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|
- Sat Oct 7 23:29:49 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
- -subjid 0051311 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UCLA_2/0051311/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
- subjid 0051311
- 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-904 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: 66074760 59175832 6898928 1758252 0 54158228
- -/+ buffers/cache: 5017604 61057156
- Swap: 0 0 0
- ########################################
- program versions used
- $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
- $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
- mri_convert.bin -all-info
- ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
- mri_convert.bin --version
- stable6
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
- ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:49-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-904 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-6.0.0/0051311
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UCLA_2/0051311/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig/001.mgz
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UCLA_2/0051311/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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/UCLA_2/0051311/session_1/anat_1/mprage.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -0, 0)
- j_ras = (-0, 1, 0)
- k_ras = (-0, -0, 1)
- writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig/001.mgz...
- #--------------------------------------------
- #@# MotionCor Sat Oct 7 23:29:52 CEST 2017
- Found 1 runs
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig.mgz --conform
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -0, 0)
- j_ras = (-0, 1, 0)
- k_ras = (-0, -0, 1)
- changing data type from short to uchar (noscale = 0)...
- MRIchangeType: Building histogram
- Reslicing using trilinear interpolation
- writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig.mgz...
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Sat Oct 7 23:30:04 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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-904 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
- Sat Oct 7 23:30:04 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.17659
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17659/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.17659/nu0.mnc -odt float
- $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
- reading from orig.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -1)
- k_ras = (0, 1, 0)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.17659/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 23:30:08 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.17659/nu0.mnc ./tmp.mri_nu_correct.mni.17659/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17659/0/ -iterations 1000 -distance 50
- [ntraut@tars-904:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/] [2017-10-07 23:30:08] 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.17659/0/ ./tmp.mri_nu_correct.mni.17659/nu0.mnc ./tmp.mri_nu_correct.mni.17659/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
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- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 43
- CV of field change: 0.000994193
-
-
-
- mri_convert ./tmp.mri_nu_correct.mni.17659/nu1.mnc orig_nu.mgz --like orig.mgz --conform
- mri_convert.bin ./tmp.mri_nu_correct.mni.17659/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.17659/nu1.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -1)
- k_ras = (0, 1, 0)
- INFO: transform src into the like-volume: orig.mgz
- changing data type from float to uchar (noscale = 0)...
- MRIchangeType: Building histogram
- writing to orig_nu.mgz...
-
-
- Sat Oct 7 23:31:23 CEST 2017
- mri_nu_correct.mni done
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- talairach_avi log file is transforms/talairach_avi.log...
- Started at Sat Oct 7 23:31:23 CEST 2017
- Ended at Sat Oct 7 23:32:13 CEST 2017
- talairach_avi done
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Sat Oct 7 23:32:15 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7533, 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-6.0.0/0051311/mri/transforms/talairach_avi.log
- tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/transforms/talairach_avi.log
- TalAviQA: 0.97768
- z-score: 0
- #--------------------------------------------
- #@# Nu Intensity Correction Sat Oct 7 23:32:15 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-6.0.0/0051311/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-904 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
- Sat Oct 7 23:32:15 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.18752
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18752/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.18752/nu0.mnc -odt float
- $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
- reading from orig.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -1)
- k_ras = (0, 1, 0)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.18752/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 23:32:18 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.18752/nu0.mnc ./tmp.mri_nu_correct.mni.18752/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18752/0/
- [ntraut@tars-904:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/] [2017-10-07 23:32:18] 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.18752/0/ ./tmp.mri_nu_correct.mni.18752/nu0.mnc ./tmp.mri_nu_correct.mni.18752/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
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- Processing:.................................................................Done
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- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 46
- CV of field change: 0.000980147
-
-
- --------------------------------------------------------
- Iteration 2 Sat Oct 7 23:33:13 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.18752/nu1.mnc ./tmp.mri_nu_correct.mni.18752/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.18752/1/
- [ntraut@tars-904:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/] [2017-10-07 23:33:13] 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.18752/1/ ./tmp.mri_nu_correct.mni.18752/nu1.mnc ./tmp.mri_nu_correct.mni.18752/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: 0.00098563
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.18752/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18752/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-6.0.0/0051311/mri
- cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.18752/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18752/ones.mgz
- sysname Linux
- hostname tars-904
- machine x86_64
- user ntraut
- input ./tmp.mri_nu_correct.mni.18752/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.18752/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.18752/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18752/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18752/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.18752/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18752/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18752/input.mean.dat
- sysname Linux
- hostname tars-904
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.18752/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.18752/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18752/ones.mgz --i ./tmp.mri_nu_correct.mni.18752/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18752/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18752/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.18752/ones.mgz --i ./tmp.mri_nu_correct.mni.18752/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18752/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18752/output.mean.dat
- sysname Linux
- hostname tars-904
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.18752/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.18752/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.18752/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.18752/nu2.mnc ./tmp.mri_nu_correct.mni.18752/nu2.mnc mul 1.04259041581368729225
- Saving result to './tmp.mri_nu_correct.mni.18752/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.18752/nu2.mnc nu.mgz --like orig.mgz
- mri_convert.bin ./tmp.mri_nu_correct.mni.18752/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.18752/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -1)
- k_ras = (0, 1, 0)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 10 seconds.
- mapping (13, 111) to ( 3, 110)
-
-
- Sat Oct 7 23:34:44 CEST 2017
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Sat Oct 7 23:34:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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
- 0.99551 -0.00649 -0.09109 2.72523;
- 0.06088 1.15020 0.24347 -5.52109;
- 0.08437 -0.28685 1.20325 -5.76160;
- 0.00000 0.00000 0.00000 1.00000;
- processing without aseg, no1d=0
- MRInormInit():
- INFO: Modifying talairach volume c_(r,a,s) based on average_305
- MRInormalize():
- MRIsplineNormalize(): npeaks = 19
- Starting OpenSpline(): npoints = 19
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 110
- white matter peak found at 109
- gm peak at 55 (55), valley at 25 (25)
- csf peak at 28, setting threshold to 46
- 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 55 (55), valley at 25 (25)
- csf peak at 28, setting threshold to 46
- 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 23:36:59 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- == Number of threads available to mri_em_register for OpenMP = 2 ==
- reading 1 input volumes...
- logging results to talairach_with_skull.log
- reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'...
- average std = 22.9 using min determinant for regularization = 52.6
- 0 singular and 9002 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- accounting for voxel sizes in initial transform
- bounding unknown intensity as < 8.7 or > 569.1
- total sample mean = 77.6 (1399 zeros)
- ************************************************
- spacing=8, using 3243 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3243, passno 0, spacing 8
- resetting wm mean[0]: 100 --> 108
- resetting gm mean[0]: 61 --> 61
- input volume #1 is the most T1-like
- using real data threshold=6.0
- skull bounding box = (45, 55, 35) --> (216, 200, 211)
- using (102, 103, 123) as brain centroid...
- mean wm in atlas = 108, using box (81,85,101) --> (123, 120,144) to find MRI wm
- before smoothing, mri peak at 107
- robust fit to distribution - 107 +- 6.1
- after smoothing, mri peak at 107, scaling input intensities by 1.009
- scaling channel 0 by 1.00935
- initial log_p = -4.577
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.470880 @ (-9.091, -9.091, -9.091)
- max log p = -4.352172 @ (4.545, -4.545, -4.545)
- max log p = -4.330606 @ (-2.273, 6.818, -2.273)
- max log p = -4.305599 @ (1.136, -1.136, 1.136)
- max log p = -4.289562 @ (-1.705, -0.568, 0.568)
- max log p = -4.289562 @ (0.000, 0.000, 0.000)
- Found translation: (-7.4, -8.5, -14.2): log p = -4.290
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.848, old_max_log_p =-4.290 (thresh=-4.3)
- 0.99144 -0.14882 -0.01959 18.62359;
- 0.14032 1.21519 0.15998 -79.52754;
- 0.00000 -0.15011 1.14016 -9.12227;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.823, old_max_log_p =-3.848 (thresh=-3.8)
- 0.91709 -0.13766 -0.01812 26.59247;
- 0.14955 1.27409 0.33049 -103.46049;
- -0.01969 -0.33049 1.19274 14.08657;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.813, old_max_log_p =-3.823 (thresh=-3.8)
- 0.98587 -0.14798 -0.01948 19.22125;
- 0.15084 1.30633 0.17198 -88.71935;
- 0.00000 -0.14926 1.13375 -7.54151;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.813, old_max_log_p =-3.813 (thresh=-3.8)
- 0.98587 -0.14798 -0.01948 19.22125;
- 0.15084 1.30633 0.17198 -88.71935;
- 0.00000 -0.14926 1.13375 -7.54151;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.731, old_max_log_p =-3.813 (thresh=-3.8)
- 0.97427 -0.06182 -0.00330 8.10079;
- 0.08319 1.25644 0.31863 -92.64512;
- -0.01532 -0.31844 1.12262 18.79496;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.719, old_max_log_p =-3.731 (thresh=-3.7)
- 0.99254 -0.06298 -0.00336 5.91127;
- 0.08364 1.26619 0.28173 -89.50504;
- -0.01235 -0.27196 1.11121 13.03175;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.719, old_max_log_p =-3.719 (thresh=-3.7)
- 1.00703 -0.11309 0.02718 5.66892;
- 0.11449 1.25435 0.20550 -84.08475;
- -0.03933 -0.18641 1.12676 3.91661;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.696, old_max_log_p =-3.719 (thresh=-3.7)
- 1.01070 -0.08697 0.00342 4.74484;
- 0.09650 1.24972 0.26105 -87.46809;
- -0.01955 -0.24966 1.11309 11.43538;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.690, old_max_log_p =-3.696 (thresh=-3.7)
- 1.00889 -0.09280 -0.01695 7.91514;
- 0.10448 1.24545 0.26970 -88.96503;
- -0.00379 -0.26096 1.10952 11.48164;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 9 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.689, old_max_log_p =-3.690 (thresh=-3.7)
- 1.00889 -0.09280 -0.01695 7.91514;
- 0.10448 1.24545 0.26970 -88.96503;
- -0.00379 -0.26065 1.10822 11.59817;
- 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
- 1.00889 -0.09280 -0.01695 7.91514;
- 0.10448 1.24545 0.26970 -88.96503;
- -0.00379 -0.26065 1.10822 11.59817;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3243
- Quasinewton: input matrix
- 1.00889 -0.09280 -0.01695 7.91514;
- 0.10448 1.24545 0.26970 -88.96503;
- -0.00379 -0.26065 1.10822 11.59817;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 012: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.00889 -0.09280 -0.01695 7.91514;
- 0.10448 1.24545 0.26970 -88.96503;
- -0.00379 -0.26065 1.10822 11.59817;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.689 (old=-4.577)
- transform before final EM align:
- 1.00889 -0.09280 -0.01695 7.91514;
- 0.10448 1.24545 0.26970 -88.96503;
- -0.00379 -0.26065 1.10822 11.59817;
- 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
- 1.00889 -0.09280 -0.01695 7.91514;
- 0.10448 1.24545 0.26970 -88.96503;
- -0.00379 -0.26065 1.10822 11.59817;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 364799
- Quasinewton: input matrix
- 1.00889 -0.09280 -0.01695 7.91514;
- 0.10448 1.24545 0.26970 -88.96503;
- -0.00379 -0.26065 1.10822 11.59817;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 014: -log(p) = 4.2 tol 0.000000
- final transform:
- 1.00889 -0.09280 -0.01695 7.91514;
- 0.10448 1.24545 0.26970 -88.96503;
- -0.00379 -0.26065 1.10822 11.59817;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach_with_skull.lta...
- mri_em_register utimesec 3121.175509
- mri_em_register stimesec 7.953790
- mri_em_register ru_maxrss 611708
- mri_em_register ru_ixrss 0
- mri_em_register ru_idrss 0
- mri_em_register ru_isrss 0
- mri_em_register ru_minflt 157528
- mri_em_register ru_majflt 0
- mri_em_register ru_nswap 0
- mri_em_register ru_inblock 0
- mri_em_register ru_oublock 32
- mri_em_register ru_msgsnd 0
- mri_em_register ru_msgrcv 0
- mri_em_register ru_nsignals 0
- mri_em_register ru_nvcsw 330534
- mri_em_register ru_nivcsw 7029
- registration took 32 minutes and 59 seconds.
- mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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=131 y=126 z=120 r=66
- first estimation of the main basin volume: 1220453 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 14 found in the rest of the brain
- global maximum in x=108, y=116, z=89, Imax=255
- CSF=20, 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=7610560721 voxels, voxel volume =1.000
- = 7610560721 mmm3 = 7610560.512 cm3
- done.
- PostAnalyze...Basin Prior
- 70 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=130,y=130, z=115, r=9258 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=47 , nb = 45657
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=40 , nb = -1034762496
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=27 , nb = -1049397912
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=50 , nb = -1078243316
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=46 , nb = 1074495890
- OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 1076229100
- Problem with the least square interpolation in GM_MIN calculation.
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 47, 35, 30, 50
- after analyzing : 24, 35, 35, 38
- RIGHT_CER
- before analyzing : 40, 33, 28, 56
- after analyzing : 21, 33, 33, 38
- LEFT_CER
- before analyzing : 27, 27, 29, 57
- after analyzing : 27, 28, 29, 35
- RIGHT_BRAIN
- before analyzing : 50, 35, 31, 48
- after analyzing : 26, 35, 35, 38
- LEFT_BRAIN
- before analyzing : 46, 35, 30, 50
- after analyzing : 22, 35, 35, 38
- OTHER
- before analyzing : 32, 59, 79, 95
- after analyzing : 32, 72, 79, 77
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...64 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.013
- curvature mean = 67.912, std = 7.762
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 5.11, sigma = 7.13
- after rotation: sse = 5.11, sigma = 7.13
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 6.64, its var is 7.68
- before Erosion-Dilatation 3.85% of inacurate vertices
- after Erosion-Dilatation 6.52% of inacurate vertices
- Validation of the shape of the surface done.
- Scaling of atlas fields onto current surface fields
- ********FINAL ITERATIVE TEMPLATE DEFORMATION********
- Compute Local values csf/gray
- Fine Segmentation...43 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1498102 voxels, voxel volume = 1.000 mm3
- = 1498102 mmm3 = 1498.102 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- mri_watershed utimesec 31.956141
- mri_watershed stimesec 0.456930
- mri_watershed ru_maxrss 818376
- mri_watershed ru_ixrss 0
- mri_watershed ru_idrss 0
- mri_watershed ru_isrss 0
- mri_watershed ru_minflt 211924
- mri_watershed ru_majflt 0
- mri_watershed ru_nswap 0
- mri_watershed ru_inblock 0
- mri_watershed ru_oublock 2456
- mri_watershed ru_msgsnd 0
- mri_watershed ru_msgrcv 0
- mri_watershed ru_nsignals 0
- mri_watershed ru_nvcsw 2115
- mri_watershed ru_nivcsw 1291
- mri_watershed done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Sun Oct 8 00:10:31 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta
- setting unknown_nbr_spacing = 3
- using MR volume brainmask.mgz to mask input volume...
- == Number of threads available to mri_em_register for OpenMP = 2 ==
- reading 1 input volumes...
- logging results to talairach.log
- reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
- average std = 7.3 using min determinant for regularization = 5.3
- 0 singular and 841 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- accounting for voxel sizes in initial transform
- bounding unknown intensity as < 6.3 or > 503.7
- total sample mean = 78.8 (1011 zeros)
- ************************************************
- spacing=8, using 2830 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 2830, passno 0, spacing 8
- resetting wm mean[0]: 98 --> 107
- resetting gm mean[0]: 61 --> 61
- input volume #1 is the most T1-like
- using real data threshold=21.0
- skull bounding box = (56, 75, 51) --> (205, 186, 197)
- using (106, 112, 124) as brain centroid...
- mean wm in atlas = 107, using box (88,98,106) --> (124, 125,141) to find MRI wm
- before smoothing, mri peak at 109
- robust fit to distribution - 107 +- 6.0
- after smoothing, mri peak at 107, scaling input intensities by 1.000
- scaling channel 0 by 1
- initial log_p = -4.185
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -3.904794 @ (-9.091, -9.091, -9.091)
- max log p = -3.764544 @ (4.545, -4.545, -4.545)
- max log p = -3.764544 @ (0.000, 0.000, 0.000)
- max log p = -3.759517 @ (1.136, 1.136, 1.136)
- max log p = -3.723667 @ (-1.705, 0.568, -0.568)
- max log p = -3.723667 @ (0.000, 0.000, 0.000)
- Found translation: (-5.1, -11.9, -13.1): log p = -3.724
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.393, old_max_log_p =-3.724 (thresh=-3.7)
- 0.99144 -0.14882 -0.01959 17.86489;
- 0.14032 1.21519 0.15998 -77.62984;
- 0.00000 -0.13885 1.05465 -1.32504;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.393, old_max_log_p =-3.393 (thresh=-3.4)
- 0.99144 -0.14882 -0.01959 17.86489;
- 0.14032 1.21519 0.15998 -77.62984;
- 0.00000 -0.13885 1.05465 -1.32504;
- 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=-3.231, old_max_log_p =-3.393 (thresh=-3.4)
- 0.95751 -0.11111 0.02399 12.46966;
- 0.10671 1.18514 0.22368 -73.13071;
- -0.04150 -0.22555 1.10131 13.81259;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.231, old_max_log_p =-3.231 (thresh=-3.2)
- 0.95751 -0.11111 0.02399 12.46966;
- 0.10671 1.18514 0.22368 -73.13071;
- -0.04150 -0.22555 1.10131 13.81259;
- 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=-3.206, old_max_log_p =-3.231 (thresh=-3.2)
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.206, old_max_log_p =-3.206 (thresh=-3.2)
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 2830 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2830
- Quasinewton: input matrix
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.206 (old=-4.185)
- transform before final EM align:
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 315557 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 315557
- Quasinewton: input matrix
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 010: -log(p) = 3.7 tol 0.000000
- final transform:
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach.lta...
- mri_em_register utimesec 1264.877709
- mri_em_register stimesec 2.041689
- mri_em_register ru_maxrss 599052
- mri_em_register ru_ixrss 0
- mri_em_register ru_idrss 0
- mri_em_register ru_isrss 0
- mri_em_register ru_minflt 158990
- mri_em_register ru_majflt 0
- mri_em_register ru_nswap 0
- mri_em_register ru_inblock 0
- mri_em_register ru_oublock 24
- mri_em_register ru_msgsnd 0
- mri_em_register ru_msgrcv 0
- mri_em_register ru_nsignals 0
- mri_em_register ru_nvcsw 143
- mri_em_register ru_nivcsw 2284
- registration took 10 minutes and 52 seconds.
- #--------------------------------------
- #@# CA Normalize Sun Oct 8 00:21:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri
- mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz
- writing control point volume to ctrl_pts.mgz
- using MR volume brainmask.mgz to mask input volume...
- reading 1 input volume
- reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
- reading transform from 'transforms/talairach.lta'...
- reading input volume from nu.mgz...
- resetting wm mean[0]: 98 --> 107
- resetting gm mean[0]: 61 --> 61
- input volume #1 is the most T1-like
- using real data threshold=21.0
- skull bounding box = (56, 75, 51) --> (205, 186, 197)
- using (106, 112, 124) as brain centroid...
- mean wm in atlas = 107, using box (88,98,106) --> (124, 125,141) to find MRI wm
- before smoothing, mri peak at 109
- robust fit to distribution - 107 +- 6.0
- after smoothing, mri peak at 107, scaling input intensities by 1.000
- scaling channel 0 by 1
- using 246344 sample points...
- INFO: compute sample coordinates transform
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- INFO: transform used
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (129, 73, 46) --> (201, 168, 193)
- Left_Cerebral_White_Matter: limiting intensities to 101.0 --> 132.0
- 0 of 68 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 77, 45) --> (132, 173, 194)
- Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0
- 0 of 50 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (134, 150, 71) --> (187, 182, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 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 (90, 150, 69) --> (135, 187, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 0 of 16 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (116, 138, 103) --> (154, 197, 130)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 0 of 13 (0.0%) samples deleted
- using 156 total control points for intensity normalization...
- bias field = 0.934 +- 0.058
- 0 of 156 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (129, 73, 46) --> (201, 168, 193)
- Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 0 of 145 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 77, 45) --> (132, 173, 194)
- Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
- 7 of 136 (5.1%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (134, 150, 71) --> (187, 182, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 7 of 79 (8.9%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (90, 150, 69) --> (135, 187, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 39 of 56 (69.6%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (116, 138, 103) --> (154, 197, 130)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 59 of 97 (60.8%) samples deleted
- using 513 total control points for intensity normalization...
- bias field = 1.000 +- 0.061
- 0 of 395 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (129, 73, 46) --> (201, 168, 193)
- Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
- 0 of 243 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 77, 45) --> (132, 173, 194)
- Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 5 of 223 (2.2%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (134, 150, 71) --> (187, 182, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 28 of 92 (30.4%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (90, 150, 69) --> (135, 187, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 65 of 95 (68.4%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (116, 138, 103) --> (154, 197, 130)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 126 of 198 (63.6%) samples deleted
- using 851 total control points for intensity normalization...
- bias field = 0.993 +- 0.050
- 0 of 625 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 Sun Oct 8 00:23:09 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri
- mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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) = 1.31 (predicted orig area = 6.1)
- label assignment complete, 0 changed (0.00%)
- freeing gibbs priors...done.
