0500, sse=11511774.0, rms=19.864 (2.962%) 015: dt: 0.0500, sse=10895926.0, rms=19.288 (2.903%) 016: dt: 0.0500, sse=10327224.0, rms=18.739 (2.843%) 017: dt: 0.0500, sse=9802535.0, rms=18.219 (2.778%) 018: dt: 0.0500, sse=9318097.0, rms=17.724 (2.714%) 019: dt: 0.0500, sse=8870694.0, rms=17.255 (2.648%) 020: dt: 0.0500, sse=8457767.0, rms=16.810 (2.578%) positioning took 1.0 minutes mean border=43.1, 43 (17) missing vertices, mean dist 1.1 [0.1 (%1.1)->1.8 (%98.9))] % 9 local maxima, %49 large gradients and %38 min vals, 1082 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=8508704.0, rms=16.873 021: dt: 0.0500, sse=8118880.0, rms=16.444 (2.546%) 022: dt: 0.0500, sse=7759770.0, rms=16.038 (2.469%) 023: dt: 0.0500, sse=7426855.5, rms=15.652 (2.406%) 024: dt: 0.0500, sse=7120417.5, rms=15.288 (2.325%) 025: dt: 0.0500, sse=6837818.5, rms=14.944 (2.248%) 026: dt: 0.0500, sse=6576751.5, rms=14.620 (2.173%) 027: dt: 0.0500, sse=6334257.0, rms=14.311 (2.109%) 028: dt: 0.0500, sse=6106522.5, rms=14.015 (2.068%) 029: dt: 0.0500, sse=5892529.5, rms=13.731 (2.027%) 030: dt: 0.0500, sse=5691462.5, rms=13.459 (1.984%) positioning took 1.0 minutes mean border=43.1, 72 (15) missing vertices, mean dist 0.9 [0.1 (%13.3)->1.7 (%86.7))] % 9 local maxima, %49 large gradients and %37 min vals, 1018 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=5751614.0, rms=13.541 031: dt: 0.5000, sse=4357317.0, rms=11.490 (15.145%) 032: dt: 0.5000, sse=3507686.8, rms=10.026 (12.744%) 033: dt: 0.5000, sse=2930481.8, rms=8.895 (11.281%) 034: dt: 0.5000, sse=2556714.2, rms=8.068 (9.300%) 035: dt: 0.5000, sse=2297326.2, rms=7.439 (7.791%) 036: dt: 0.5000, sse=2121850.8, rms=6.977 (6.205%) 037: dt: 0.5000, sse=1982105.9, rms=6.589 (5.564%) 038: dt: 0.5000, sse=1880865.2, rms=6.292 (4.519%) 039: dt: 0.5000, sse=1791780.5, rms=6.021 (4.292%) 040: dt: 0.5000, sse=1727753.2, rms=5.817 (3.390%) 041: dt: 0.5000, sse=1673792.0, rms=5.641 (3.026%) 042: dt: 0.5000, sse=1637054.6, rms=5.518 (2.187%) 043: dt: 0.5000, sse=1607963.5, rms=5.419 (1.798%) 044: dt: 0.5000, sse=1591021.0, rms=5.358 (1.120%) 045: dt: 0.5000, sse=1573600.2, rms=5.298 (1.123%) rms = 5.26, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1564385.1, rms=5.263 (0.655%) 047: dt: 0.2500, sse=1524605.2, rms=5.085 (3.376%) rms = 5.05, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=1514425.6, rms=5.046 (0.776%) rms = 5.03, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=1510806.8, rms=5.028 (0.347%) positioning took 2.5 minutes mean border=42.2, 2060 (8) missing vertices, mean dist 0.2 [0.2 (%51.7)->0.9 (%48.3))] %19 local maxima, %42 large gradients and %33 min vals, 484 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=1669011.8, rms=4.907 050: dt: 0.5000, sse=1533905.5, rms=4.371 (10.932%) 051: dt: 0.5000, sse=1475522.5, rms=4.143 (5.212%) 052: dt: 0.5000, sse=1450389.0, rms=4.038 (2.538%) 053: dt: 0.5000, sse=1432187.4, rms=3.966 (1.770%) rms = 3.92, time step reduction 1 of 3 to 0.250... 054: dt: 0.5000, sse=1421202.6, rms=3.919 (1.198%) 055: dt: 0.2500, sse=1373399.2, rms=3.624 (7.517%) 056: dt: 0.2500, sse=1359503.8, rms=3.551 (2.013%) rms = 3.54, time step reduction 2 of 3 to 0.125... 057: dt: 0.2500, sse=1356757.5, rms=3.537 (0.408%) rms = 3.50, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1351586.8, rms=3.505 (0.913%) positioning took 1.4 minutes mean border=41.2, 2345 (6) missing vertices, mean dist 0.2 [0.2 (%50.3)->0.7 (%49.7))] %30 local maxima, %31 large gradients and %33 min vals, 594 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=1466584.2, rms=3.921 059: dt: 0.5000, sse=1432055.2, rms=3.761 (4.079%) 060: dt: 0.5000, sse=1407547.6, rms=3.701 (1.602%) rms = 3.74, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1375830.8, rms=3.501 (5.393%) 062: dt: 0.2500, sse=1364383.6, rms=3.426 (2.155%) rms = 3.42, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1362220.2, rms=3.415 (0.302%) rms = 3.38, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1356173.1, rms=3.378 (1.100%) positioning took 1.1 minutes mean border=40.4, 4527 (6) missing vertices, mean dist 0.1 [0.2 (%47.8)->0.5 (%52.2))] %37 local maxima, %24 large gradients and %32 min vals, 584 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-6.0.0/0050750/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1412613.0, rms=3.588 rms = 3.56, time step reduction 1 of 3 to 0.250... 065: dt: 0.5000, sse=1404258.9, rms=3.559 (0.806%) 066: dt: 0.2500, sse=1366045.6, rms=3.351 (5.830%) 067: dt: 0.2500, sse=1352106.4, rms=3.283 (2.052%) rms = 3.27, time step reduction 2 of 3 to 0.125... 068: dt: 0.2500, sse=1350149.5, rms=3.275 (0.237%) rms = 3.23, time step reduction 3 of 3 to 0.062... 069: dt: 0.1250, sse=1342470.9, rms=3.227 (1.471%) positioning took 0.9 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.area.pial vertex spacing 1.06 +- 0.47 (0.05-->6.81) (max @ vno 100083 --> 100051) face area 0.44 +- 0.36 (0.00-->7.43) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 143025 vertices processed 25000 of 143025 vertices processed 50000 of 143025 vertices processed 75000 of 143025 vertices processed 100000 of 143025 vertices processed 125000 of 143025 vertices processed 0 of 143025 vertices processed 25000 of 143025 vertices processed 50000 of 143025 vertices processed 75000 of 143025 vertices processed 100000 of 143025 vertices processed 125000 of 143025 vertices processed thickness calculation complete, 373:1329 truncations. 27176 vertices at 0 distance 94933 vertices at 1 distance 90927 vertices at 2 distance 39948 vertices at 3 distance 13221 vertices at 4 distance 4421 vertices at 5 distance 1412 vertices at 6 distance 520 vertices at 7 distance 239 vertices at 8 distance 149 vertices at 9 distance 85 vertices at 10 distance 72 vertices at 11 distance 66 vertices at 12 distance 28 vertices at 13 distance 15 vertices at 14 distance 20 vertices at 15 distance 21 vertices at 16 distance 9 vertices at 17 distance 8 vertices at 18 distance 9 vertices at 19 distance 13 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.thickness positioning took 16.5 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050750 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-6.0.0/0050750/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... 17276 bright wm thresholded. 1249 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.orig... computing class statistics... border white: 265437 voxels (1.58%) border gray 306999 voxels (1.83%) WM (96.0): 96.5 +- 9.6 [70.0 --> 110.0] GM (63.0) : 62.7 +- 11.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.4 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 31.7 (was 40) setting MAX_GRAY to 92.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 43.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.1 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-7.0, GM=55+-9.6 mean inside = 90.9, mean outside = 67.5 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 0.92 +- 0.25 (0.02-->3.61) (max @ vno 130905 --> 135482) face area 0.35 +- 0.16 (0.00-->3.24) mean absolute distance = 0.41 +- 0.67 2027 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 120 points - only 0.00% unknown deleting segment 1 with 16 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 35 points - only 0.00% unknown deleting segment 9 with 16 points - only 0.00% unknown deleting segment 10 with 358 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown deleting segment 12 with 24 points - only 0.00% unknown deleting segment 13 with 20 points - only 0.00% unknown deleting segment 14 with 19 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown deleting segment 16 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 17 with 2 points - only 0.00% unknown deleting segment 18 with 11 points - only 0.00% unknown deleting segment 19 with 5 points - only 0.00% unknown deleting segment 20 with 9 points - only 0.00% unknown deleting segment 21 with 6 points - only 0.00% unknown mean border=71.3, 74 (71) missing vertices, mean dist 0.2 [0.5 (%16.9)->0.4 (%83.1))] %76 local maxima, %19 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 0.94 +- 0.26 (0.12-->3.76) (max @ vno 105206 --> 102985) face area 0.35 +- 0.17 (0.00-->3.52) mean absolute distance = 0.25 +- 0.47 1749 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2366562.0, rms=7.760 001: dt: 0.5000, sse=1372404.9, rms=4.884 (37.052%) 002: dt: 0.5000, sse=1199521.6, rms=4.207 (13.878%) rms = 4.32, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=962027.9, rms=2.975 (29.282%) 004: dt: 0.2500, sse=880865.1, rms=2.401 (19.296%) 005: dt: 0.2500, sse=847019.8, rms=2.129 (11.328%) 006: dt: 0.2500, sse=838569.8, rms=2.043 (4.049%) 007: dt: 0.2500, sse=831005.8, rms=1.974 (3.349%) rms = 1.94, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=828047.4, rms=1.940 (1.734%) 009: dt: 0.1250, sse=818693.8, rms=1.839 (5.230%) rms = 1.82, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=817389.2, rms=1.825 (0.750%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 106 points - only 0.00% unknown deleting segment 1 with 14 points - only 0.00% unknown deleting segment 2 with 10 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 37 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 190 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 10 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown deleting segment 14 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown deleting segment 16 with 9 points - only 0.00% unknown deleting segment 17 with 5 points - only 0.00% unknown deleting segment 18 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 19 with 3 points - only 0.00% unknown mean border=74.2, 68 (12) missing vertices, mean dist -0.1 [0.3 (%71.0)->0.2 (%29.0))] %83 local maxima, %13 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 0.93 +- 0.26 (0.10-->3.95) (max @ vno 105206 --> 102985) face area 0.37 +- 0.17 (0.00-->3.61) mean absolute distance = 0.21 +- 0.38 2081 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1262547.6, rms=4.270 011: dt: 0.5000, sse=1068012.9, rms=3.314 (22.394%) rms = 4.03, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=890738.7, rms=2.154 (35.009%) 013: dt: 0.2500, sse=846320.3, rms=1.725 (19.923%) 014: dt: 0.2500, sse=830724.2, rms=1.560 (9.572%) rms = 1.55, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=828659.0, rms=1.547 (0.810%) 016: dt: 0.1250, sse=819351.2, rms=1.427 (7.779%) rms = 1.42, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=819484.3, rms=1.423 (0.235%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 56 points - only 0.00% unknown deleting segment 1 with 14 points - only 0.00% unknown deleting segment 2 with 8 points - only 0.00% unknown deleting segment 3 with 44 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 38 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 284 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown deleting segment 12 with 10 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 15 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown deleting segment 17 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 18 with 2 points - only 0.00% unknown deleting segment 19 with 9 points - only 0.00% unknown deleting segment 20 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 21 with 3 points - only 0.00% unknown deleting segment 22 with 6 points - only 0.00% unknown mean border=76.1, 77 (11) missing vertices, mean dist -0.1 [0.2 (%65.2)->0.2 (%34.8))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.92 +- 0.26 (0.12-->3.97) (max @ vno 105206 --> 102985) face area 0.36 +- 0.17 (0.00-->3.42) mean absolute distance = 0.21 +- 0.32 2195 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=955177.7, rms=2.768 rms = 3.37, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=837609.2, rms=1.819 (34.265%) 019: dt: 0.2500, sse=799523.1, rms=1.366 (24.909%) rms = 1.35, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=795925.4, rms=1.352 (1.047%) 021: dt: 0.1250, sse=789136.7, rms=1.261 (6.746%) rms = 1.27, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=789882.2, rms=1.267 (-0.463%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 58 points - only 0.00% unknown deleting segment 1 with 15 points - only 0.00% unknown deleting segment 2 with 8 points - only 0.00% unknown deleting segment 3 with 42 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 38 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 9 points - only 0.00% unknown deleting segment 9 with 345 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown deleting segment 12 with 10 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown deleting segment 16 with 5 points - only 0.00% unknown deleting segment 17 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 18 with 2 points - only 0.00% unknown deleting segment 19 with 9 points - only 0.00% unknown deleting segment 20 with 5 points - only 0.00% unknown deleting segment 21 with 9 points - only 0.00% unknown deleting segment 22 with 6 points - only 0.00% unknown mean border=77.0, 73 (8) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=813864.2, rms=1.679 rms = 2.43, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=770446.1, rms=1.100 (34.490%) 024: dt: 0.2500, sse=761571.3, rms=0.955 (13.145%) rms = 0.96, time step reduction 2 of 3 to 0.125... rms = 0.95, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=762369.1, rms=0.950 (0.589%) positioning took 0.5 minutes generating cortex label... 6 non-cortical segments detected only using segment with 7955 vertices erasing segment 0 (vno[0] = 41928) erasing segment 2 (vno[0] = 88923) erasing segment 3 (vno[0] = 105129) erasing segment 4 (vno[0] = 108396) erasing segment 5 (vno[0] = 112326) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.area vertex spacing 0.92 +- 0.26 (0.02-->3.94) (max @ vno 102985 --> 105206) face area 0.36 +- 0.17 (0.00-->3.28) 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 40 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=42.6, 74 (74) missing vertices, mean dist 1.5 [0.0 (%0.0)->2.8 (%100.0))] % 8 local maxima, %43 large gradients and %45 min vals, 1032 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=34197168.0, rms=35.051 001: dt: 0.0500, sse=29838878.0, rms=32.689 (6.738%) 002: dt: 0.0500, sse=26677880.0, rms=30.863 (5.586%) 003: dt: 0.0500, sse=24243994.0, rms=29.380 (4.806%) 004: dt: 0.0500, sse=22268864.0, rms=28.119 (4.293%) 005: dt: 0.0500, sse=20606374.0, rms=27.012 (3.938%) 006: dt: 0.0500, sse=19168120.0, rms=26.016 (3.687%) 007: dt: 0.0500, sse=17900718.0, rms=25.105 (3.500%) 008: dt: 0.0500, sse=16767187.0, rms=24.262 (3.359%) 009: dt: 0.0500, sse=15743167.0, rms=23.474 (3.248%) 010: dt: 0.0500, sse=14810905.0, rms=22.733 (3.157%) positioning took 1.0 minutes mean border=42.5, 74 (45) missing vertices, mean dist 1.2 [0.0 (%0.0)->2.3 (%100.0))] % 8 local maxima, %43 large gradients and %44 min vals, 987 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=15391951.0, rms=23.202 011: dt: 0.0500, sse=14534965.0, rms=22.513 (2.968%) 012: dt: 0.0500, sse=13747022.0, rms=21.861 (2.898%) 013: dt: 0.0500, sse=13019656.0, rms=21.241 (2.836%) 014: dt: 0.0500, sse=12347419.0, rms=20.651 (2.776%) 015: dt: 0.0500, sse=11726162.0, rms=20.091 (2.714%) 016: dt: 0.0500, sse=11151391.0, rms=19.558 (2.653%) 017: dt: 0.0500, sse=10618876.0, rms=19.050 (2.593%) 018: dt: 0.0500, sse=10126076.0, rms=18.569 (2.529%) 019: dt: 0.0500, sse=9669503.0, rms=18.111 (2.466%) 020: dt: 0.0500, sse=9246920.0, rms=17.676 (2.399%) positioning took 1.0 minutes mean border=42.4, 80 (28) missing vertices, mean dist 1.1 [0.1 (%0.9)->2.0 (%99.1))] % 8 local maxima, %44 large gradients and %43 min vals, 1022 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=9312618.0, rms=17.752 021: dt: 0.0500, sse=8914159.0, rms=17.334 (2.355%) 022: dt: 0.0500, sse=8545490.0, rms=16.938 (2.285%) 023: dt: 0.0500, sse=8202636.0, rms=16.561 (2.225%) 024: dt: 0.0500, sse=7885542.0, rms=16.204 (2.153%) 025: dt: 0.0500, sse=7592061.0, rms=15.867 (2.081%) 026: dt: 0.0500, sse=7319711.0, rms=15.548 (2.014%) 027: dt: 0.0500, sse=7065310.0, rms=15.243 (1.960%) 028: dt: 0.0500, sse=6825486.0, rms=14.950 (1.923%) 029: dt: 0.0500, sse=6599129.0, rms=14.668 (1.887%) 030: dt: 0.0500, sse=6385639.0, rms=14.396 (1.850%) positioning took 1.0 minutes mean border=42.4, 109 (25) missing vertices, mean dist 0.9 [0.1 (%11.1)->1.9 (%88.9))] % 9 local maxima, %44 large gradients and %43 min vals, 913 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=6453574.5, rms=14.485 031: dt: 0.5000, sse=4969109.0, rms=12.450 (14.049%) 032: dt: 0.5000, sse=4024440.2, rms=10.949 (12.051%) 033: dt: 0.5000, sse=3369399.5, rms=9.773 (10.740%) 034: dt: 0.5000, sse=2929851.8, rms=8.889 (9.053%) 035: dt: 0.5000, sse=2619711.5, rms=8.206 (7.681%) 036: dt: 0.5000, sse=2401341.2, rms=7.685 (6.344%) 037: dt: 0.5000, sse=2218214.5, rms=7.224 (5.999%) 038: dt: 0.5000, sse=2075052.0, rms=6.840 (5.316%) 039: dt: 0.5000, sse=1946198.2, rms=6.481 (5.259%) 040: dt: 0.5000, sse=1847029.6, rms=6.186 (4.538%) 041: dt: 0.5000, sse=1770185.0, rms=5.951 (3.800%) 042: dt: 0.5000, sse=1724508.6, rms=5.805 (2.461%) 043: dt: 0.5000, sse=1687071.2, rms=5.684 (2.081%) 044: dt: 0.5000, sse=1663560.8, rms=5.604 (1.410%) 045: dt: 0.5000, sse=1643948.1, rms=5.540 (1.150%) rms = 5.50, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1633908.4, rms=5.503 (0.663%) 047: dt: 0.2500, sse=1592508.9, rms=5.328 (3.176%) rms = 5.29, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=1581102.5, rms=5.286 (0.795%) rms = 5.26, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=1575886.4, rms=5.263 (0.426%) positioning took 2.6 minutes mean border=41.6, 2295 (12) missing vertices, mean dist 0.2 [0.2 (%52.4)->0.9 (%47.6))] %17 local maxima, %38 large gradients and %39 min vals, 414 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=1720444.2, rms=5.052 050: dt: 0.5000, sse=1599348.1, rms=4.591 (9.124%) 051: dt: 0.5000, sse=1553303.1, rms=4.430 (3.508%) 052: dt: 0.5000, sse=1533743.1, rms=4.356 (1.651%) rms = 4.31, time step reduction 1 of 3 to 0.250... 053: dt: 0.5000, sse=1519625.1, rms=4.307 (1.145%) 054: dt: 0.2500, sse=1474718.2, rms=4.050 (5.953%) 055: dt: 0.2500, sse=1459697.4, rms=3.980 (1.726%) rms = 3.97, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1456634.6, rms=3.966 (0.352%) rms = 3.93, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1449937.4, rms=3.929 (0.943%) positioning took 1.4 minutes mean border=40.9, 2683 (6) missing vertices, mean dist 0.1 [0.2 (%51.9)->0.7 (%48.1))] %27 local maxima, %29 large gradients and %38 min vals, 508 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=1533284.5, rms=4.191 rms = 4.14, time step reduction 1 of 3 to 0.250... 058: dt: 0.5000, sse=1519066.5, rms=4.141 (1.188%) 059: dt: 0.2500, sse=1480443.1, rms=3.962 (4.329%) 060: dt: 0.2500, sse=1465890.1, rms=3.897 (1.635%) rms = 3.88, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1461434.9, rms=3.879 (0.458%) 062: dt: 0.1250, sse=1450960.8, rms=3.824 (1.426%) rms = 3.81, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1447308.5, rms=3.808 (0.406%) positioning took 1.1 minutes mean border=40.2, 5196 (4) missing vertices, mean dist 0.1 [0.2 (%48.7)->0.5 (%51.3))] %33 local maxima, %22 large gradients and %37 min vals, 481 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-6.0.0/0050750/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1491097.4, rms=3.944 rms = 3.91, time step reduction 1 of 3 to 0.250... 064: dt: 0.5000, sse=1480492.5, rms=3.915 (0.747%) 065: dt: 0.2500, sse=1436951.0, rms=3.702 (5.435%) 066: dt: 0.2500, sse=1421338.1, rms=3.630 (1.933%) rms = 3.61, time step reduction 2 of 3 to 0.125... 067: dt: 0.2500, sse=1415824.8, rms=3.607 (0.639%) 068: dt: 0.1250, sse=1405581.5, rms=3.550 (1.580%) rms = 3.54, time step reduction 3 of 3 to 0.062... 