- average std[0] = 5.0
- **************** pass 1 of 1 ************************
- enabling zero nodes
- setting smoothness coefficient to 0.039
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.843, neg=0, invalid=762
- 0001: dt=186.891676, rms=0.786 (6.672%), neg=0, invalid=762
- 0002: dt=221.952000, rms=0.774 (1.504%), neg=0, invalid=762
- 0003: dt=295.936000, rms=0.763 (1.440%), neg=0, invalid=762
- 0004: dt=154.613861, rms=0.758 (0.678%), neg=0, invalid=762
- 0005: dt=517.888000, rms=0.747 (1.531%), neg=0, invalid=762
- 0006: dt=129.472000, rms=0.743 (0.480%), neg=0, invalid=762
- 0007: dt=1183.744000, rms=0.731 (1.590%), neg=0, invalid=762
- 0008: dt=110.976000, rms=0.727 (0.511%), neg=0, invalid=762
- 0009: dt=1479.680000, rms=0.721 (0.890%), neg=0, invalid=762
- 0010: dt=221.952000, rms=0.717 (0.571%), neg=0, invalid=762
- 0011: dt=295.936000, rms=0.716 (0.175%), neg=0, invalid=762
- 0012: dt=295.936000, rms=0.715 (0.149%), neg=0, invalid=762
- 0013: dt=295.936000, rms=0.712 (0.353%), neg=0, invalid=762
- 0014: dt=295.936000, rms=0.710 (0.263%), neg=0, invalid=762
- 0015: dt=295.936000, rms=0.707 (0.468%), neg=0, invalid=762
- 0016: dt=295.936000, rms=0.703 (0.475%), neg=0, invalid=762
- 0017: dt=295.936000, rms=0.701 (0.296%), neg=0, invalid=762
- 0018: dt=295.936000, rms=0.698 (0.417%), neg=0, invalid=762
- 0019: dt=295.936000, rms=0.696 (0.383%), neg=0, invalid=762
- 0020: dt=295.936000, rms=0.694 (0.204%), neg=0, invalid=762
- 0021: dt=295.936000, rms=0.692 (0.359%), neg=0, invalid=762
- 0022: dt=295.936000, rms=0.690 (0.238%), neg=0, invalid=762
- 0023: dt=295.936000, rms=0.689 (0.151%), neg=0, invalid=762
- 0024: dt=295.936000, rms=0.688 (0.238%), neg=0, invalid=762
- 0025: dt=295.936000, rms=0.686 (0.215%), neg=0, invalid=762
- 0026: dt=295.936000, rms=0.685 (0.164%), neg=0, invalid=762
- 0027: dt=295.936000, rms=0.684 (0.195%), neg=0, invalid=762
- 0028: dt=295.936000, rms=0.682 (0.178%), neg=0, invalid=762
- 0029: dt=295.936000, rms=0.681 (0.126%), neg=0, invalid=762
- 0030: dt=295.936000, rms=0.680 (0.173%), neg=0, invalid=762
- 0031: dt=295.936000, rms=0.679 (0.184%), neg=0, invalid=762
- 0032: dt=295.936000, rms=0.678 (0.126%), neg=0, invalid=762
- 0033: dt=295.936000, rms=0.677 (0.116%), neg=0, invalid=762
- 0034: dt=295.936000, rms=0.676 (0.154%), neg=0, invalid=762
- 0035: dt=295.936000, rms=0.676 (0.095%), neg=0, invalid=762
- 0036: dt=295.936000, rms=0.675 (0.088%), neg=0, invalid=762
- 0037: dt=129.472000, rms=0.675 (0.026%), neg=0, invalid=762
- 0038: dt=129.472000, rms=0.675 (0.001%), neg=0, invalid=762
- 0039: dt=129.472000, rms=0.675 (0.006%), neg=0, invalid=762
- 0040: dt=129.472000, rms=0.675 (0.015%), neg=0, invalid=762
- 0041: dt=129.472000, rms=0.675 (0.015%), neg=0, invalid=762
- 0042: dt=129.472000, rms=0.675 (0.019%), neg=0, invalid=762
- 0043: dt=129.472000, rms=0.674 (0.017%), neg=0, invalid=762
- 0044: dt=129.472000, rms=0.674 (0.020%), neg=0, invalid=762
- 0045: dt=129.472000, rms=0.674 (0.021%), neg=0, invalid=762
- 0046: dt=129.472000, rms=0.674 (0.023%), neg=0, invalid=762
- 0047: dt=129.472000, rms=0.674 (0.022%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.675, neg=0, invalid=762
- 0048: dt=110.976000, rms=0.674 (0.150%), neg=0, invalid=762
- 0049: dt=295.936000, rms=0.673 (0.044%), neg=0, invalid=762
- 0050: dt=295.936000, rms=0.673 (0.070%), neg=0, invalid=762
- 0051: dt=295.936000, rms=0.672 (0.087%), neg=0, invalid=762
- 0052: dt=295.936000, rms=0.672 (0.069%), neg=0, invalid=762
- 0053: dt=295.936000, rms=0.671 (0.071%), neg=0, invalid=762
- 0054: dt=295.936000, rms=0.671 (0.085%), neg=0, invalid=762
- 0055: dt=295.936000, rms=0.670 (0.070%), neg=0, invalid=762
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.679, neg=0, invalid=762
- 0056: dt=144.941176, rms=0.674 (0.697%), neg=0, invalid=762
- 0057: dt=248.832000, rms=0.668 (0.923%), neg=0, invalid=762
- 0058: dt=69.304813, rms=0.664 (0.622%), neg=0, invalid=762
- 0059: dt=145.152000, rms=0.661 (0.380%), neg=0, invalid=762
- 0060: dt=121.081081, rms=0.659 (0.424%), neg=0, invalid=762
- 0061: dt=36.288000, rms=0.658 (0.175%), neg=0, invalid=762
- 0062: dt=36.288000, rms=0.657 (0.108%), neg=0, invalid=762
- 0063: dt=36.288000, rms=0.656 (0.162%), neg=0, invalid=762
- 0064: dt=36.288000, rms=0.654 (0.233%), neg=0, invalid=762
- 0065: dt=36.288000, rms=0.652 (0.310%), neg=0, invalid=762
- 0066: dt=36.288000, rms=0.650 (0.343%), neg=0, invalid=762
- 0067: dt=36.288000, rms=0.648 (0.332%), neg=0, invalid=762
- 0068: dt=36.288000, rms=0.646 (0.326%), neg=0, invalid=762
- 0069: dt=36.288000, rms=0.644 (0.331%), neg=0, invalid=762
- 0070: dt=36.288000, rms=0.642 (0.318%), neg=0, invalid=762
- 0071: dt=36.288000, rms=0.640 (0.305%), neg=0, invalid=762
- 0072: dt=36.288000, rms=0.638 (0.279%), neg=0, invalid=762
- 0073: dt=36.288000, rms=0.636 (0.255%), neg=0, invalid=762
- 0074: dt=36.288000, rms=0.635 (0.223%), neg=0, invalid=762
- 0075: dt=36.288000, rms=0.633 (0.198%), neg=0, invalid=762
- 0076: dt=36.288000, rms=0.632 (0.192%), neg=0, invalid=762
- 0077: dt=36.288000, rms=0.631 (0.189%), neg=0, invalid=762
- 0078: dt=36.288000, rms=0.630 (0.170%), neg=0, invalid=762
- 0079: dt=36.288000, rms=0.629 (0.150%), neg=0, invalid=762
- 0080: dt=36.288000, rms=0.628 (0.138%), neg=0, invalid=762
- 0081: dt=36.288000, rms=0.627 (0.118%), neg=0, invalid=762
- 0082: dt=36.288000, rms=0.627 (0.109%), neg=0, invalid=762
- 0083: dt=145.152000, rms=0.626 (0.048%), neg=0, invalid=762
- 0084: dt=145.152000, rms=0.626 (-0.059%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.627, neg=0, invalid=762
- 0085: dt=82.944000, rms=0.626 (0.242%), neg=0, invalid=762
- 0086: dt=103.680000, rms=0.625 (0.104%), neg=0, invalid=762
- 0087: dt=103.680000, rms=0.625 (-0.121%), neg=0, invalid=762
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.651, neg=0, invalid=762
- 0088: dt=0.700000, rms=0.650 (0.114%), neg=0, invalid=762
- 0089: dt=0.700000, rms=0.650 (0.003%), neg=0, invalid=762
- 0090: dt=0.700000, rms=0.650 (0.000%), neg=0, invalid=762
- 0091: dt=0.700000, rms=0.650 (-0.005%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.651, neg=0, invalid=762
- 0092: dt=0.000000, rms=0.650 (0.113%), neg=0, invalid=762
- 0093: dt=0.000000, rms=0.650 (0.000%), neg=0, invalid=762
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.725, neg=0, invalid=762
- 0094: dt=5.647416, rms=0.704 (2.859%), neg=0, invalid=762
- 0095: dt=3.178571, rms=0.703 (0.143%), neg=0, invalid=762
- 0096: dt=3.178571, rms=0.703 (-0.048%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.704, neg=0, invalid=762
- 0097: dt=0.000000, rms=0.703 (0.083%), neg=0, invalid=762
- 0098: dt=0.000000, rms=0.703 (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=0.779, neg=0, invalid=762
- 0099: dt=1.280000, rms=0.776 (0.430%), neg=0, invalid=762
- 0100: dt=2.431655, rms=0.768 (0.975%), neg=0, invalid=762
- 0101: dt=0.320000, rms=0.768 (0.024%), neg=0, invalid=762
- 0102: dt=0.320000, rms=0.768 (0.024%), neg=0, invalid=762
- 0103: dt=0.320000, rms=0.767 (0.030%), neg=0, invalid=762
- 0104: dt=0.320000, rms=0.767 (0.045%), neg=0, invalid=762
- 0105: dt=0.320000, rms=0.766 (0.082%), neg=0, invalid=762
- 0106: dt=0.320000, rms=0.766 (0.110%), neg=0, invalid=762
- 0107: dt=0.320000, rms=0.765 (0.091%), neg=0, invalid=762
- 0108: dt=0.320000, rms=0.765 (0.027%), neg=0, invalid=762
- 0109: dt=1.024000, rms=0.765 (0.011%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.765, neg=0, invalid=762
- 0110: dt=1.820896, rms=0.762 (0.395%), neg=0, invalid=762
- 0111: dt=0.000000, rms=0.762 (-0.001%), neg=0, invalid=762
- 0112: dt=0.100000, rms=0.762 (-0.003%), 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=0.718, neg=0, invalid=762
- 0113: dt=0.975596, rms=0.694 (3.456%), neg=0, invalid=762
- 0114: dt=0.096000, rms=0.692 (0.167%), neg=0, invalid=762
- 0115: dt=0.096000, rms=0.692 (-0.134%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.693, neg=0, invalid=762
- 0116: dt=0.028000, rms=0.692 (0.103%), neg=0, invalid=762
- 0117: dt=0.001750, rms=0.692 (0.000%), neg=0, invalid=762
- 0118: dt=0.001750, rms=0.692 (-0.000%), neg=0, invalid=762
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.10027 (20)
- mri peak = 0.21687 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (985 voxels, overlap=0.019)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (985 voxels, peak = 7), gca=8.0
- gca peak = 0.15565 (16)
- mri peak = 0.14998 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (800 voxels, overlap=0.148)
- Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (800 voxels, peak = 7), gca=7.0
- gca peak = 0.26829 (96)
- mri peak = 0.07790 (88)
- Right_Pallidum (52): linear fit = 0.94 x + 0.0 (664 voxels, overlap=0.718)
- Right_Pallidum (52): linear fit = 0.94 x + 0.0 (664 voxels, peak = 91), gca=90.7
- gca peak = 0.20183 (93)
- mri peak = 0.08094 (89)
- Left_Pallidum (13): linear fit = 0.94 x + 0.0 (578 voxels, overlap=1.005)
- Left_Pallidum (13): linear fit = 0.94 x + 0.0 (578 voxels, peak = 88), gca=87.9
- gca peak = 0.21683 (55)
- mri peak = 0.08208 (56)
- Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (398 voxels, overlap=0.998)
- Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (398 voxels, peak = 57), gca=57.5
- gca peak = 0.30730 (58)
- mri peak = 0.11605 (56)
- Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (475 voxels, overlap=0.963)
- Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (475 voxels, peak = 54), gca=54.2
- gca peak = 0.11430 (101)
- mri peak = 0.07889 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (46529 voxels, overlap=0.619)
- Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (46529 voxels, peak = 108), gca=107.6
- gca peak = 0.12076 (102)
- mri peak = 0.07761 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (46020 voxels, overlap=0.656)
- Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (46020 voxels, peak = 109), gca=108.6
- gca peak = 0.14995 (59)
- mri peak = 0.05668 (50)
- Left_Cerebral_Cortex (3): linear fit = 0.87 x + 0.0 (13708 voxels, overlap=0.316)
- Left_Cerebral_Cortex (3): linear fit = 0.87 x + 0.0 (13708 voxels, peak = 51), gca=51.0
- gca peak = 0.15082 (58)
- mri peak = 0.05744 (50)
- Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (13402 voxels, overlap=0.615)
- Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (13402 voxels, peak = 52), gca=51.9