069: dt: 0.1250, sse=1402350.9, rms=3.537 (0.377%) positioning took 1.1 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.area.pial vertex spacing 1.06 +- 0.49 (0.08-->7.38) (max @ vno 104291 --> 103225) face area 0.44 +- 0.37 (0.00-->5.89) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 142876 vertices processed 25000 of 142876 vertices processed 50000 of 142876 vertices processed 75000 of 142876 vertices processed 100000 of 142876 vertices processed 125000 of 142876 vertices processed 0 of 142876 vertices processed 25000 of 142876 vertices processed 50000 of 142876 vertices processed 75000 of 142876 vertices processed 100000 of 142876 vertices processed 125000 of 142876 vertices processed thickness calculation complete, 413:1294 truncations. 26162 vertices at 0 distance 91249 vertices at 1 distance 91243 vertices at 2 distance 41762 vertices at 3 distance 14404 vertices at 4 distance 4789 vertices at 5 distance 1667 vertices at 6 distance 631 vertices at 7 distance 249 vertices at 8 distance 120 vertices at 9 distance 65 vertices at 10 distance 52 vertices at 11 distance 34 vertices at 12 distance 45 vertices at 13 distance 35 vertices at 14 distance 47 vertices at 15 distance 20 vertices at 16 distance 19 vertices at 17 distance 10 vertices at 18 distance 7 vertices at 19 distance 2 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.thickness positioning took 16.8 minutes PIDs (31198 31201) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 00:21:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0050750 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/lh.cortex.label Total face volume 277198 Total vertex volume 273347 (mask=0) #@# 0050750 lh 273347 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 00:21:07 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0050750 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/rh.cortex.label Total face volume 282100 Total vertex volume 278317 (mask=0) #@# 0050750 rh 278317 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 00:21:10 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0050750 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 = 312 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/ribbon.mgz mris_volmask took 15.16 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 00:36:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0050750 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 0050750 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 00:36:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0050750 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 0050750 rh pial Waiting for PID 32599 of (32599 32602 32605 32608) to complete... Waiting for PID 32602 of (32599 32602 32605 32608) to complete... Waiting for PID 32605 of (32599 32602 32605 32608) to complete... Waiting for PID 32608 of (32599 32602 32605 32608) 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 0050750 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 277198 Total vertex volume 273347 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 1947 1374 3795 2.796 0.484 0.117 0.021 16 1.7 bankssts 861 574 1746 2.515 0.733 0.132 0.017 13 0.6 caudalanteriorcingulate 3313 2319 6271 2.403 0.672 0.126 0.028 34 3.8 caudalmiddlefrontal 1981 1409 3191 2.115 0.411 0.158 0.035 33 3.0 cuneus 646 477 1840 2.987 0.818 0.138 0.032 8 0.9 entorhinal 4984 3550 11150 2.690 0.646 0.138 0.031 74 6.3 fusiform 8188 5908 16153 2.434 0.615 0.130 0.027 99 9.8 inferiorparietal 4670 3431 9743 2.398 0.715 0.130 0.028 63 5.7 inferiortemporal 1865 1253 3912 2.681 0.806 0.131 0.034 29 2.1 isthmuscingulate 7978 5668 13103 2.199 0.545 0.152 0.033 115 11.1 lateraloccipital 4175 3005 8488 2.609 0.669 0.146 0.040 59 7.0 lateralorbitofrontal 4611 3321 8539 2.402 0.581 0.145 0.032 60 6.2 lingual 2768 1989 6115 2.602 0.845 0.117 0.028 35 3.3 medialorbitofrontal 4962 3613 13806 2.996 0.648 0.133 0.031 68 6.6 middletemporal 1024 687 2055 2.606 0.842 0.095 0.017 7 0.6 parahippocampal 2380 1594 4702 2.638 0.627 0.119 0.024 19 2.4 paracentral 2235 1578 4634 2.553 0.573 0.118 0.025 24 2.0 parsopercularis 1109 794 2638 2.650 0.766 0.154 0.033 19 1.6 parsorbitalis 1746 1230 3225 2.266 0.591 0.123 0.023 16 1.9 parstriangularis 1817 1298 2281 1.916 0.521 0.138 0.031 21 2.5 pericalcarine 7729 5419 14214 2.211 0.667 0.134 0.030 91 9.4 postcentral 1961 1395 4370 2.709 0.902 0.144 0.029 33 2.6 posteriorcingulate 8201 5691 15731 2.418 0.620 0.119 0.022 74 7.6 precentral 6913 4902 13502 2.668 0.597 0.139 0.031 88 9.5 precuneus 1208 852 2945 3.095 1.023 0.129 0.030 18 1.3 rostralanteriorcingulate 8121 5975 15002 2.088 0.644 0.151 0.042 137 15.4 rostralmiddlefrontal 10755 7781 24441 2.673 0.741 0.134 0.032 121 14.1 superiorfrontal 8802 6273 15859 2.235 0.616 0.135 0.026 110 9.7 superiorparietal 5978 4207 14464 2.920 0.692 0.116 0.023 61 5.9 superiortemporal 6523 4797 12527 2.343 0.602 0.134 0.031 89 9.0 supramarginal 359 278 1036 2.718 0.581 0.176 0.056 9 0.9 frontalpole 775 556 2941 3.376 1.002 0.147 0.056 14 1.9 temporalpole 559 375 1139 2.773 0.459 0.117 0.026 6 0.5 transversetemporal 3591 2493 7780 3.081 0.685 0.123 0.033 38 4.5 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050750 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 277198 Total vertex volume 273347 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 1947 1321 3795 2.796 0.484 0.144 0.042 31 3.9 bankssts 861 773 1746 2.515 0.733 0.167 0.039 26 1.4 caudalanteriorcingulate 3313 2842 6271 2.403 0.672 0.161 0.041 44 6.4 caudalmiddlefrontal 1981 1685 3191 2.115 0.411 0.153 0.037 38 3.1 cuneus 646 726 1840 2.987 0.818 0.180 0.046 12 1.3 entorhinal 4984 4635 11150 2.690 0.646 0.170 0.042 79 10.1 fusiform 8188 7306 16153 2.434 0.615 0.157 0.036 102 13.2 inferiorparietal 4670 4529 9743 2.398 0.715 0.173 0.045 61 9.7 inferiortemporal 1865 1643 3912 2.681 0.806 0.164 0.045 41 3.5 isthmuscingulate 7978 6539 13103 2.199 0.545 0.153 0.038 122 13.6 lateraloccipital 4175 3739 8488 2.609 0.669 0.177 0.050 81 9.4 lateralorbitofrontal 4611 4045 8539 2.402 0.581 0.156 0.037 66 8.2 lingual 2768 2755 6115 2.602 0.845 0.177 0.044 38 5.8 medialorbitofrontal 4962 5519 13806 2.996 0.648 0.188 0.044 66 10.4 middletemporal 1024 955 2055 2.606 0.842 0.158 0.038 11 2.0 parahippocampal 2380 1954 4702 2.638 0.627 0.137 0.032 27 3.4 paracentral 2235 2020 4634 2.553 0.573 0.167 0.039 31 4.2 parsopercularis 1109 1193 2638 2.650 0.766 0.190 0.037 14 2.1 parsorbitalis 1746 1633 3225 2.266 0.591 0.176 0.041 24 3.3 parstriangularis 1817 1130 2281 1.916 0.521 0.124 0.035 25 2.7 pericalcarine 7729 7239 14214 2.211 0.667 0.168 0.041 96 14.7 postcentral 1961 1742 4370 2.709 0.902 0.171 0.047 62 3.9 posteriorcingulate 8201 7149 15731 2.418 0.620 0.149 0.034 110 13.4 precentral 6913 5390 13502 2.668 0.597 0.151 0.040 119 12.4 precuneus 1208 1151 2945 3.095 1.023 0.173 0.053 20 2.6 rostralanteriorcingulate 8121 8175 15002 2.088 0.644 0.198 0.050 138 20.6 rostralmiddlefrontal 10755 10253 24441 2.673 0.741 0.175 0.046 168 22.8 superiorfrontal 8802 7695 15859 2.235 0.616 0.155 0.037 111 15.5 superiorparietal 5978 5508 14464 2.920 0.692 0.158 0.037 87 10.5 superiortemporal 6523 5861 12527 2.343 0.602 0.168 0.041 102 12.4 supramarginal 359 440 1036 2.718 0.581 0.226 0.058 5 0.9 frontalpole 775 1085 2941 3.376 1.002 0.240 0.056 11 2.2 temporalpole 559 462 1139 2.773 0.459 0.137 0.036 4 0.9 transversetemporal 3591 2374 7780 3.081 0.685 0.142 0.042 77 6.5 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 0050750 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 282100 Total vertex volume 278317 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 1855 1303 3448 2.635 0.563 0.113 0.024 19 1.8 bankssts 977 670 1834 2.377 0.734 0.124 0.020 13 0.7 caudalanteriorcingulate 3414 2406 7538 2.726 0.668 0.124 0.024 34 3.7 caudalmiddlefrontal 2396 1669 3878 2.163 0.486 0.170 0.042 41 4.5 cuneus 600 451 2028 3.225 0.850 0.156 0.050 14 1.1 entorhinal 4119 2882 9328 2.728 0.590 0.133 0.031 54 5.4 fusiform 9367 6756 18945 2.472 0.614 0.134 0.029 123 11.2 inferiorparietal 5151 3726 11318 2.571 0.683 0.145 0.040 79 9.1 inferiortemporal 1681 1123 3383 2.608 0.899 0.129 0.029 25 1.8 isthmuscingulate 6762 4848 11395 2.095 0.550 0.156 0.038 103 11.1 lateraloccipital 3880 2795 7987 2.554 0.730 0.149 0.041 62 6.0 lateralorbitofrontal 4932 3400 9063 2.402 0.695 0.146 0.033 70 7.1 lingual 2925 2162 6504 2.499 0.747 0.138 0.037 44 4.4 medialorbitofrontal 5820 4297 15301 2.857 0.664 0.138 0.034 95 8.7 middletemporal 1070 707 2143 2.636 0.789 0.103 0.021 9 0.8 parahippocampal 2483 1714 4658 2.441 0.527 0.121 0.022 22 2.3 paracentral 2024 1415 4529 2.864 0.541 0.124 0.026 22 2.0 parsopercularis 1233 884 2736 2.519 0.670 0.147 0.034 21 1.6 parsorbitalis 2021 1408 3867 2.479 0.650 0.121 0.026 23 2.2 parstriangularis 2071 1458 2669 1.950 0.498 0.144 0.032 28 2.9 pericalcarine 7101 4923 13113 2.307 0.738 0.135 0.028 83 8.5 postcentral 2149 1464 4218 2.558 0.935 0.140 0.028 37 2.6 posteriorcingulate 8171 5602 16460 2.633 0.675 0.116 0.022 72 7.3 precentral 7111 5051 14158 2.715 0.626 0.144 0.033 106 9.7 precuneus 816 572 1760 2.830 0.636 0.138 0.030 12 0.9 rostralanteriorcingulate 7949 5799 16925 2.425 0.682 0.150 0.041 117 14.5 rostralmiddlefrontal 10772 7909 25608 2.662 0.711 0.142 0.035 136 15.7 superiorfrontal 8291 5849 14853 2.261 0.599 0.136 0.027 103 9.9 superiorparietal 5860 4019 13637 3.031 0.723 0.115 0.024 54 6.4 superiortemporal 5860 4203 11853 2.471 0.658 0.143 0.033 86 8.6 supramarginal 438 339 1671 3.188 0.505 0.201 0.071 9 1.5 frontalpole 653 481 2480 3.439 0.828 0.146 0.049 9 1.4 temporalpole 534 333 1042 2.799 0.517 0.141 0.038 8 0.7 transversetemporal 3513 2429 7985 3.251 0.667 0.128 0.037 39 5.2 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 0050750 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 282100 Total vertex volume 278317 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 1855 1296 3448 2.635 0.563 0.141 0.041 31 3.3 bankssts 977 817 1834 2.377 0.734 0.137 0.038 16 1.3 caudalanteriorcingulate 3414 3010 7538 2.726 0.668 0.159 0.039 53 6.2 caudalmiddlefrontal 2396 2056 3878 2.163 0.486 0.158 0.043 30 4.7 cuneus 600 855 2028 3.225 0.850 0.260 0.068 15 2.1 entorhinal 4119 3844 9328 2.728 0.590 0.194 0.045 22424 8.9 fusiform 9367 8560 18945 2.472 0.614 0.166 0.037 119 16.1 inferiorparietal 5151 5027 11318 2.571 0.683 0.195 0.054 222 13.5 inferiortemporal 1681 1428 3383 2.608 0.899 0.159 0.041 51 2.6 isthmuscingulate 6762 6144 11395 2.095 0.550 0.173 0.042 102 13.7 lateraloccipital 3880 3523 7987 2.554 0.730 0.195 0.057 86 10.3 lateralorbitofrontal 4932 4193 9063 2.402 0.695 0.157 0.063 130 17.7 lingual 2925 3009 6504 2.499 0.747 0.190 0.046 50 6.8 medialorbitofrontal 5820 6294 15301 2.857 0.664 0.187 0.046 80 12.9 middletemporal 1070 925 2143 2.636 0.789 0.153 0.037 15 1.9 parahippocampal 2483 2066 4658 2.441 0.527 0.143 0.035 33 3.9 paracentral 2024 1698 4529 2.864 0.541 0.155 0.040 28 3.8 parsopercularis 1233 1325 2736 2.519 0.670 0.189 0.047 17 2.8 parsorbitalis 2021 1733 3867 2.479 0.650 0.157 0.034 23 3.2 parstriangularis 2071 1356 2669 1.950 0.498 0.146 0.038 31 3.8 pericalcarine 7101 6339 13113 2.307 0.738 0.151 0.037 93 12.2 postcentral 2149 1786 4218 2.558 0.935 0.161 0.042 39 4.3 posteriorcingulate 8171 6633 16460 2.633 0.675 0.134 0.032 107 11.7 precentral 7111 5589 14158 2.715 0.626 0.153 0.041 133 13.3 precuneus 816 706 1760 2.830 0.636 0.159 0.043 13 1.6 rostralanteriorcingulate 7949 7990 16925 2.425 0.682 0.194 0.049 123 19.2 rostralmiddlefrontal 10772 10793 25608 2.662 0.711 0.185 0.048 163 24.9 superiorfrontal 8291 7163 14853 2.261 0.599 0.156 0.038 111 14.5 superiorparietal 5860 5058 13637 3.031 0.723 0.164 0.043 193 12.1 superiortemporal 5860 5329 11853 2.471 0.658 0.174 0.046 88 12.2 supramarginal 438 677 1671 3.188 0.505 0.284 0.065 7 1.6 frontalpole 653 986 2480 3.439 0.828 0.269 0.064 14 2.3 temporalpole 534 419 1042 2.799 0.517 0.129 0.034 3 0.8 transversetemporal 3513 2303 7985 3.251 0.667 0.148 0.044 70 7.0 insula PIDs (32599 32602 32605 32608) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 00:37:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050750 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Sun Oct 8 00:37:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050750 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 32705 of (32705 32708) to complete... Waiting for PID 32708 of (32705 32708) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050750 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... 10 labels changed using aseg relabeling using gibbs priors... 000: 9265 changed, 143025 examined... 001: 2148 changed, 36305 examined... 002: 624 changed, 11363 examined... 003: 255 changed, 3484 examined... 004: 121 changed, 1461 examined... 005: 55 changed, 661 examined... 006: 29 changed, 313 examined... 007: 13 changed, 166 examined... 008: 6 changed, 79 examined... 009: 2 changed, 35 examined... 010: 1 changed, 16 examined... 011: 1 changed, 7 examined... 012: 2 changed, 7 examined... 013: 0 changed, 11 examined... 2 labels changed using aseg 000: 251 total segments, 163 labels (2125 vertices) changed 001: 99 total segments, 12 labels (93 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 950 vertices marked for relabeling... 950 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 19 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050750 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... 31 labels changed using aseg relabeling using gibbs priors... 000: 9524 changed, 142876 examined... 001: 2173 changed, 36988 examined... 002: 601 changed, 11240 examined... 003: 243 changed, 3478 examined... 004: 101 changed, 1342 examined... 005: 48 changed, 589 examined... 006: 29 changed, 273 examined... 007: 13 changed, 156 examined... 008: 6 changed, 86 examined... 009: 1 changed, 31 examined... 010: 2 changed, 7 examined... 011: 0 changed, 11 examined... 5 labels changed using aseg 000: 255 total segments, 170 labels (2406 vertices) changed 001: 93 total segments, 9 labels (38 vertices) changed 002: 85 total segments, 1 labels (1 vertices) changed 003: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 659 vertices marked for relabeling... 659 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 19 seconds. PIDs (32705 32708) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 00:37:55 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0050750 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 00:37:55 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0050750 rh white Waiting for PID 32757 of (32757 32760) to complete... Waiting for PID 32760 of (32757 32760) 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 0050750 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 277198 Total vertex volume 273347 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 1145 833 1897 2.046 0.614 0.156 0.046 20 2.3 G&S_frontomargin 1760 1231 3263 2.417 0.532 0.153 0.030 26 2.1 G&S_occipital_inf 1838 1231 3567 2.314 0.650 0.120 0.025 16 1.8 G&S_paracentral 1679 1227 4500 2.806 0.696 0.146 0.032 24 2.3 G&S_subcentral 490 374 1556 2.738 0.626 0.175 0.079 13 1.3 G&S_transv_frontopol 2170 1571 5086 2.831 0.772 0.127 0.027 23 2.5 G&S_cingul-Ant 1356 978 2732 2.682 0.578 0.114 0.019 11 1.1 G&S_cingul-Mid-Ant 1432 997 3093 2.940 0.648 0.114 0.022 12 1.2 G&S_cingul-Mid-Post 841 601 2641 3.385 0.603 0.163 0.042 16 1.5 G_cingul-Post-dorsal 340 236 934 2.801 0.673 0.143 0.042 7 0.4 G_cingul-Post-ventral 1839 1346 3126 2.031 0.378 0.165 0.037 34 3.2 G_cuneus 1229 888 3363 2.823 0.496 0.129 0.030 18 1.4 G_front_inf-Opercular 427 306 1216 3.001 0.625 0.168 0.036 9 0.7 G_front_inf-Orbital 970 674 2287 2.574 0.547 0.137 0.034 12 1.3 G_front_inf-Triangul 4445 3300 10344 2.362 0.697 0.164 0.048 89 9.3 G_front_middle 7581 5473 19657 2.817 0.727 0.148 0.038 106 12.1 G_front_sup 796 565 1894 3.244 0.649 0.150 0.044 13 1.4 G_Ins_lg&S_cent_ins 853 569 2667 3.500 0.705 0.130 0.043 14 1.3 G_insular_short 2362 1645 5330 2.551 0.574 0.156 0.035 41 3.6 G_occipital_middle 1189 841 1814 1.956 0.410 0.148 0.035 18 1.6 G_occipital_sup 2098 1471 5160 2.808 0.575 0.144 0.034 39 2.9 G_oc-temp_lat-fusifor 3202 2333 6304 2.341 0.649 0.168 0.041 54 5.6 G_oc-temp_med-Lingual 1412 969 3666 2.933 0.838 0.133 0.033 18 2.1 G_oc-temp_med-Parahip 2679 1985 6666 2.502 0.655 0.169 0.050 59 5.8 G_orbital 3144 2421 7931 2.563 0.689 0.163 0.040 60 5.7 G_pariet_inf-Angular 3067 2358 7644 2.521 0.625 0.157 0.039 60 5.6 G_pariet_inf-Supramar 3716 2711 8510 2.462 0.696 0.147 0.030 57 4.6 G_parietal_sup 3189 2205 6570 2.290 0.647 0.147 0.036 47 4.7 G_postcentral 2785 1950 7039 2.583 0.722 0.131 0.027 33 3.1 G_precentral 3434 2503 8392 2.732 0.587 0.160 0.037 59 5.7 G_precuneus 954 770 3000 2.780 0.847 0.172 0.040 25 1.7 G_rectus 568 357 1051 2.482 1.260 0.064 0.027 4 0.5 G_subcallosal 427 286 1050 2.919 0.515 0.119 0.025 4 0.5 G_temp_sup-G_T_transv 2025 1462 6481 3.043 0.693 0.143 0.035 34 3.1 G_temp_sup-Lateral 786 549 2619 3.782 0.796 0.103 0.025 6 0.7 G_temp_sup-Plan_polar 999 727 2055 2.463 0.702 0.084 0.012 4 0.4 G_temp_sup-Plan_tempo 2237 1637 5122 2.397 0.689 0.142 0.037 40 3.5 G_temporal_inf 2880 2119 9486 3.098 0.642 0.150 0.038 50 4.7 G_temporal_middle 257 179 341 1.892 0.469 0.098 0.015 1 0.1 Lat_Fis-ant-Horizont 294 205 484 2.418 0.489 0.129 0.023 2 0.3 Lat_Fis-ant-Vertical 1105 746 1398 2.415 0.426 0.126 0.024 10 1.1 Lat_Fis-post 1882 1465 3348 1.975 0.535 0.163 0.038 30 3.3 Pole_occipital 1568 1219 6204 3.169 0.962 0.168 0.053 36 3.5 Pole_temporal 2545 1789 3529 2.200 0.648 0.128 0.029 27 3.2 S_calcarine 3649 2498 4385 1.987 0.437 0.111 0.021 25 3.1 S_central 1306 931 2231 2.587 0.593 0.131 0.031 14 2.0 S_cingul-Marginalis 663 443 1078 2.974 0.447 0.103 0.026 3 0.7 S_circular_insula_ant 1263 892 2098 2.855 0.637 0.092 0.015 5 0.9 S_circular_insula_inf 1873 1287 2734 2.584 0.502 0.101 0.017 9 1.3 S_circular_insula_sup 918 657 1444 2.336 0.698 0.110 0.018 6 0.7 S_collat_transv_ant 667 467 851 2.311 0.303 0.128 0.024 5 0.7 S_collat_transv_post 1988 1403 2834 1.928 0.527 0.097 0.014 12 1.2 S_front_inf 1518 1128 2262 1.963 0.568 0.133 0.033 17 2.3 S_front_middle 2946 2132 4644 2.242 0.638 0.121 0.027 23 3.3 S_front_sup 419 276 466 1.924 0.525 0.092 0.014 2 0.3 S_interm_prim-Jensen 3227 2284 4381 2.050 0.516 0.117 0.020 29 3.0 S_intrapariet&P_trans 1186 793 1357 2.015 0.424 0.113 0.022 8 1.0 S_oc_middle&Lunatus 1143 778 1409 2.131 0.382 0.110 0.021 8 0.9 S_oc_sup&transversal 1085 742 1374 2.300 0.423 0.126 0.022 10 1.0 S_occipital_ant 1174 866 2042 2.346 0.651 0.131 0.026 13 1.4 S_oc-temp_lat 2256 1570 3601 2.451 0.485 0.101 0.014 14 1.4 S_oc-temp_med&Lingual 445 308 431 1.455 0.202 0.108 0.017 3 0.3 S_orbital_lateral 719 509 989 2.280 0.628 0.113 0.022 6 0.5 S_orbital_med-olfact 1523 1079 2729 2.577 0.761 0.138 0.034 14 2.2 S_orbital-H_Shaped 2135 1487 3284 2.512 0.551 0.131 0.024 24 2.2 S_parieto_occipital 1351 815 1233 1.991 0.889 0.134 0.024 30 1.0 S_pericallosal 3841 2628 4968 2.141 0.470 0.111 0.022 29 3.2 S_postcentral 1841 1257 2779 2.388 0.530 0.104 0.016 11 1.2 S_precentral-inf-part 1570 1120 2041 2.067 0.475 0.119 0.020 11 1.5 S_precentral-sup-part 665 461 1117 2.744 0.808 0.097 0.018 4 0.5 S_suborbital 1828 1250 2893 2.626 0.509 0.114 0.026 14 1.8 S_subparietal 1619 1164 2600 2.447 0.672 0.102 0.017 9 1.1 S_temporal_inf 7536 5259 13480 2.639 0.568 0.110 0.020 56 6.0 S_temporal_sup 395 285 601 2.507 0.486 0.129 0.018 4 0.3 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 0050750 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 282100 Total vertex volume 278317 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 825 604 2086 2.769 0.615 0.154 0.044 11 1.7 G&S_frontomargin 1196 847 2261 2.270 0.645 0.149 0.036 19 1.9 G&S_occipital_inf 1646 1126 3496 2.484 0.604 0.125 0.027 17 1.8 G&S_paracentral 1911 1340 4506 2.886 0.637 0.132 0.025 22 1.9 G&S_subcentral 1003 791 2851 2.470 0.694 0.189 0.068 23 2.8 G&S_transv_frontopol 3233 2317 6537 2.559 0.627 0.135 0.031 42 4.0 G&S_cingul-Ant 1310 928 2757 2.828 0.569 0.112 0.021 11 1.0 G&S_cingul-Mid-Ant 1474 1060 2890 2.653 0.628 0.131 0.026 19 1.5 G&S_cingul-Mid-Post 891 585 2513 3.295 0.736 0.168 0.040 19 1.5 G_cingul-Post-dorsal 276 200 792 2.712 0.690 0.150 0.038 5 0.4 G_cingul-Post-ventral 2091 1497 3457 2.072 0.488 0.177 0.046 38 4.2 G_cuneus 1342 960 3764 3.083 0.562 0.140 0.030 20 1.6 G_front_inf-Opercular 435 312 1065 2.549 0.495 0.132 0.031 6 