- gca peak = 0.14161 (67)
- mri peak = 0.10451 (64)
- Right_Caudate (50): linear fit = 0.93 x + 0.0 (540 voxels, overlap=0.525)
- Right_Caudate (50): linear fit = 0.93 x + 0.0 (540 voxels, peak = 62), gca=62.0
- gca peak = 0.15243 (71)
- mri peak = 0.09446 (67)
- Left_Caudate (11): linear fit = 0.90 x + 0.0 (604 voxels, overlap=0.540)
- Left_Caudate (11): linear fit = 0.90 x + 0.0 (604 voxels, peak = 64), gca=64.3
- gca peak = 0.13336 (57)
- mri peak = 0.04103 (50)
- Left_Cerebellum_Cortex (8): linear fit = 0.93 x + 0.0 (12771 voxels, overlap=0.813)
- Left_Cerebellum_Cortex (8): linear fit = 0.93 x + 0.0 (12771 voxels, peak = 53), gca=52.7
- gca peak = 0.13252 (56)
- mri peak = 0.04318 (55)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (13347 voxels, overlap=0.994)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (13347 voxels, peak = 53), gca=52.9
- gca peak = 0.18181 (84)
- mri peak = 0.07788 (88)
- Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5369 voxels, overlap=0.633)
- Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5369 voxels, peak = 90), gca=90.3
- gca peak = 0.20573 (83)
- mri peak = 0.06807 (86)
- Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4956 voxels, overlap=0.872)
- Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4956 voxels, peak = 85), gca=85.1
- gca peak = 0.21969 (57)
- mri peak = 0.11021 (54)
- Left_Amygdala (18): linear fit = 0.94 x + 0.0 (267 voxels, overlap=0.992)
- Left_Amygdala (18): linear fit = 0.94 x + 0.0 (267 voxels, peak = 54), gca=53.9
- gca peak = 0.39313 (56)
- mri peak = 0.10429 (56)
- Right_Amygdala (54): linear fit = 0.99 x + 0.0 (372 voxels, overlap=1.003)
- Right_Amygdala (54): linear fit = 0.99 x + 0.0 (372 voxels, peak = 55), gca=55.2
- gca peak = 0.14181 (85)
- mri peak = 0.06244 (82)
- Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4412 voxels, overlap=0.969)
- Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4412 voxels, peak = 81), gca=81.2
- gca peak = 0.11978 (83)
- mri peak = 0.06269 (81)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3664 voxels, overlap=0.923)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3664 voxels, peak = 84), gca=84.2
- gca peak = 0.13399 (79)
- mri peak = 0.06625 (73)
- Left_Putamen (12): linear fit = 0.94 x + 0.0 (1887 voxels, overlap=0.752)
- Left_Putamen (12): linear fit = 0.94 x + 0.0 (1887 voxels, peak = 74), gca=73.9
- gca peak = 0.14159 (79)
- mri peak = 0.07276 (73)
- Right_Putamen (51): linear fit = 0.94 x + 0.0 (2031 voxels, overlap=0.888)
- Right_Putamen (51): linear fit = 0.94 x + 0.0 (2031 voxels, peak = 74), gca=73.9
- gca peak = 0.10025 (80)
- mri peak = 0.09548 (83)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (9084 voxels, overlap=0.402)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (9084 voxels, peak = 88), gca=87.6
- gca peak = 0.13281 (86)
- mri peak = 0.06018 (90)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (780 voxels, overlap=0.728)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (780 voxels, peak = 93), gca=93.3
- gca peak = 0.12801 (89)
- mri peak = 0.07684 (91)
- Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1151 voxels, overlap=0.850)
- Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1151 voxels, peak = 93), gca=93.0
- gca peak = 0.20494 (23)
- mri peak = 0.19780 (13)
- gca peak = 0.15061 (21)
- mri peak = 0.17648 (12)
- Fourth_Ventricle (15): linear fit = 0.61 x + 0.0 (326 voxels, overlap=0.293)
- Fourth_Ventricle (15): linear fit = 0.61 x + 0.0 (326 voxels, peak = 13), gca=12.7
- 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 0.94 x + 0.0
- estimating mean wm scale to be 1.07 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=0.730, neg=0, invalid=762
- 0119: dt=129.472000, rms=0.723 (0.985%), neg=0, invalid=762
- 0120: dt=134.826667, rms=0.720 (0.409%), neg=0, invalid=762
- 0121: dt=129.472000, rms=0.719 (0.188%), neg=0, invalid=762
- 0122: dt=129.472000, rms=0.717 (0.199%), neg=0, invalid=762
- 0123: dt=129.472000, rms=0.716 (0.126%), neg=0, invalid=762
- 0124: dt=369.920000, rms=0.715 (0.236%), neg=0, invalid=762
- 0125: dt=73.984000, rms=0.714 (0.126%), neg=0, invalid=762
- 0126: dt=1775.616000, rms=0.710 (0.510%), neg=0, invalid=762
- 0127: dt=92.480000, rms=0.710 (0.055%), neg=0, invalid=762
- 0128: dt=517.888000, rms=0.708 (0.208%), neg=0, invalid=762
- 0129: dt=73.984000, rms=0.708 (0.045%), neg=0, invalid=762
- 0130: dt=73.984000, rms=0.708 (0.024%), neg=0, invalid=762
- 0131: dt=73.984000, rms=0.707 (0.040%), neg=0, invalid=762
- 0132: dt=73.984000, rms=0.707 (0.055%), neg=0, invalid=762
- 0133: dt=73.984000, rms=0.706 (0.069%), neg=0, invalid=762
- 0134: dt=73.984000, rms=0.706 (0.079%), neg=0, invalid=762
- 0135: dt=73.984000, rms=0.705 (0.083%), neg=0, invalid=762
- 0136: dt=73.984000, rms=0.705 (0.079%), neg=0, invalid=762
- 0137: dt=73.984000, rms=0.704 (0.075%), neg=0, invalid=762
- 0138: dt=73.984000, rms=0.704 (0.072%), neg=0, invalid=762
- 0139: dt=73.984000, rms=0.703 (0.068%), neg=0, invalid=762
- 0140: dt=73.984000, rms=0.703 (0.068%), neg=0, invalid=762
- 0141: dt=73.984000, rms=0.702 (0.073%), neg=0, invalid=762
- 0142: dt=73.984000, rms=0.702 (0.080%), neg=0, invalid=762
- 0143: dt=73.984000, rms=0.701 (0.074%), neg=0, invalid=762
- 0144: dt=73.984000, rms=0.701 (0.073%), neg=0, invalid=762
- 0145: dt=73.984000, rms=0.700 (0.069%), neg=0, invalid=762
- 0146: dt=73.984000, rms=0.700 (0.062%), neg=0, invalid=762
- 0147: dt=73.984000, rms=0.699 (0.065%), neg=0, invalid=762
- 0148: dt=73.984000, rms=0.699 (0.062%), neg=0, invalid=762
- 0149: dt=73.984000, rms=0.698 (0.062%), neg=0, invalid=762
- 0150: dt=73.984000, rms=0.698 (0.061%), neg=0, invalid=762
- 0151: dt=73.984000, rms=0.698 (0.062%), neg=0, invalid=762
- 0152: dt=73.984000, rms=0.697 (0.063%), neg=0, invalid=762
- 0153: dt=73.984000, rms=0.697 (0.065%), neg=0, invalid=762
- 0154: dt=73.984000, rms=0.696 (0.062%), neg=0, invalid=762
- 0155: dt=73.984000, rms=0.696 (0.058%), neg=0, invalid=762
- 0156: dt=73.984000, rms=0.695 (0.053%), neg=0, invalid=762
- 0157: dt=73.984000, rms=0.695 (0.048%), neg=0, invalid=762
- 0158: dt=73.984000, rms=0.695 (0.047%), neg=0, invalid=762
- 0159: dt=73.984000, rms=0.694 (0.049%), neg=0, invalid=762
- 0160: dt=73.984000, rms=0.694 (0.046%), neg=0, invalid=762
- 0161: dt=73.984000, rms=0.694 (0.041%), neg=0, invalid=762
- 0162: dt=73.984000, rms=0.694 (0.038%), neg=0, invalid=762
- 0163: dt=73.984000, rms=0.693 (0.038%), neg=0, invalid=762
- 0164: dt=73.984000, rms=0.693 (0.037%), neg=0, invalid=762
- 0165: dt=73.984000, rms=0.693 (0.035%), neg=0, invalid=762
- 0166: dt=73.984000, rms=0.693 (0.032%), neg=0, invalid=762
- 0167: dt=73.984000, rms=0.692 (0.029%), neg=0, invalid=762
- 0168: dt=73.984000, rms=0.692 (0.029%), neg=0, invalid=762
- 0169: dt=73.984000, rms=0.692 (0.031%), neg=0, invalid=762
- 0170: dt=73.984000, rms=0.692 (0.032%), neg=0, invalid=762
- 0171: dt=73.984000, rms=0.692 (0.031%), neg=0, invalid=762
- 0172: dt=73.984000, rms=0.691 (0.030%), neg=0, invalid=762
- 0173: dt=73.984000, rms=0.691 (0.029%), neg=0, invalid=762
- 0174: dt=73.984000, rms=0.691 (0.028%), neg=0, invalid=762
- 0175: dt=73.984000, rms=0.691 (0.028%), neg=0, invalid=762
- 0176: dt=73.984000, rms=0.691 (0.029%), neg=0, invalid=762
- 0177: dt=73.984000, rms=0.690 (0.031%), neg=0, invalid=762
- 0178: dt=73.984000, rms=0.690 (0.032%), neg=0, invalid=762
- 0179: dt=73.984000, rms=0.690 (0.030%), neg=0, invalid=762
- 0180: dt=73.984000, rms=0.690 (0.029%), neg=0, invalid=762
- 0181: dt=73.984000, rms=0.690 (0.028%), neg=0, invalid=762
- 0182: dt=73.984000, rms=0.689 (0.029%), neg=0, invalid=762
- 0183: dt=73.984000, rms=0.689 (0.030%), neg=0, invalid=762
- 0184: dt=73.984000, rms=0.689 (0.029%), neg=0, invalid=762
- 0185: dt=73.984000, rms=0.689 (0.026%), neg=0, invalid=762
- 0186: dt=73.984000, rms=0.689 (0.023%), neg=0, invalid=762
- 0187: dt=73.984000, rms=0.688 (0.022%), neg=0, invalid=762
- 0188: dt=8286.208000, rms=0.687 (0.214%), neg=0, invalid=762
- 0189: dt=55.488000, rms=0.687 (0.034%), neg=0, invalid=762
- 0190: dt=55.488000, rms=0.687 (0.002%), neg=0, invalid=762
- 0191: dt=55.488000, rms=0.687 (-0.016%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.688, neg=0, invalid=762
- 0192: dt=129.472000, rms=0.686 (0.234%), neg=0, invalid=762
- 0193: dt=369.920000, rms=0.685 (0.099%), neg=0, invalid=762
- 0194: dt=129.472000, rms=0.685 (0.084%), neg=0, invalid=762
- 0195: dt=129.472000, rms=0.685 (0.028%), neg=0, invalid=762
- 0196: dt=129.472000, rms=0.684 (0.031%), neg=0, invalid=762
- 0197: dt=129.472000, rms=0.684 (0.038%), neg=0, invalid=762
- 0198: dt=129.472000, rms=0.684 (0.052%), neg=0, invalid=762
- 0199: dt=129.472000, rms=0.683 (0.051%), neg=0, invalid=762
- 0200: dt=129.472000, rms=0.683 (0.061%), neg=0, invalid=762
- 0201: dt=129.472000, rms=0.683 (0.059%), neg=0, invalid=762
- 0202: dt=129.472000, rms=0.682 (0.053%), neg=0, invalid=762
- 0203: dt=129.472000, rms=0.682 (0.047%), neg=0, invalid=762
- 0204: dt=129.472000, rms=0.682 (0.038%), neg=0, invalid=762
- 0205: dt=129.472000, rms=0.681 (0.040%), neg=0, invalid=762
- 0206: dt=129.472000, rms=0.681 (0.038%), neg=0, invalid=762
- 0207: dt=129.472000, rms=0.681 (0.031%), neg=0, invalid=762
- 0208: dt=129.472000, rms=0.681 (0.024%), neg=0, invalid=762
- 0209: dt=129.472000, rms=0.680 (0.027%), neg=0, invalid=762
- 0210: dt=129.472000, rms=0.680 (0.028%), neg=0, invalid=762
- 0211: dt=129.472000, rms=0.680 (0.027%), neg=0, invalid=762
- 0212: dt=129.472000, rms=0.680 (0.025%), neg=0, invalid=762
- 0213: dt=129.472000, rms=0.680 (0.024%), neg=0, invalid=762
- 0214: dt=517.888000, rms=0.680 (0.014%), neg=0, invalid=762
- 0215: dt=517.888000, rms=0.680 (-0.246%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.682, neg=0, invalid=762
- 0216: dt=107.354839, rms=0.677 (0.662%), neg=0, invalid=762
- 0217: dt=116.822535, rms=0.672 (0.685%), neg=0, invalid=762
- 0218: dt=36.288000, rms=0.670 (0.411%), neg=0, invalid=762
- 0219: dt=497.664000, rms=0.661 (1.318%), neg=0, invalid=762
- 0220: dt=70.268041, rms=0.655 (0.904%), neg=0, invalid=762
- 0221: dt=36.288000, rms=0.653 (0.234%), neg=0, invalid=762
- 0222: dt=580.608000, rms=0.647 (1.005%), neg=0, invalid=762
- 0223: dt=69.041575, rms=0.642 (0.659%), neg=0, invalid=762
- 0224: dt=36.288000, rms=0.642 (0.064%), neg=0, invalid=762