0.6 G_front_inf-Orbital 751 525 1840 2.771 0.633 0.138 0.033 12 1.0 G_front_inf-Triangul 3605 2653 10079 2.736 0.772 0.159 0.041 65 6.5 G_front_middle 7075 5192 19349 2.797 0.749 0.153 0.039 100 11.8 G_front_sup 628 441 1723 3.431 0.570 0.138 0.040 8 1.1 G_Ins_lg&S_cent_ins 859 569 2613 3.561 0.803 0.162 0.063 19 2.2 G_insular_short 2385 1751 5301 2.393 0.533 0.169 0.042 45 4.1 G_occipital_middle 1476 1059 2212 1.902 0.402 0.144 0.030 20 1.9 G_occipital_sup 1735 1199 4810 2.831 0.566 0.143 0.035 30 2.3 G_oc-temp_lat-fusifor 2982 2032 6409 2.539 0.730 0.157 0.038 51 4.6 G_oc-temp_med-Lingual 1303 915 3736 3.034 0.849 0.150 0.047 24 2.5 G_oc-temp_med-Parahip 2709 2015 7168 2.665 0.743 0.168 0.049 62 5.0 G_orbital 3643 2783 9838 2.624 0.708 0.170 0.042 84 7.0 G_pariet_inf-Angular 3056 2181 7358 2.620 0.684 0.156 0.037 58 5.1 G_pariet_inf-Supramar 2661 1937 6427 2.463 0.702 0.151 0.033 43 3.8 G_parietal_sup 2438 1709 5490 2.434 0.741 0.152 0.035 35 3.6 G_postcentral 2936 2028 8192 2.832 0.726 0.126 0.027 35 3.1 G_precentral 3268 2437 8466 2.844 0.627 0.171 0.044 73 6.3 G_precuneus 765 614 2106 2.332 0.650 0.185 0.061 19 1.9 G_rectus 276 191 797 3.220 0.650 0.086 0.023 2 0.3 G_subcallosal 431 261 917 2.930 0.695 0.146 0.041 7 0.7 G_temp_sup-G_T_transv 2116 1441 6253 3.187 0.773 0.137 0.031 30 2.7 G_temp_sup-Lateral 831 586 2316 3.336 0.813 0.103 0.031 6 0.9 G_temp_sup-Plan_polar 748 556 1450 2.337 0.461 0.095 0.016 4 0.5 G_temp_sup-Plan_tempo 2805 2075 7176 2.579 0.697 0.161 0.051 59 6.6 G_temporal_inf 3421 2609 10502 2.923 0.677 0.158 0.043 74 6.6 G_temporal_middle 402 264 471 2.137 0.373 0.085 0.012 2 0.2 Lat_Fis-ant-Horizont 272 205 562 2.743 0.739 0.118 0.028 1 0.3 Lat_Fis-ant-Vertical 1443 963 2102 2.729 0.483 0.112 0.021 9 1.2 Lat_Fis-post 3307 2389 5231 1.954 0.528 0.172 0.044 61 7.1 Pole_occipital 1640 1288 6358 3.256 0.898 0.181 0.058 35 4.2 Pole_temporal 2600 1808 3541 2.274 0.721 0.128 0.026 27 2.8 S_calcarine 3255 2222 3826 2.014 0.562 0.117 0.023 24 3.1 S_central 1507 1050 2434 2.399 0.571 0.107 0.019 10 1.2 S_cingul-Marginalis 601 421 1021 2.857 0.721 0.138 0.038 6 1.0 S_circular_insula_ant 1209 823 1944 2.922 0.577 0.096 0.017 6 0.9 S_circular_insula_inf 1364 957 2403 2.955 0.549 0.102 0.017 6 1.0 S_circular_insula_sup 1082 750 1712 2.579 0.470 0.110 0.023 6 1.1 S_collat_transv_ant 370 240 551 2.412 0.504 0.143 0.034 4 0.5 S_collat_transv_post 1934 1361 3277 2.372 0.504 0.107 0.020 16 1.6 S_front_inf 2293 1667 4232 2.244 0.645 0.146 0.042 30 4.6 S_front_middle 2937 2100 4751 2.360 0.529 0.120 0.027 25 3.1 S_front_sup 247 177 380 2.391 0.512 0.129 0.042 2 0.3 S_interm_prim-Jensen 4020 2780 5366 2.089 0.461 0.119 0.020 37 3.5 S_intrapariet&P_trans 927 642 1103 1.968 0.483 0.125 0.025 7 1.0 S_oc_middle&Lunatus 993 690 1327 2.118 0.384 0.112 0.021 7 0.7 S_oc_sup&transversal 680 483 1000 2.237 0.537 0.123 0.023 6 0.7 S_occipital_ant 1007 707 1478 2.468 0.478 0.113 0.020 7 0.7 S_oc-temp_lat 2068 1413 3108 2.465 0.497 0.097 0.016 11 1.4 S_oc-temp_med&Lingual 530 373 763 2.201 0.643 0.128 0.023 5 0.5 S_orbital_lateral 770 544 1047 2.181 0.838 0.103 0.017 5 0.4 S_orbital_med-olfact 1518 1058 2640 2.470 0.667 0.135 0.036 16 2.1 S_orbital-H_Shaped 2454 1649 3583 2.495 0.535 0.131 0.025 27 2.6 S_parieto_occipital 1660 1013 1307 1.739 0.644 0.117 0.018 26 0.9 S_pericallosal 3111 2134 4191 2.230 0.538 0.123 0.025 28 3.2 S_postcentral 2071 1417 3315 2.679 0.479 0.107 0.019 14 1.6 S_precentral-inf-part 1384 980 1941 2.193 0.431 0.108 0.016 9 0.9 S_precentral-sup-part 333 262 736 2.404 0.686 0.127 0.022 3 0.3 S_suborbital 1662 1161 2841 2.740 0.678 0.121 0.023 12 1.5 S_subparietal 1722 1175 2373 2.455 0.548 0.114 0.018 11 1.4 S_temporal_inf 7820 5361 13435 2.654 0.580 0.103 0.019 50 6.2 S_temporal_sup 258 182 464 3.227 0.454 0.134 0.020 3 0.2 S_temporal_transverse PIDs (32757 32760) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 00:38:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050750 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Sun Oct 8 00:38:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050750 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 359 of (359 362) to complete... Waiting for PID 362 of (359 362) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050750 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... 1248 labels changed using aseg relabeling using gibbs priors... 000: 2090 changed, 143025 examined... 001: 519 changed, 9603 examined... 002: 153 changed, 2871 examined... 003: 59 changed, 865 examined... 004: 29 changed, 372 examined... 005: 15 changed, 174 examined... 006: 11 changed, 92 examined... 007: 5 changed, 67 examined... 008: 2 changed, 26 examined... 009: 1 changed, 13 examined... 010: 0 changed, 7 examined... 221 labels changed using aseg 000: 53 total segments, 20 labels (136 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 15 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 657 vertices marked for relabeling... 657 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050750 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... 1181 labels changed using aseg relabeling using gibbs priors... 000: 2096 changed, 142876 examined... 001: 452 changed, 9694 examined... 002: 98 changed, 2648 examined... 003: 43 changed, 579 examined... 004: 22 changed, 244 examined... 005: 15 changed, 135 examined... 006: 6 changed, 83 examined... 007: 8 changed, 39 examined... 008: 7 changed, 47 examined... 009: 7 changed, 39 examined... 010: 2 changed, 31 examined... 011: 0 changed, 16 examined... 201 labels changed using aseg 000: 58 total segments, 25 labels (201 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, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 553 vertices marked for relabeling... 553 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. PIDs (359 362) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 00:38:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0050750 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 00:38:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0050750 rh white Waiting for PID 410 of (410 413) to complete... Waiting for PID 413 of (410 413) 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 0050750 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 277198 Total vertex volume 273347 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 1603 1102 3202 2.495 0.655 0.126 0.021 22 1.4 caudalanteriorcingulate 3641 2557 6957 2.394 0.678 0.126 0.028 37 4.3 caudalmiddlefrontal 2795 1991 4412 2.128 0.405 0.151 0.033 43 3.9 cuneus 586 433 1597 2.954 0.789 0.132 0.029 7 0.8 entorhinal 4671 3300 9838 2.663 0.594 0.135 0.029 66 5.6 fusiform 8124 5876 15965 2.405 0.611 0.131 0.027 99 9.8 inferiorparietal 4797 3522 10779 2.453 0.775 0.135 0.031 68 6.5 inferiortemporal 1765 1194 3736 2.672 0.797 0.133 0.035 29 2.1 isthmuscingulate 7802 5518 12877 2.188 0.546 0.150 0.033 112 10.5 lateraloccipital 4501 3234 9263 2.530 0.676 0.155 0.045 75 8.5 lateralorbitofrontal 4696 3397 8671 2.391 0.576 0.146 0.032 62 6.4 lingual 2227 1637 5326 2.632 0.872 0.118 0.030 32 2.9 medialorbitofrontal 6739 4866 16910 2.894 0.648 0.128 0.028 83 8.0 middletemporal 1075 727 2166 2.601 0.833 0.096 0.017 7 0.7 parahippocampal 2840 1919 5598 2.662 0.616 0.120 0.024 23 2.9 paracentral 2131 1505 4497 2.591 0.542 0.120 0.025 24 2.0 parsopercularis 1114 773 2479 2.817 0.658 0.131 0.027 14 1.3 parsorbitalis 2060 1441 3429 2.145 0.625 0.123 0.024 19 2.1 parstriangularis 1768 1268 2198 1.919 0.533 0.136 0.030 19 2.4 pericalcarine 8597 6051 15548 2.224 0.659 0.134 0.030 99 10.6 postcentral 2107 1493 4558 2.735 0.887 0.141 0.029 33 2.7 posteriorcingulate 8088 5613 15535 2.428 0.621 0.119 0.022 73 7.5 precentral 6764 4810 13608 2.683 0.593 0.144 0.033 92 9.7 precuneus 1916 1353 4645 3.034 0.928 0.131 0.029 26 2.2 rostralanteriorcingulate 5990 4447 11342 2.113 0.651 0.149 0.040 99 10.8 rostralmiddlefrontal 11197 8117 24920 2.570 0.767 0.139 0.036 141 16.5 superiorfrontal 7408 5249 13392 2.240 0.636 0.131 0.026 89 7.9 superiorparietal 8103 5717 20212 2.978 0.727 0.121 0.027 90 9.3 superiortemporal 5936 4357 11556 2.358 0.607 0.135 0.032 82 8.3 supramarginal 557 373 1124 2.758 0.452 0.118 0.026 6 0.6 transversetemporal 3146 2229 7005 3.082 0.660 0.121 0.029 30 3.8 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 0050750 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 282100 Total vertex volume 278317 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 1039 717 1918 2.345 0.752 0.124 0.019 14 0.7 caudalanteriorcingulate 3544 2502 7843 2.723 0.674 0.124 0.024 35 3.8 caudalmiddlefrontal 2816 1958 4359 2.135 0.482 0.160 0.037 45 4.3 cuneus 530 383 1731 3.276 0.827 0.146 0.049 12 0.8 entorhinal 3795 2633 8165 2.708 0.541 0.131 0.030 47 4.7 fusiform 9204 6666 18644 2.469 0.619 0.133 0.028 119 10.9 inferiorparietal 5461 3979 12263 2.577 0.693 0.145 0.040 84 9.5 inferiortemporal 1643 1099 3325 2.638 0.887 0.130 0.029 24 1.8 isthmuscingulate 6893 4924 11459 2.072 0.541 0.156 0.038 105 11.5 lateraloccipital 4238 3073 9520 2.571 0.753 0.152 0.043 70 7.3 lateralorbitofrontal 4770 3293 8787 2.401 0.698 0.144 0.032 66 6.6 lingual 2080 1537 4882 2.444 0.798 0.140 0.040 34 3.2 medialorbitofrontal 7158 5215 17841 2.830 0.659 0.133 0.032 105 10.1 middletemporal 1133 756 2323 2.646 0.773 0.106 0.022 10 0.9 parahippocampal 2580 1789 4910 2.452 0.529 0.122 0.023 23 2.4 paracentral 2370 1676 5387 2.860 0.543 0.128 0.026 27 2.4 parsopercularis 1069 762 2452 2.566 0.651 0.135 0.032 16 1.3 parsorbitalis 1903 1306 3366 2.420 0.616 0.123 0.026 20 2.1 parstriangularis 2135 1503 2779 1.943 0.476 0.151 0.035 31 3.5 pericalcarine 7863 5450 14466 2.326 0.723 0.134 0.028 90 9.2 postcentral 2190 1492 4293 2.564 0.926 0.140 0.028 38 2.6 posteriorcingulate 7768 5319 15824 2.651 0.674 0.117 0.023 69 7.0 precentral 7281 5184 14713 2.716 0.622 0.144 0.033 109 10.1 precuneus 1193 833 2463 2.780 0.630 0.132 0.028 17 1.2 rostralanteriorcingulate 5710 4165 12062 2.418 0.697 0.151 0.040 89 10.4 rostralmiddlefrontal 13625 10019 31596 2.622 0.701 0.144 0.037 175 20.9 superiorfrontal 6973 4925 12545 2.262 0.604 0.137 0.028 89 8.6 superiorparietal 7591 5273 18561 3.022 0.744 0.122 0.029 81 9.6 superiortemporal 5509 3933 11165 2.470 0.651 0.143 0.033 82 7.8 supramarginal 553 348 1101 2.841 0.540 0.140 0.037 8 0.8 transversetemporal 3370 2325 7576 3.261 0.655 0.129 0.036 38 5.1 insula PIDs (410 413) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 00:39:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts pctsurfcon --s 0050750 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 00:39:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts pctsurfcon --s 0050750 --rh-only Waiting for PID 483 of (483 495) to complete... Waiting for PID 495 of (483 495) to complete... pctsurfcon --s 0050750 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts/pctsurfcon.log Sun Oct 8 00:39:28 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-6.0.0/0050750/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-540 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-6.0.0/0050750/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.483/lh.wm.mgh --regheader 0050750 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99877 0.04919 0.00547 0.00000; -0.00977 0.08760 0.99611 0.00005; 0.04852 -0.99494 0.08798 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 = 78412 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.483/lh.wm.mgh Dim: 143025 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.483/lh.gm.mgh --projfrac 0.3 --regheader 0050750 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99877 0.04919 0.00547 0.00000; -0.00977 0.08760 0.99611 0.00005; 0.04852 -0.99494 0.08798 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 = 91140 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.483/lh.gm.mgh Dim: 143025 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.483/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.483/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.w-g.pct.mgh --annot 0050750 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/surf/lh.w-g.pct.mgh --annot 0050750 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-540 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/surf/lh.w-g.pct.mgh Vertex Area is 0.709679 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 0050750 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/scripts/pctsurfcon.log Sun Oct 8 00:39:28 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-6.0.0/0050750/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-540 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-6.0.0/0050750/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.495/rh.wm.mgh --regheader 0050750 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99877 0.04919 0.00547 0.00000; -0.00977 0.08760 0.99611 0.00005; 0.04852 -0.99494 0.08798 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 = 77797 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.495/rh.wm.mgh Dim: 142876 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.495/rh.gm.mgh --projfrac 0.3 --regheader 0050750 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99877 0.04919 0.00547 0.00000; -0.00977 0.08760 0.99611 0.00005; 0.04852 -0.99494 0.08798 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 = 90468 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.495/rh.gm.mgh Dim: 142876 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.495/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/tmp.pctsurfcon.495/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.w-g.pct.mgh --annot 0050750 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/surf/rh.w-g.pct.mgh --annot 0050750 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-540 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/surf/rh.w-g.pct.mgh Vertex Area is 0.705824 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 (483 495) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 00:39:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1255 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1546 voxels changed to hypointensity... 3468 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 00:39:55 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750 mri_aparc2aseg --s 0050750 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt #----------------------------------------- #@# AParc-to-ASeg a2009s Sun Oct 8 00:39:55 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750 mri_aparc2aseg --s 0050750 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s #----------------------------------------- #@# AParc-to-ASeg DKTatlas Sun Oct 8 00:39:55 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750 mri_aparc2aseg --s 0050750 --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 646 of (646 649 652) to complete... Waiting for PID 649 of (646 649 652) to complete... Waiting for PID 652 of (646 649 652) to complete... mri_aparc2aseg --s 0050750 --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 0050750 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/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-6.0.0/0050750/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.79 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 45 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 25 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 50 rescaling Left_Thalamus from 94 --> 90 rescaling Left_Thalamus_Proper from 84 --> 91 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 6 rescaling Fourth_Ventricle from 22 --> 4 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 62 rescaling CSF from 32 --> 8 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 106 rescaling Right_Cerebral_Cortex from 58 --> 46 rescaling Right_Lateral_Ventricle from 13 --> 3 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 88 rescaling Right_Cerebellum_Cortex from 59 --> 49 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 65 rescaling Right_Putamen from 80 --> 71 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 52 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 64 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 8 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 548495 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 146 changed. pass 2: 8 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/aparc+aseg.mgz mri_aparc2aseg --s 0050750 --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 0050750 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/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-6.0.0/0050750/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.79 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 45 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 25 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 50 rescaling Left_Thalamus from 94 --> 90 rescaling Left_Thalamus_Proper from 84 --> 91 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 6 rescaling Fourth_Ventricle from 22 --> 4 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 62 rescaling CSF from 32 --> 8 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 106 rescaling Right_Cerebral_Cortex from 58 --> 46 rescaling Right_Lateral_Ventricle from 13 --> 3 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 88 rescaling Right_Cerebellum_Cortex from 59 --> 49 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 65 rescaling Right_Putamen from 80 --> 71 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 52 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 64 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 8 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 548466 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 146 changed. pass 2: 8 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0050750 --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 0050750 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/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-6.0.0/0050750/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.79 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 45 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 25 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 50 rescaling Left_Thalamus from 94 --> 90 rescaling Left_Thalamus_Proper from 84 --> 91 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 6 rescaling Fourth_Ventricle from 22 --> 4 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 62 rescaling CSF from 32 --> 8 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 106 rescaling Right_Cerebral_Cortex from 58 --> 46 rescaling Right_Lateral_Ventricle from 13 --> 3 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 88 rescaling Right_Cerebellum_Cortex from 59 --> 49 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 65 rescaling Right_Putamen from 80 --> 71 rescaling Right_Pallidum from 97 --> 90 rescaling Right_Hippocampus from 53 --> 52 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 64 rescaling Right_VentralDC from 86 --> 100 rescaling Fifth_Ventricle from 40 --> 8 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 548466 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 146 changed. pass 2: 8 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (646 649 652) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 00:47:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 00:47:05 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-540 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-6.0.0/0050750/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-540 machine x86_64 user ntraut input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Sun Oct 8 00:47:05 CEST 2017 Ended at Sun Oct 8 00:47:11 CEST 2017 Apas2aseg-Run-Time-Sec 6 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 00:47:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750 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 0050750 $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 0050750 sysname Linux hostname tars-540 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1537738 mm^3 (det: 1.266865 ) Computing euler number orig.nofix lheno = -74, rheno = -64 orig.nofix lhholes = 38, rhholes = 33 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Sun Oct 8 00:48:41 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750 mri_aparc2aseg --s 0050750 --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 0050750 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-6.0.0/0050750/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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-6.0.0/0050750/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8290 vertices from left hemi Ripped 8877 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-6.0.0/0050750/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 = 1056662 Used brute-force search on 480 voxels Fixing Parahip LH WM Found 11 clusters 0 k 15.000000 1 k 1.000000 2 k 1504.000000 3 k 2.