- 0225: dt=580.608000, rms=0.639 (0.431%), neg=0, invalid=762
- 0226: dt=70.479574, rms=0.636 (0.451%), neg=0, invalid=762
- 0227: dt=36.288000, rms=0.636 (0.065%), neg=0, invalid=762
- 0228: dt=580.608000, rms=0.633 (0.424%), neg=0, invalid=762
- 0229: dt=65.647525, rms=0.631 (0.361%), neg=0, invalid=762
- 0230: dt=36.288000, rms=0.631 (0.029%), neg=0, invalid=762
- 0231: dt=36.288000, rms=0.631 (0.029%), neg=0, invalid=762
- 0232: dt=36.288000, rms=0.630 (0.053%), neg=0, invalid=762
- 0233: dt=36.288000, rms=0.630 (0.075%), neg=0, invalid=762
- 0234: dt=36.288000, rms=0.629 (0.095%), neg=0, invalid=762
- 0235: dt=36.288000, rms=0.628 (0.118%), neg=0, invalid=762
- 0236: dt=36.288000, rms=0.628 (0.132%), neg=0, invalid=762
- 0237: dt=36.288000, rms=0.627 (0.146%), neg=0, invalid=762
- 0238: dt=36.288000, rms=0.626 (0.155%), neg=0, invalid=762
- 0239: dt=36.288000, rms=0.625 (0.164%), neg=0, invalid=762
- 0240: dt=36.288000, rms=0.625 (0.030%), neg=0, invalid=762
- 0241: dt=36.288000, rms=0.624 (0.050%), neg=0, invalid=762
- 0242: dt=36.288000, rms=0.624 (0.062%), neg=0, invalid=762
- 0243: dt=36.288000, rms=0.624 (0.017%), neg=0, invalid=762
- 0244: dt=36.288000, rms=0.624 (0.020%), neg=0, invalid=762
- 0245: dt=1.134000, rms=0.624 (0.001%), neg=0, invalid=762
- 0246: dt=0.141750, rms=0.624 (0.000%), neg=0, invalid=762
- 0247: dt=0.035437, rms=0.624 (0.000%), neg=0, invalid=762
- 0248: dt=0.017719, rms=0.624 (0.000%), neg=0, invalid=762
- 0249: dt=0.000069, rms=0.624 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.625, neg=0, invalid=762
- 0250: dt=145.152000, rms=0.620 (0.751%), neg=0, invalid=762
- 0251: dt=36.288000, rms=0.619 (0.119%), neg=0, invalid=762
- 0252: dt=331.776000, rms=0.618 (0.239%), neg=0, invalid=762
- 0253: dt=36.288000, rms=0.617 (0.162%), neg=0, invalid=762
- 0254: dt=145.152000, rms=0.616 (0.125%), neg=0, invalid=762
- 0255: dt=82.944000, rms=0.616 (0.053%), neg=0, invalid=762
- 0256: dt=145.152000, rms=0.615 (0.106%), neg=0, invalid=762
- 0257: dt=36.288000, rms=0.615 (0.030%), neg=0, invalid=762
- 0258: dt=36.288000, rms=0.615 (0.022%), neg=0, invalid=762
- 0259: dt=36.288000, rms=0.615 (0.040%), neg=0, invalid=762
- 0260: dt=36.288000, rms=0.614 (0.059%), neg=0, invalid=762
- 0261: dt=36.288000, rms=0.614 (0.074%), neg=0, invalid=762
- 0262: dt=36.288000, rms=0.613 (0.086%), neg=0, invalid=762
- 0263: dt=36.288000, rms=0.613 (0.091%), neg=0, invalid=762
- 0264: dt=36.288000, rms=0.612 (0.094%), neg=0, invalid=762
- 0265: dt=36.288000, rms=0.612 (0.094%), neg=0, invalid=762
- 0266: dt=36.288000, rms=0.611 (0.095%), neg=0, invalid=762
- 0267: dt=36.288000, rms=0.610 (0.099%), neg=0, invalid=762
- 0268: dt=36.288000, rms=0.610 (0.016%), neg=0, invalid=762
- 0269: dt=36.288000, rms=0.610 (0.027%), neg=0, invalid=762
- 0270: dt=36.288000, rms=0.610 (0.038%), neg=0, invalid=762
- 0271: dt=36.288000, rms=0.610 (0.048%), neg=0, invalid=762
- 0272: dt=36.288000, rms=0.609 (0.053%), neg=0, invalid=762
- 0273: dt=36.288000, rms=0.609 (0.061%), neg=0, invalid=762
- 0274: dt=36.288000, rms=0.608 (0.066%), neg=0, invalid=762
- 0275: dt=36.288000, rms=0.608 (0.068%), neg=0, invalid=762
- 0276: dt=36.288000, rms=0.608 (0.072%), neg=0, invalid=762
- 0277: dt=36.288000, rms=0.607 (0.078%), neg=0, invalid=762
- 0278: dt=36.288000, rms=0.607 (0.080%), neg=0, invalid=762
- 0279: dt=36.288000, rms=0.606 (0.082%), neg=0, invalid=762
- 0280: dt=36.288000, rms=0.606 (0.010%), neg=0, invalid=762
- 0281: dt=18.144000, rms=0.606 (0.005%), neg=0, invalid=762
- 0282: dt=2.268000, rms=0.606 (0.001%), neg=0, invalid=762
- 0283: dt=0.283500, rms=0.606 (0.000%), neg=0, invalid=762
- 0284: dt=0.141750, rms=0.606 (0.000%), neg=0, invalid=762
- 0285: dt=0.070875, rms=0.606 (0.000%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.614, neg=0, invalid=762
- 0286: dt=87.183673, rms=0.602 (1.826%), neg=0, invalid=762
- 0287: dt=2.800000, rms=0.602 (0.154%), neg=0, invalid=762
- 0288: dt=2.800000, rms=0.601 (0.145%), neg=0, invalid=762
- 0289: dt=0.010937, rms=0.601 (0.002%), neg=0, invalid=762
- 0290: dt=0.010937, rms=0.601 (0.001%), neg=0, invalid=762
- 0291: dt=0.002734, rms=0.601 (0.000%), neg=0, invalid=762
- 0292: dt=0.001367, rms=0.601 (0.000%), neg=0, invalid=762
- 0293: dt=0.000684, rms=0.601 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.602, neg=0, invalid=762
- 0294: dt=44.800000, rms=0.589 (2.188%), neg=0, invalid=762
- 0295: dt=58.140845, rms=0.584 (0.849%), neg=0, invalid=762
- 0296: dt=31.888889, rms=0.579 (0.714%), neg=0, invalid=762
- 0297: dt=38.400000, rms=0.577 (0.485%), neg=0, invalid=762
- 0298: dt=32.000000, rms=0.574 (0.415%), neg=0, invalid=762
- 0299: dt=32.000000, rms=0.572 (0.363%), neg=0, invalid=762
- 0300: dt=11.200000, rms=0.571 (0.196%), neg=0, invalid=762
- 0301: dt=11.200000, rms=0.570 (0.125%), neg=0, invalid=762
- 0302: dt=2.800000, rms=0.570 (0.031%), neg=0, invalid=762
- 0303: dt=2.800000, rms=0.570 (0.026%), neg=0, invalid=762
- 0304: dt=1.400000, rms=0.570 (0.013%), neg=0, invalid=762
- 0305: dt=0.700000, rms=0.570 (0.006%), neg=0, invalid=762
- 0306: dt=0.043750, rms=0.570 (0.000%), neg=0, invalid=762
- 0307: dt=0.005469, rms=0.570 (0.000%), neg=0, invalid=762
- 0308: dt=0.000684, rms=0.570 (0.000%), neg=0, invalid=762
- 0309: dt=0.000342, rms=0.570 (0.000%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.589, neg=0, invalid=762
- 0310: dt=7.144033, rms=0.586 (0.455%), neg=0, invalid=762
- 0311: dt=12.571429, rms=0.584 (0.261%), neg=0, invalid=762
- 0312: dt=16.128000, rms=0.582 (0.459%), neg=0, invalid=762
- 0313: dt=4.032000, rms=0.581 (0.088%), neg=0, invalid=762
- 0314: dt=1.008000, rms=0.581 (0.018%), neg=0, invalid=762
- 0315: dt=0.252000, rms=0.581 (0.005%), neg=0, invalid=762
- 0316: dt=0.063000, rms=0.581 (0.001%), neg=0, invalid=762
- 0317: dt=0.003938, rms=0.581 (0.000%), neg=0, invalid=762
- 0318: dt=0.002813, rms=0.581 (0.000%), neg=0, invalid=762
- 0319: dt=0.000246, rms=0.581 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.582, neg=0, invalid=762
- 0320: dt=11.520000, rms=0.580 (0.368%), neg=0, invalid=762
- 0321: dt=16.128000, rms=0.579 (0.090%), neg=0, invalid=762
- 0322: dt=16.128000, rms=0.578 (0.211%), neg=0, invalid=762
- 0323: dt=10.514286, rms=0.578 (0.042%), neg=0, invalid=762
- 0324: dt=10.514286, rms=0.577 (0.137%), neg=0, invalid=762
- 0325: dt=10.514286, rms=0.577 (0.060%), neg=0, invalid=762
- 0326: dt=10.514286, rms=0.576 (0.159%), neg=0, invalid=762
- 0327: dt=10.514286, rms=0.575 (0.084%), neg=0, invalid=762
- 0328: dt=10.514286, rms=0.575 (0.128%), neg=0, invalid=762
- 0329: dt=10.514286, rms=0.574 (0.034%), neg=0, invalid=762
- 0330: dt=10.514286, rms=0.574 (0.110%), neg=0, invalid=762
- 0331: dt=10.514286, rms=0.573 (0.149%), neg=0, invalid=762
- 0332: dt=10.514286, rms=0.572 (0.162%), neg=0, invalid=762
- 0333: dt=10.514286, rms=0.571 (0.168%), neg=0, invalid=762
- 0334: dt=10.514286, rms=0.570 (0.189%), neg=0, invalid=762
- 0335: dt=10.514286, rms=0.569 (0.155%), neg=0, invalid=762
- 0336: dt=10.514286, rms=0.568 (0.131%), neg=0, invalid=762
- 0337: dt=10.514286, rms=0.568 (0.015%), neg=0, invalid=762
- 0338: dt=10.514286, rms=0.568 (-0.012%), neg=0, invalid=762
- 0339: dt=4.032000, rms=0.568 (0.005%), neg=0, invalid=762
- 0340: dt=8.000000, rms=0.568 (0.007%), neg=0, invalid=762
- 0341: dt=16.128000, rms=0.568 (0.009%), neg=0, invalid=762
- 0342: dt=3.456000, rms=0.568 (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=0.587, neg=0, invalid=762
- 0343: dt=0.000000, rms=0.586 (0.164%), neg=0, invalid=762
- 0344: dt=0.000000, rms=0.586 (0.000%), neg=0, invalid=762
- 0345: dt=0.100000, rms=0.586 (-0.180%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.587, neg=0, invalid=762
- 0346: dt=0.000000, rms=0.586 (0.164%), neg=0, invalid=762
- 0347: dt=0.000000, rms=0.586 (0.000%), neg=0, invalid=762
- 0348: dt=0.100000, rms=0.586 (-0.164%), 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=0.557, neg=0, invalid=762
- 0349: dt=0.384000, rms=0.540 (2.990%), neg=0, invalid=762
- 0350: dt=0.448000, rms=0.534 (1.223%), neg=0, invalid=762
- 0351: dt=0.448000, rms=0.531 (0.516%), neg=0, invalid=762
- 0352: dt=0.448000, rms=0.529 (0.320%), neg=0, invalid=762
- 0353: dt=0.448000, rms=0.528 (0.246%), neg=0, invalid=762
- 0354: dt=0.448000, rms=0.527 (0.170%), neg=0, invalid=762
- 0355: dt=0.448000, rms=0.526 (0.155%), neg=0, invalid=762
- 0356: dt=0.448000, rms=0.526 (0.101%), neg=0, invalid=762
- 0357: dt=0.448000, rms=0.525 (0.111%), neg=0, invalid=762
- 0358: dt=0.448000, rms=0.525 (0.068%), neg=0, invalid=762
- 0359: dt=0.448000, rms=0.524 (0.084%), neg=0, invalid=762
- 0360: dt=0.448000, rms=0.524 (0.045%), neg=0, invalid=762
- 0361: dt=0.448000, rms=0.524 (0.067%), neg=0, invalid=762
- 0362: dt=0.448000, rms=0.523 (0.091%), neg=0, invalid=762
- 0363: dt=0.224000, rms=0.523 (0.019%), neg=0, invalid=762
- 0364: dt=0.224000, rms=0.523 (0.045%), neg=0, invalid=762
- 0365: dt=0.224000, rms=0.523 (0.020%), neg=0, invalid=762
- 0366: dt=0.224000, rms=0.523 (0.028%), neg=0, invalid=762
- 0367: dt=0.224000, rms=0.523 (0.035%), neg=0, invalid=762
- 0368: dt=0.224000, rms=0.522 (0.049%), neg=0, invalid=762
- 0369: dt=0.224000, rms=0.522 (0.056%), neg=0, invalid=762
- 0370: dt=0.224000, rms=0.522 (0.007%), neg=0, invalid=762
- 0371: dt=0.224000, rms=0.522 (0.012%), neg=0, invalid=762
- 0372: dt=0.224000, rms=0.522 (0.020%), neg=0, invalid=762
- 0373: dt=0.224000, rms=0.522 (0.022%), neg=0, invalid=762
- 0374: dt=0.224000, rms=0.522 (0.027%), neg=0, invalid=762
- 0375: dt=0.224000, rms=0.521 (0.026%), neg=0, invalid=762
- 0376: dt=0.224000, rms=0.521 (0.028%), neg=0, invalid=762
- 0377: dt=0.224000, rms=0.521 (0.024%), neg=0, invalid=762
- 0378: dt=0.224000, rms=0.521 (0.024%), neg=0, invalid=762
- 0379: dt=0.320000, rms=0.521 (0.003%), neg=0, invalid=762
- 0380: dt=0.320000, rms=0.521 (-0.003%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.522, neg=0, invalid=762
- 0381: dt=0.384000, rms=0.516 (1.232%), neg=0, invalid=762
- 0382: dt=0.384000, rms=0.515 (0.214%), neg=0, invalid=762
- 0383: dt=0.384000, rms=0.514 (0.043%), neg=0, invalid=762
- 0384: dt=0.384000, rms=0.514 (0.007%), neg=0, invalid=762
- 0385: dt=0.384000, rms=0.514 (-0.001%), 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=0.513, neg=0, invalid=762