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 19.000000 9 k 1.000000 10 k 1.000000 Fixing Parahip RH WM Found 9 clusters 0 k 1.000000 1 k 1.000000 2 k 3.000000 3 k 2.000000 4 k 1.000000 5 k 2.000000 6 k 21.000000 7 k 1729.000000 8 k 1.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050750 --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 0050750 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-540 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1537738 mm^3 (det: 1.266865 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 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-6.0.0/0050750/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 00:57:04 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 0050750 --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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 1521 of (1521 1527 1533 1538 1545) to complete... Waiting for PID 1527 of (1521 1527 1533 1538 1545) to complete... Waiting for PID 1533 of (1521 1527 1533 1538 1545) to complete... Waiting for PID 1538 of (1521 1527 1533 1538 1545) to complete... Waiting for PID 1545 of (1521 1527 1533 1538 1545) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 577 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4706 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 1160 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 9069 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 221 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4298 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 572 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6555 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 454 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6238 mri_label2label: Done PIDs (1521 1527 1533 1538 1545) 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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 1603 of (1603 1609 1615 1621) to complete... Waiting for PID 1609 of (1603 1609 1615 1621) to complete... Waiting for PID 1615 of (1603 1609 1615 1621) to complete... Waiting for PID 1621 of (1603 1609 1615 1621) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 273 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4343 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 1376 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14965 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 298 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4479 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 519 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3941 mri_label2label: Done PIDs (1603 1609 1615 1621) 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 0050750 --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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 1665 of (1665 1671 1677 1682 1689) to complete... Waiting for PID 1671 of (1665 1671 1677 1682 1689) to complete... Waiting for PID 1677 of (1665 1671 1677 1682 1689) to complete... Waiting for PID 1682 of (1665 1671 1677 1682 1689) to complete... Waiting for PID 1689 of (1665 1671 1677 1682 1689) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 951 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5592 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 2710 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10824 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 570 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2588 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1421 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 156 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1355 mri_label2label: Done PIDs (1665 1671 1677 1682 1689) 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 0050750 --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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 1742 of (1742 1748 1754 1759 1766) to complete... Waiting for PID 1748 of (1742 1748 1754 1759 1766) to complete... Waiting for PID 1754 of (1742 1748 1754 1759 1766) to complete... Waiting for PID 1759 of (1742 1748 1754 1759 1766) to complete... Waiting for PID 1766 of (1742 1748 1754 1759 1766) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 173 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1187 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 473 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2565 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 84 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1588 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 142 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2138 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2460 mri_label2label: Done PIDs (1742 1748 1754 1759 1766) 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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 1823 of (1823 1829 1835 1840) to complete... Waiting for PID 1829 of (1823 1829 1835 1840) to complete... Waiting for PID 1835 of (1823 1829 1835 1840) to complete... Waiting for PID 1840 of (1823 1829 1835 1840) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 102 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1651 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 622 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7657 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2033 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 134 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1285 mri_label2label: Done PIDs (1823 1829 1835 1840) 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 0050750 --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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 1885 of (1885 1891 1897 1902 1909) to complete... Waiting for PID 1891 of (1885 1891 1897 1902 1909) to complete... Waiting for PID 1897 of (1885 1891 1897 1902 1909) to complete... Waiting for PID 1902 of (1885 1891 1897 1902 1909) to complete... Waiting for PID 1909 of (1885 1891 1897 1902 1909) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 653 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4058 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 1145 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4479 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 149 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 662 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 508 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 143025 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 538 mri_label2label: Done PIDs (1885 1891 1897 1902 1909) completed and logs appended. mris_label2annot --s 0050750 --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-6.0.0/0050750/label cmdline mris_label2annot --s 0050750 --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-540 machine x86_64 user ntraut subject 0050750 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-6.0.0/0050750/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 99148 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/lh.BA_exvivo.annot mris_label2annot --s 0050750 --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-6.0.0/0050750/label cmdline mris_label2annot --s 0050750 --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-540 machine x86_64 user ntraut subject 0050750 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-6.0.0/0050750/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 117711 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0050750 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 277198 Total vertex volume 273347 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 1356 947 3396 2.536 0.688 0.147 0.035 18 1.8 BA1_exvivo 5305 3678 8082 2.188 0.538 0.125 0.028 54 6.0 BA2_exvivo 1235 803 1307 1.978 0.501 0.129 0.028 11 1.3 BA3a_exvivo 2641 1861 4460 2.048 0.618 0.130 0.027 29 3.1 BA3b_exvivo 1772 1207 3612 2.597 0.608 0.120 0.027 14 1.9 BA4a_exvivo 1448 985 2275 2.326 0.432 0.101 0.019 8 1.1 BA4p_exvivo 9901 7054 21825 2.579 0.749 0.135 0.030 116 12.3 BA6_exvivo 2330 1650 5095 2.635 0.562 0.110 0.021 22 1.9 BA44_exvivo 2707 1894 5105 2.220 0.664 0.135 0.031 33 3.6 BA45_exvivo 3108 2354 4700 1.947 0.507 0.153 0.036 46 5.0 V1_exvivo 8395 5961 13900 2.199 0.557 0.159 0.037 131 13.4 V2_exvivo 2305 1597 4393 2.559 0.514 0.135 0.026 27 2.3 MT_exvivo 586 403 1574 3.100 0.762 0.121 0.033 7 0.9 perirhinal_exvivo 788 562 2089 2.789 0.880 0.150 0.046 13 1.5 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050750 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 277198 Total vertex volume 273347 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 944 611 2393 2.671 0.619 0.159 0.040 16 1.4 BA1_exvivo 2251 1560 3569 2.156 0.538 0.130 0.032 27 2.9 BA2_exvivo 1018 656 999 1.926 0.414 0.131 0.029 9 1.0 BA3a_exvivo 1563 1118 2021 1.717 0.337 0.108 0.020 11 1.3 BA3b_exvivo 1694 1162 3292 2.535 0.574 0.114 0.025 12 1.7 BA4a_exvivo 1180 809 1806 2.294 0.392 0.106 0.021 8 1.0 BA4p_exvivo 5443 3859 12090 2.569 0.798 0.134 0.029 60 6.6 BA6_exvivo 1428 1024 3166 2.655 0.498 0.119 0.025 16 1.4 BA44_exvivo 986 688 2128 2.398 0.635 0.141 0.029 13 1.2 BA45_exvivo 3343 2539 5157 1.957 0.497 0.156 0.040 51 6.1 V1_exvivo 4095 2971 6624 2.135 0.543 0.165 0.038 69 6.8 V2_exvivo 614 421 1248 2.618 0.583 0.129 0.024 7 0.7 MT_exvivo 299 201 902 3.281 