- 0386: dt=0.000000, rms=0.512 (0.219%), neg=0, invalid=762
- 0387: dt=0.000000, rms=0.512 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.513, neg=0, invalid=762
- 0388: dt=221.952000, rms=0.511 (0.291%), neg=0, invalid=762
- 0389: dt=129.472000, rms=0.511 (0.021%), neg=0, invalid=762
- 0390: dt=129.472000, rms=0.511 (0.021%), neg=0, invalid=762
- 0391: dt=129.472000, rms=0.511 (0.035%), neg=0, invalid=762
- 0392: dt=129.472000, rms=0.511 (0.027%), neg=0, invalid=762
- 0393: dt=129.472000, rms=0.510 (0.030%), neg=0, invalid=762
- 0394: dt=129.472000, rms=0.510 (0.021%), neg=0, invalid=762
- 0395: dt=92.480000, rms=0.510 (0.018%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.511, neg=0, invalid=762
- 0396: dt=15.552000, rms=0.510 (0.248%), neg=0, invalid=762
- 0397: dt=9.072000, rms=0.510 (0.008%), neg=0, invalid=762
- 0398: dt=9.072000, rms=0.510 (0.002%), neg=0, invalid=762
- 0399: dt=9.072000, rms=0.510 (-0.007%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.511, neg=0, invalid=762
- 0400: dt=145.152000, rms=0.508 (0.671%), neg=0, invalid=762
- 0401: dt=25.920000, rms=0.507 (0.141%), neg=0, invalid=762
- 0402: dt=25.920000, rms=0.507 (0.047%), neg=0, invalid=762
- 0403: dt=25.920000, rms=0.507 (0.050%), neg=0, invalid=762
- 0404: dt=25.920000, rms=0.506 (0.062%), neg=0, invalid=762
- 0405: dt=25.920000, rms=0.506 (0.095%), neg=0, invalid=762
- 0406: dt=25.920000, rms=0.505 (0.114%), neg=0, invalid=762
- 0407: dt=25.920000, rms=0.505 (0.111%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0408: dt=25.920000, rms=0.504 (0.096%), neg=0, invalid=762
- 0409: dt=36.288000, rms=0.504 (0.012%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.505, neg=0, invalid=762
- iter 0, gcam->neg = 6
- after 1 iterations, nbhd size=0, neg = 0
- 0410: dt=38.020906, rms=0.501 (0.801%), neg=0, invalid=762
- iter 0, gcam->neg = 33
- after 10 iterations, nbhd size=1, neg = 0
- 0411: dt=82.800000, rms=0.498 (0.676%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 2 iterations, nbhd size=0, neg = 0
- 0412: dt=24.356688, rms=0.497 (0.285%), neg=0, invalid=762
- iter 0, gcam->neg = 16
- after 12 iterations, nbhd size=1, neg = 0
- 0413: dt=38.400000, rms=0.495 (0.234%), neg=0, invalid=762
- iter 0, gcam->neg = 6
- after 1 iterations, nbhd size=0, neg = 0
- 0414: dt=38.400000, rms=0.495 (-0.006%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.497, neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0415: dt=38.400000, rms=0.490 (1.342%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0416: dt=21.960784, rms=0.488 (0.553%), neg=0, invalid=762
- 0417: dt=38.400000, rms=0.486 (0.310%), neg=0, invalid=762
- 0418: dt=11.200000, rms=0.485 (0.197%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0419: dt=11.200000, rms=0.485 (0.089%), neg=0, invalid=762
- 0420: dt=11.200000, rms=0.484 (0.117%), neg=0, invalid=762
- 0421: dt=11.200000, rms=0.483 (0.169%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0422: dt=11.200000, rms=0.482 (0.180%), neg=0, invalid=762
- 0423: dt=11.200000, rms=0.481 (0.190%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 3 iterations, nbhd size=0, neg = 0
- 0424: dt=11.200000, rms=0.481 (0.193%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0425: dt=11.200000, rms=0.480 (0.180%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 3 iterations, nbhd size=0, neg = 0
- 0426: dt=11.200000, rms=0.479 (0.170%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0427: dt=11.200000, rms=0.478 (0.176%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0428: dt=11.200000, rms=0.477 (0.164%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 2 iterations, nbhd size=0, neg = 0
- 0429: dt=11.200000, rms=0.476 (0.162%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 2 iterations, nbhd size=0, neg = 0
- 0430: dt=11.200000, rms=0.476 (0.151%), neg=0, invalid=762
- 0431: dt=11.200000, rms=0.475 (0.137%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0432: dt=11.200000, rms=0.474 (0.137%), neg=0, invalid=762
- 0433: dt=11.200000, rms=0.474 (0.117%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 9 iterations, nbhd size=1, neg = 0
- 0434: dt=11.200000, rms=0.473 (0.103%), neg=0, invalid=762
- 0435: dt=38.400000, rms=0.473 (0.024%), neg=0, invalid=762
- 0436: dt=38.400000, rms=0.473 (-0.056%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.480, neg=0, invalid=762
- 0437: dt=1.008000, rms=0.478 (0.260%), neg=0, invalid=762
- 0438: dt=0.252000, rms=0.478 (-0.002%), neg=0, invalid=762
- 0439: dt=0.252000, rms=0.478 (0.000%), neg=0, invalid=762
- 0440: dt=0.252000, rms=0.478 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.480, neg=0, invalid=762
- 0441: dt=0.864000, rms=0.478 (0.252%), neg=0, invalid=762
- 0442: dt=0.432000, rms=0.478 (0.001%), neg=0, invalid=762
- 0443: dt=0.432000, rms=0.478 (-0.001%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.489, neg=0, invalid=762
- 0444: dt=0.448000, rms=0.488 (0.289%), neg=0, invalid=762
- 0445: dt=0.320000, rms=0.488 (0.013%), neg=0, invalid=762
- 0446: dt=0.320000, rms=0.488 (-0.006%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.489, neg=0, invalid=762
- 0447: dt=1.280000, rms=0.487 (0.402%), neg=0, invalid=762
- 0448: dt=0.448000, rms=0.487 (0.017%), neg=0, invalid=762
- 0449: dt=0.448000, rms=0.487 (0.007%), neg=0, invalid=762
- 0450: dt=0.448000, rms=0.487 (-0.028%), 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=0.478, neg=0, invalid=762
- iter 0, gcam->neg = 1463
- after 16 iterations, nbhd size=1, neg = 0
- 0451: dt=2.219166, rms=0.442 (7.514%), neg=0, invalid=762
- 0452: dt=0.080000, rms=0.442 (0.051%), neg=0, invalid=762
- 0453: dt=0.080000, rms=0.442 (-0.060%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.443, neg=0, invalid=762
- 0454: dt=0.080000, rms=0.442 (0.353%), neg=0, invalid=762
- 0455: dt=0.003000, rms=0.441 (0.003%), neg=0, invalid=762
- 0456: dt=0.003000, rms=0.441 (-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=0.427, neg=0, invalid=762
- 0457: dt=0.000000, 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
- 0458: dt=-0.009615, rms=0.427 (0.000%), neg=0, invalid=762
- 0459: dt=0.000000, rms=0.427 (0.000%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.427, neg=0, invalid=762
- 0460: dt=0.001420, rms=0.427 (0.000%), neg=0, invalid=762
- 0461: dt=0.000000, 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
- 0462: dt=25.920000, rms=0.427 (0.019%), neg=0, invalid=762
- 0463: dt=36.288000, rms=0.427 (0.008%), neg=0, invalid=762
- 0464: dt=36.288000, rms=0.427 (0.009%), neg=0, invalid=762
- 0465: dt=36.288000, rms=0.427 (0.006%), neg=0, invalid=762
- 0466: dt=36.288000, rms=0.427 (-0.005%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.428, neg=0, invalid=762
- 0467: dt=11.200000, rms=0.427 (0.068%), neg=0, invalid=762
- 0468: dt=2.800000, rms=0.427 (0.004%), neg=0, invalid=762
- 0469: dt=2.800000, rms=0.427 (0.000%), neg=0, invalid=762
- 0470: dt=2.800000, rms=0.427 (-0.012%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.427, neg=0, invalid=762
- 0471: dt=78.800000, rms=0.424 (0.734%), neg=0, invalid=762
- 0472: dt=24.615385, rms=0.423 (0.297%), neg=0, invalid=762
- 0473: dt=44.800000, rms=0.422 (0.130%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0474: dt=44.800000, rms=0.422 (0.059%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0475: dt=44.800000, rms=0.421 (0.300%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 8 iterations, nbhd size=1, neg = 0
- 0476: dt=44.800000, rms=0.420 (0.214%), neg=0, invalid=762
- iter 0, gcam->neg = 10
- after 2 iterations, nbhd size=0, neg = 0
- 0477: dt=44.800000, rms=0.419 (0.202%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 8 iterations, nbhd size=1, neg = 0
- 0478: dt=44.800000, rms=0.418 (0.248%), neg=0, invalid=762
- iter 0, gcam->neg = 14
- after 13 iterations, nbhd size=1, neg = 0
- 0479: dt=44.800000, rms=0.417 (0.162%), neg=0, invalid=762
- iter 0, gcam->neg = 20
- after 14 iterations, nbhd size=1, neg = 0
- 0480: dt=44.800000, rms=0.417 (0.077%), neg=0, invalid=762
- iter 0, gcam->neg = 23
- after 15 iterations, nbhd size=1, neg = 0
- 0481: dt=44.800000, rms=0.416 (0.148%), neg=0, invalid=762
- iter 0, gcam->neg = 15
- after 2 iterations, nbhd size=0, neg = 0
- 0482: dt=44.800000, rms=0.416 (0.124%), neg=0, invalid=762
- iter 0, gcam->neg = 22
- after 10 iterations, nbhd size=1, neg = 0
- 0483: dt=44.800000, rms=0.416 (0.025%), neg=0, invalid=762
- 0484: dt=11.200000, rms=0.416 (0.051%), neg=0, invalid=762
- 0485: dt=38.400000, rms=0.415 (0.031%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0486: dt=38.400000, rms=0.415 (0.010%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 1 iterations, nbhd size=0, neg = 0
- 0487: dt=38.400000, rms=0.415 (0.035%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0488: dt=38.400000, rms=0.415 (0.011%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0489: dt=38.400000, rms=0.415 (0.022%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0490: dt=38.400000, rms=0.415 (0.010%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.420, neg=0, invalid=762
- 0491: dt=0.000211, rms=0.420 (0.000%), neg=0, invalid=762
- 0492: dt=0.000000, rms=0.420 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.420, neg=0, invalid=762
- 0493: dt=2.304000, rms=0.420 (0.010%), neg=0, invalid=762
- 0494: dt=1.008000, rms=0.420 (0.002%), neg=0, invalid=762
- 0495: dt=1.008000, rms=0.420 (0.001%), neg=0, invalid=762
- 0496: dt=1.008000, rms=0.420 (-0.004%), 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
- 0497: 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
- 0498: 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=0.414, neg=0, invalid=762
- iter 0, gcam->neg = 830
- after 19 iterations, nbhd size=1, neg = 0
- 0499: dt=1.195958, rms=0.403 (2.471%), neg=0, invalid=762
- 0500: dt=0.000023, rms=0.403 (0.000%), neg=0, invalid=762
- 0501: dt=0.000023, rms=0.403 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.403, neg=0, invalid=762
- 0502: dt=0.112000, rms=0.403 (0.062%), neg=0, invalid=762
- 0503: dt=0.080000, rms=0.403 (0.016%), neg=0, invalid=762
- 0504: dt=0.080000, rms=0.403 (0.011%), neg=0, invalid=762
- 0505: dt=0.080000, rms=0.403 (-0.019%), neg=0, invalid=762
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- mri_ca_register took 2 hours, 38 minutes and 21 seconds.
- mri_ca_register utimesec 10647.572322
- mri_ca_register stimesec 9.580543
- mri_ca_register ru_maxrss 1337888
- mri_ca_register ru_ixrss 0
- mri_ca_register ru_idrss 0
- mri_ca_register ru_isrss 0
- mri_ca_register ru_minflt 5317668
- mri_ca_register ru_majflt 0
- mri_ca_register ru_nswap 0
- mri_ca_register ru_inblock 0
- mri_ca_register ru_oublock 62944
- mri_ca_register ru_msgsnd 0
- mri_ca_register ru_msgrcv 0
- mri_ca_register ru_nsignals 0
- mri_ca_register ru_nvcsw 6758
- mri_ca_register ru_nivcsw 15682
- FSRUNTIME@ mri_ca_register 2.6391 hours 2 threads
- #--------------------------------------
- #@# SubCort Seg Sun Oct 8 03:01:29 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-904
- 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-6.0.0/0051311/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 6.09
- 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 = 0.14817 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (1828 voxels, overlap=0.015)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1828 voxels, peak = 7), gca=8.0
- gca peak = 0.17677 (13)
- mri peak = 0.14591 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (1289 voxels, overlap=0.424)
- Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (1289 voxels, peak = 7), gca=6.7
- gca peak = 0.28129 (95)
- mri peak = 0.08311 (92)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (561 voxels, overlap=1.016)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (561 voxels, peak = 91), gca=90.7
- gca peak = 0.16930 (96)
- mri peak = 0.08997 (92)
- Left_Pallidum (13): linear fit = 0.95 x + 0.0 (577 voxels, overlap=0.978)
- Left_Pallidum (13): linear fit = 0.95 x + 0.0 (577 voxels, peak = 92), gca=91.7
- gca peak = 0.24553 (55)
- mri peak = 0.08241 (61)
- Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (517 voxels, overlap=1.006)
- Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (517 voxels, peak = 56), gca=56.4
- gca peak = 0.30264 (59)
- mri peak = 0.10548 (54)
- Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (551 voxels, overlap=1.009)
- Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (551 voxels, peak = 55), gca=55.2
- gca peak = 0.07580 (103)
- mri peak = 0.08118 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (31077 voxels, overlap=0.597)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (31077 voxels, peak = 108), gca=107.6
- gca peak = 0.07714 (104)
- mri peak = 0.07867 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (30677 voxels, overlap=0.612)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (30677 voxels, peak = 109), gca=108.7
- gca peak = 0.09712 (58)
- mri peak = 0.06003 (50)
- Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (17820 voxels, overlap=0.456)
- Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (17820 voxels, peak = 50), gca=49.6
- gca peak = 0.11620 (58)
- mri peak = 0.05601 (52)
- Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (16657 voxels, overlap=0.679)
- Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (16657 voxels, peak = 52), gca=51.9
- gca peak = 0.30970 (66)
- mri peak = 0.10903 (67)
- Right_Caudate (50): linear fit = 0.95 x + 0.0 (960 voxels, overlap=1.010)
- Right_Caudate (50): linear fit = 0.95 x + 0.0 (960 voxels, peak = 63), gca=63.0
- gca peak = 0.15280 (69)
- mri peak = 0.09378 (63)
- Left_Caudate (11): linear fit = 0.88 x + 0.0 (979 voxels, overlap=0.343)
- Left_Caudate (11): linear fit = 0.88 x + 0.0 (979 voxels, peak = 61), gca=61.1
- gca peak = 0.13902 (56)
- mri peak = 0.05154 (50)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (11705 voxels, overlap=0.987)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (11705 voxels, peak = 53), gca=52.9
- gca peak = 0.14777 (55)
- mri peak = 0.05120 (53)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (13724 voxels, overlap=0.988)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (13724 voxels, peak = 53), gca=53.1
- gca peak = 0.16765 (84)
- mri peak = 0.09098 (88)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4588 voxels, overlap=0.810)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4588 voxels, peak = 89), gca=89.5
- gca peak = 0.18739 (84)
- mri peak = 0.08287 (86)
- Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (4881 voxels, overlap=0.911)
- Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (4881 voxels, peak = 88), gca=87.8
- gca peak = 0.29869 (57)
- mri peak = 0.09573 (56)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (426 voxels, overlap=1.020)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (426 voxels, peak = 53), gca=52.7
- gca peak = 0.33601 (57)
- mri peak = 0.12093 (59)
- Right_Amygdala (54): linear fit = 1.04 x + 0.0 (223 voxels, overlap=1.025)
- Right_Amygdala (54): linear fit = 1.04 x + 0.0 (223 voxels, peak = 60), gca=59.6
- gca peak = 0.11131 (90)
- mri peak = 0.07111 (82)
- Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3991 voxels, overlap=0.915)
- Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3991 voxels, peak = 86), gca=85.9
- gca peak = 0.11793 (83)
- mri peak = 0.06214 (80)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4116 voxels, overlap=0.978)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4116 voxels, peak = 83), gca=82.6
- gca peak = 0.08324 (81)
- mri peak = 0.07414 (75)
- Left_Putamen (12): linear fit = 0.93 x + 0.0 (2162 voxels, overlap=0.654)
- Left_Putamen (12): linear fit = 0.93 x + 0.0 (2162 voxels, peak = 75), gca=74.9
- gca peak = 0.10360 (77)
- mri peak = 0.07462 (74)
- Right_Putamen (51): linear fit = 0.94 x + 0.0 (2329 voxels, overlap=0.771)
- Right_Putamen (51): linear fit = 0.94 x + 0.0 (2329 voxels, peak = 72), gca=72.0
- gca peak = 0.08424 (78)
- mri peak = 0.09689 (83)
- Brain_Stem (16): linear fit = 1.05 x + 0.0 (9447 voxels, overlap=0.476)
- Brain_Stem (16): linear fit = 1.05 x + 0.0 (9447 voxels, peak = 82), gca=82.3
- gca peak = 0.12631 (89)
- mri peak = 0.06168 (96)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1008 voxels, overlap=0.814)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1008 voxels, peak = 97), gca=96.6
- gca peak = 0.14500 (87)
- mri peak = 0.07095 (91)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1092 voxels, overlap=0.916)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1092 voxels, peak = 90), gca=90.0
- gca peak = 0.14975 (24)
- mri peak = 0.12230 ( 9)
- Third_Ventricle (14): linear fit = 0.38 x + 0.0 (139 voxels, overlap=0.048)
- Third_Ventricle (14): linear fit = 0.38 x + 0.0 (139 voxels, peak = 9), gca=9.0
- gca peak = 0.19357 (14)
- mri peak = 0.13376 (14)
- Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (157 voxels, overlap=0.486)
- Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (157 voxels, peak = 10), gca=9.9
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.16825 (27)
- gca peak Left_Thalamus = 1.00000 (94)
- gca peak Third_Ventricle = 0.14975 (24)
- gca peak CSF = 0.23379 (36)
- gca peak Left_Accumbens_area = 0.70037 (62)
- gca peak Left_undetermined = 1.00000 (26)
- gca peak Left_vessel = 0.75997 (52)
- gca peak Left_choroid_plexus = 0.12089 (35)
- gca peak Right_Inf_Lat_Vent = 0.24655 (23)
- gca peak Right_Accumbens_area = 0.45042 (65)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14516 (37)
- gca peak Fifth_Ventricle = 0.65475 (32)
- gca peak WM_hypointensities = 0.07854 (76)
- gca peak non_WM_hypointensities = 0.08491 (43)
- gca peak Optic_Chiasm = 0.71127 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.95 x + 0.0
- estimating mean wm scale to be 1.04 x + 0.0
- estimating mean csf scale to be 0.54 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.30836 ( 7)
- mri peak = 0.14817 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (1828 voxels, overlap=0.999)
- Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (1828 voxels, peak = 6), gca=6.3
- gca peak = 0.29638 ( 7)
- mri peak = 0.14591 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (1289 voxels, overlap=0.965)
- Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (1289 voxels, peak = 8), gca=7.5
- gca peak = 0.25679 (90)
- mri peak = 0.08311 (92)
- Right_Pallidum (52): linear fit = 1.01 x + 0.0 (561 voxels, overlap=1.008)
- Right_Pallidum (52): linear fit = 1.01 x + 0.0 (561 voxels, peak = 91), gca=91.3
- gca peak = 0.18583 (92)
- mri peak = 0.08997 (92)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (577 voxels, overlap=1.006)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (577 voxels, peak = 92), gca=91.5
- gca peak = 0.29045 (57)
- mri peak = 0.08241 (61)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (517 voxels, overlap=1.005)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (517 voxels, peak = 57), gca=57.0
- gca peak = 0.27564 (53)
- mri peak = 0.10548 (54)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (551 voxels, overlap=1.007)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (551 voxels, peak = 53), gca=53.0
- gca peak = 0.07601 (108)
- mri peak = 0.08118 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31077 voxels, overlap=0.784)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31077 voxels, peak = 107), gca=107.5
- gca peak = 0.07787 (109)
- mri peak = 0.07867 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30677 voxels, overlap=0.788)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30677 voxels, peak = 108), gca=108.5
- gca peak = 0.11313 (50)
- mri peak = 0.06003 (50)
- Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (17820 voxels, overlap=0.998)
- Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (17820 voxels, peak = 49), gca=48.8
- gca peak = 0.12882 (52)
- mri peak = 0.05601 (52)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (16657 voxels, overlap=0.999)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (16657 voxels, peak = 51), gca=51.2
- gca peak = 0.34160 (63)
- mri peak = 0.10903 (67)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (960 voxels, overlap=1.007)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (960 voxels, peak = 63), gca=63.0
- gca peak = 0.13671 (61)
- mri peak = 0.09378 (63)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (979 voxels, overlap=0.972)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (979 voxels, peak = 61), gca=61.0
- gca peak = 0.14834 (52)
- mri peak = 0.05154 (50)
- Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (11705 voxels, overlap=1.000)
- Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (11705 voxels, peak = 51), gca=50.7
- gca peak = 0.15622 (53)
- mri peak = 0.05120 (53)
- Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (13724 voxels, overlap=1.000)
- Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (13724 voxels, peak = 53), gca=53.0
- gca peak = 0.15873 (90)