0.714 0.096 0.017 2 0.2 perirhinal_exvivo 456 321 984 2.858 0.764 0.141 0.035 6 0.5 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 00:59:59 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 0050750 --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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 2025 of (2025 2031 2037 2043 2048) to complete... Waiting for PID 2031 of (2025 2031 2037 2043 2048) to complete... Waiting for PID 2037 of (2025 2031 2037 2043 2048) to complete... Waiting for PID 2043 of (2025 2031 2037 2043 2048) to complete... Waiting for PID 2048 of (2025 2031 2037 2043 2048) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 366 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4328 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 579 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7266 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 159 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4139 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 310 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4832 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 334 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6081 mri_label2label: Done PIDs (2025 2031 2037 2043 2048) 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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 2121 of (2121 2127 2133 2139) to complete... Waiting for PID 2127 of (2121 2127 2133 2139) to complete... Waiting for PID 2133 of (2121 2127 2133 2139) to complete... Waiting for PID 2139 of (2121 2127 2133 2139) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 196 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4669 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 1022 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13278 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 902 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7814 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 636 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5991 mri_label2label: Done PIDs (2121 2127 2133 2139) 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 0050750 --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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 2315 of (2315 2321 2327 2333 2338) to complete... Waiting for PID 2321 of (2315 2321 2327 2333 2338) to complete... Waiting for PID 2327 of (2315 2321 2327 2333 2338) to complete... Waiting for PID 2333 of (2315 2321 2327 2333 2338) to complete... Waiting for PID 2338 of (2315 2321 2327 2333 2338) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 1312 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6039 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 2474 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10490 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 402 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2334 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1171 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 124 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 876 mri_label2label: Done PIDs (2315 2321 2327 2333 2338) 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 0050750 --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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 2404 of (2404 2410 2416 2422 2427) to complete... Waiting for PID 2410 of (2404 2410 2416 2422 2427) to complete... Waiting for PID 2416 of (2404 2410 2416 2422 2427) to complete... Waiting for PID 2422 of (2404 2410 2416 2422 2427) to complete... Waiting for PID 2427 of (2404 2410 2416 2422 2427) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 93 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 969 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 238 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2926 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 79 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1777 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 137 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2320 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1469 mri_label2label: Done PIDs (2404 2410 2416 2422 2427) 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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 2491 of (2491 2497 2503 2508) to complete... Waiting for PID 2497 of (2491 2497 2503 2508) to complete... Waiting for PID 2503 of (2491 2497 2503 2508) to complete... Waiting for PID 2508 of (2491 2497 2503 2508) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1547 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 572 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7531 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1160 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1248 mri_label2label: Done PIDs (2491 2497 2503 2508) 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 0050750 --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 0050750 --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 0050750 --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 0050750 --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 0050750 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 2551 of (2551 2557 2563 2568 2574) to complete... Waiting for PID 2557 of (2551 2557 2563 2568 2574) to complete... Waiting for PID 2563 of (2551 2557 2563 2568 2574) to complete... Waiting for PID 2568 of (2551 2557 2563 2568 2574) to complete... Waiting for PID 2574 of (2551 2557 2563 2568 2574) 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 846 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4078 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 1162 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4599 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 312 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 793 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 0050750 --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 = 0050750 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-6.0.0/0050750/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 142876 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 349 mri_label2label: Done PIDs (2551 2557 2563 2568 2574) completed and logs appended. mris_label2annot --s 0050750 --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-6.0.0/0050750/label cmdline mris_label2annot --s 0050750 --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-540 machine x86_64 user ntraut subject 0050750 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-6.0.0/0050750/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 100519 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/label/rh.BA_exvivo.annot mris_label2annot --s 0050750 --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-6.0.0/0050750/label cmdline mris_label2annot --s 0050750 --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-540 machine x86_64 user ntraut subject 0050750 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-6.0.0/0050750/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 119196 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/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 0050750 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 282100 Total vertex volume 278317 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 992 691 2824 2.816 0.731 0.157 0.036 15 1.3 BA1_exvivo 3849 2721 6499 2.275 0.614 0.139 0.029 46 4.9 BA2_exvivo 1226 791 1231 2.023 0.486 0.139 0.034 13 1.7 BA3a_exvivo 2185 1526 3265 1.902 0.597 0.122 0.025 21 2.3 BA3b_exvivo 1559 1081 3204 2.564 0.475 0.105 0.019 10 1.1 BA4a_exvivo 1260 885 2127 2.458 0.510 0.110 0.020 8 1.0 BA4p_exvivo 8462 6022 20249 2.701 0.686 0.132 0.028 92 9.7 BA6_exvivo 4309 2971 8629 2.737 0.558 0.113 0.020 38 3.4 BA44_exvivo 3644 2599 7449 2.450 0.647 0.134 0.031 50 4.6 BA45_exvivo 3765 2757 5724 1.921 0.516 0.165 0.041 65 7.7 V1_exvivo 8040 5546 13274 2.241 0.643 0.155 0.037 120 12.2 V2_exvivo 2039 1463 3593 2.389 0.556 0.137 0.033 23 2.9 MT_exvivo 642 469 2146 3.162 0.876 0.139 0.040 11 1.0 perirhinal_exvivo 385 280 904 2.492 0.679 0.192 0.065 9 1.2 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 0050750 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050750/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 282100 Total vertex volume 278317 (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) = 1537738 mm^3 (det: 1.266865 ) lhCtxGM: 272442.513 272596.000 diff= -153.5 pctdiff=-0.056 rhCtxGM: 277283.776 277024.000 diff= 259.8 pctdiff= 0.094 lhCtxWM: 255939.612 255727.000 diff= 212.6 pctdiff= 0.083 rhCtxWM: 253701.624 254207.000 diff= -505.4 pctdiff=-0.199 SubCortGMVol 67367.000 SupraTentVol 1145502.525 (1143462.000) diff=2040.525 pctdiff=0.178 SupraTentVolNotVent 1129140.525 (1127100.000) diff=2040.525 pctdiff=0.181 BrainSegVol 1286712.000 (1284887.000) diff=1825.000 pctdiff=0.142 BrainSegVolNotVent 1268035.000 (1267636.525) diff=398.475 pctdiff=0.031 BrainSegVolNotVent 1268035.000 CerebellumVol 140723.000 VentChorVol 16362.000 3rd4th5thCSF 2315.000 CSFVol 490.000, OptChiasmVol 212.000 MaskVol 1758188.000 722 483 2019 2.784 0.756 0.156 0.034 11 1.1 BA1_exvivo 2163 1552 3728 2.190 0.608 0.136 0.028 25 2.7 BA2_exvivo 1085 694 954 1.988 0.442 0.139 0.033 11 1.5 BA3a_exvivo 1700 1192 2143 1.701 0.443 0.115 0.024 15 1.7 BA3b_exvivo 985 688 2219 2.619 0.480 0.117 0.022 7 0.8 BA4a_exvivo 1011 717 1632 2.425 0.458 0.105 0.018 6 0.7 BA4p_exvivo 5445 3853 12993 2.677 0.712 0.132 0.028 60 6.4 BA6_exvivo 943 668 2455 3.020 0.503 0.128 0.029 11 0.9 BA44_exvivo 853 643 2251 2.815 0.692 0.159 0.036 15 1.4 BA45_exvivo 3590 2628 5364 1.924 0.520 0.162 0.040 60 7.3 V1_exvivo 4236 2971 7193 2.201 0.651 0.162 0.037 69 6.5 V2_exvivo 267 199 635 2.500 0.354 0.141 0.037 3 0.3 MT_exvivo 399 282 1313 3.273 0.898 0.122 0.035 6 0.6 perirhinal_exvivo 281 204 656 2.618 0.659 0.201 0.055 6 0.8 entorhinal_exvivo Started at Sat Oct 7 16:52:34 CEST 2017 Ended at Sun Oct 8 01:02:55 CEST 2017 #@#%# recon-all-run-time-hours 8.172 recon-all -s 0050750 finished without error at Sun Oct 8 01:02:55 CEST 2017