- mri peak = 0.09098 (88)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4588 voxels, overlap=0.975)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4588 voxels, peak = 90), gca=89.6
- gca peak = 0.16966 (88)
- mri peak = 0.08287 (86)
- Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4881 voxels, overlap=0.985)
- Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4881 voxels, peak = 87), gca=86.7
- gca peak = 0.35242 (54)
- mri peak = 0.09573 (56)
- Left_Amygdala (18): linear fit = 1.01 x + 0.0 (426 voxels, overlap=1.024)
- Left_Amygdala (18): linear fit = 1.01 x + 0.0 (426 voxels, peak = 55), gca=54.8
- gca peak = 0.28990 (60)
- mri peak = 0.12093 (59)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (223 voxels, overlap=1.014)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (223 voxels, peak = 60), gca=60.0
- gca peak = 0.11465 (86)
- mri peak = 0.07111 (82)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3991 voxels, overlap=0.957)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3991 voxels, peak = 86), gca=85.6
- gca peak = 0.09952 (80)
- mri peak = 0.06214 (80)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4116 voxels, overlap=0.972)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4116 voxels, peak = 81), gca=81.2
- gca peak = 0.09421 (70)
- mri peak = 0.07414 (75)
- Left_Putamen (12): linear fit = 0.99 x + 0.0 (2162 voxels, overlap=0.999)
- Left_Putamen (12): linear fit = 0.99 x + 0.0 (2162 voxels, peak = 69), gca=69.0
- gca peak = 0.09691 (72)
- mri peak = 0.07462 (74)
- Right_Putamen (51): linear fit = 1.01 x + 0.0 (2329 voxels, overlap=0.958)
- Right_Putamen (51): linear fit = 1.01 x + 0.0 (2329 voxels, peak = 73), gca=73.1
- gca peak = 0.07599 (83)
- mri peak = 0.09689 (83)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (9447 voxels, overlap=0.714)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (9447 voxels, peak = 83), gca=82.6
- gca peak = 0.10974 (96)
- mri peak = 0.06168 (96)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1008 voxels, overlap=0.911)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1008 voxels, peak = 96), gca=95.5
- gca peak = 0.15222 (88)
- mri peak = 0.07095 (91)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1092 voxels, overlap=0.952)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1092 voxels, peak = 88), gca=87.6
- gca peak = 0.28896 (14)
- mri peak = 0.12230 ( 9)
- Third_Ventricle (14): linear fit = 0.86 x + 0.0 (139 voxels, overlap=0.962)
- Third_Ventricle (14): linear fit = 0.86 x + 0.0 (139 voxels, peak = 12), gca=12.0
- gca peak = 0.26059 (10)
- mri peak = 0.13376 (14)
- Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (157 voxels, overlap=0.834)
- Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (157 voxels, peak = 10), gca=10.4
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.17854 (25)
- gca peak Left_Thalamus = 1.00000 (89)
- gca peak CSF = 0.26466 (20)
- gca peak Left_Accumbens_area = 0.81130 (55)
- gca peak Left_undetermined = 1.00000 (26)
- gca peak Left_vessel = 0.70074 (52)
- gca peak Left_choroid_plexus = 0.12089 (35)
- gca peak Right_Inf_Lat_Vent = 0.18913 (24)
- gca peak Right_Accumbens_area = 0.34583 (62)
- gca peak Right_vessel = 0.81794 (52)
- gca peak Right_choroid_plexus = 0.14516 (37)
- gca peak Fifth_Ventricle = 0.89470 (17)
- gca peak WM_hypointensities = 0.06869 (81)
- gca peak non_WM_hypointensities = 0.08561 (45)
- gca peak Optic_Chiasm = 0.70906 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.00 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.97 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
- 60115 voxels changed in iteration 0 of unlikely voxel relabeling
- 172 voxels changed in iteration 1 of unlikely voxel relabeling
- 15 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 22493 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels)
- 527 hippocampal voxels changed.
- 0 amygdala voxels changed.
- pass 1: 64681 changed. image ll: -2.105, PF=0.500
- pass 2: 18839 changed. image ll: -2.105, PF=0.500
- pass 3: 5774 changed.
- pass 4: 2131 changed.
- 33775 voxels changed in iteration 0 of unlikely voxel relabeling
- 159 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
- 4737 voxels changed in iteration 0 of unlikely voxel relabeling
- 32 voxels changed in iteration 1 of unlikely voxel relabeling
- 0 voxels changed in iteration 2 of unlikely voxel relabeling
- 5200 voxels changed in iteration 0 of unlikely voxel relabeling
- 37 voxels changed in iteration 1 of unlikely voxel relabeling
- 0 voxels changed in iteration 2 of unlikely voxel relabeling
- 4667 voxels changed in iteration 0 of unlikely voxel relabeling
- 29 voxels changed in iteration 1 of unlikely voxel relabeling
- 0 voxels changed in iteration 2 of unlikely voxel relabeling
- MRItoUCHAR: min=0, max=85
- MRItoUCHAR: converting to UCHAR
- writing labeled volume to aseg.auto_noCCseg.mgz
- mri_ca_label utimesec 3540.188809
- mri_ca_label stimesec 1.728737
- mri_ca_label ru_maxrss 2130748
- mri_ca_label ru_ixrss 0
- mri_ca_label ru_idrss 0
- mri_ca_label ru_isrss 0
- mri_ca_label ru_minflt 765133
- mri_ca_label ru_majflt 0
- mri_ca_label ru_nswap 0
- mri_ca_label ru_inblock 62936
- mri_ca_label ru_oublock 448
- mri_ca_label ru_msgsnd 0
- mri_ca_label ru_msgrcv 0
- mri_ca_label ru_nsignals 0
- mri_ca_label ru_nvcsw 267
- mri_ca_label ru_nivcsw 7961
- auto-labeling took 58 minutes and 18 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/transforms/cc_up.lta 0051311
- 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-6.0.0/0051311/mri/transforms/cc_up.lta
- reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aseg.auto_noCCseg.mgz
- reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/norm.mgz
- 31420 voxels in left wm, 27692 in right wm, xrange [125, 134]
- searching rotation angles z=[-2 12], y=[-7 7]
-
searching scale 1 Z rot -2.1
searching scale 1 Z rot -1.8
searching scale 1 Z rot -1.6
searching scale 1 Z rot -1.3
searching scale 1 Z rot -1.1
searching scale 1 Z rot -0.8
searching scale 1 Z rot -0.6
searching scale 1 Z rot -0.3
searching scale 1 Z rot -0.1
searching scale 1 Z rot 0.2
searching scale 1 Z rot 0.4
searching scale 1 Z rot 0.7
searching scale 1 Z rot 0.9
searching scale 1 Z rot 1.2
searching scale 1 Z rot 1.4
searching scale 1 Z rot 1.7
searching scale 1 Z rot 1.9
searching scale 1 Z rot 2.2
searching scale 1 Z rot 2.4
searching scale 1 Z rot 2.7
searching scale 1 Z rot 2.9
searching scale 1 Z rot 3.2
searching scale 1 Z rot 3.4
searching scale 1 Z rot 3.7
searching scale 1 Z rot 3.9
searching scale 1 Z rot 4.2
searching scale 1 Z rot 4.4
searching scale 1 Z rot 4.7
searching scale 1 Z rot 4.9
searching scale 1 Z rot 5.2
searching scale 1 Z rot 5.4
searching scale 1 Z rot 5.7
searching scale 1 Z rot 5.9
searching scale 1 Z rot 6.2
searching scale 1 Z rot 6.4
searching scale 1 Z rot 6.7
searching scale 1 Z rot 6.9
searching scale 1 Z rot 7.2
searching scale 1 Z rot 7.4
searching scale 1 Z rot 7.7
searching scale 1 Z rot 7.9
searching scale 1 Z rot 8.2
searching scale 1 Z rot 8.4
searching scale 1 Z rot 8.7
searching scale 1 Z rot 8.9
searching scale 1 Z rot 9.2
searching scale 1 Z rot 9.4
searching scale 1 Z rot 9.7
searching scale 1 Z rot 9.9
searching scale 1 Z rot 10.2
searching scale 1 Z rot 10.4
searching scale 1 Z rot 10.7
searching scale 1 Z rot 10.9
searching scale 1 Z rot 11.2
searching scale 1 Z rot 11.4
searching scale 1 Z rot 11.7 global minimum found at slice 129.2, rotations (0.47, 4.92)
- final transformation (x=129.2, yr=0.469, zr=4.923):
- 0.99628 -0.08581 0.00815 8.44840;
- 0.08581 0.99631 0.00070 0.26983;
- -0.00818 -0.00000 0.99997 20.06056;
- 0.00000 0.00000 0.00000 1.00000;
- updating x range to be [124, 130] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 117 109
- eigenvectors:
- 0.00082 0.00225 1.00000;
- -0.03438 -0.99941 0.00228;
- 0.99941 -0.03438 -0.00074;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aseg.auto.mgz...
- corpus callosum segmentation took 0.7 minutes
- #--------------------------------------
- #@# Merge ASeg Sun Oct 8 04:00:32 CEST 2017
- cp aseg.auto.mgz aseg.presurf.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Sun Oct 8 04:00:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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...
- 1597 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 54 (54), valley at 20 (20)
- csf peak at 27, setting threshold to 45
- 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 55 (55), valley at 19 (19)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 3 minutes and 20 seconds.
- #--------------------------------------------
- #@# Mask BFS Sun Oct 8 04:03:54 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1443268 voxels in mask (pct= 8.60)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Sun Oct 8 04:03:56 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 (108.0): 107.7 +- 5.3 [79.0 --> 125.0]
- GM (63.0) : 63.3 +- 10.0 [30.0 --> 95.0]
- setting bottom of white matter range to 73.3
- setting top of gray matter range to 83.3
- 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...
- 9148 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 7763 filled
- 88 bright non-wm voxels segmented.
- 4646 diagonally connected voxels added...
- white matter segmentation took 1.4 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 0.61 minutes
- reading wm segmentation from wm.seg.mgz...
- 405 voxels added to wm to prevent paths from MTL structures to cortex
- 1961 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 48316 voxels turned on, 39597 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 102 new 102
- 115,126,128 old 102 new 102
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 12 found - 12 modified | TOTAL: 12
- pass 2 (xy+): 0 found - 12 modified | TOTAL: 12
- pass 1 (xy-): 12 found - 12 modified | TOTAL: 24
- pass 2 (xy-): 0 found - 12 modified | TOTAL: 24
- pass 1 (yz+): 17 found - 17 modified | TOTAL: 41
- pass 2 (yz+): 0 found - 17 modified | TOTAL: 41
- pass 1 (yz-): 29 found - 29 modified | TOTAL: 70
- pass 2 (yz-): 0 found - 29 modified | TOTAL: 70
- pass 1 (xz+): 13 found - 13 modified | TOTAL: 83
- pass 2 (xz+): 0 found - 13 modified | TOTAL: 83
- pass 1 (xz-): 15 found - 15 modified | TOTAL: 98
- pass 2 (xz-): 0 found - 15 modified | TOTAL: 98
- Iteration Number : 1
- pass 1 (+++): 18 found - 18 modified | TOTAL: 18
- pass 2 (+++): 0 found - 18 modified | TOTAL: 18
- pass 1 (+++): 14 found - 14 modified | TOTAL: 32
- pass 2 (+++): 0 found - 14 modified | TOTAL: 32
- pass 1 (+++): 6 found - 6 modified | TOTAL: 38
- pass 2 (+++): 0 found - 6 modified | TOTAL: 38
- pass 1 (+++): 11 found - 11 modified | TOTAL: 49
- pass 2 (+++): 0 found - 11 modified | TOTAL: 49
- Iteration Number : 1
- pass 1 (++): 235 found - 235 modified | TOTAL: 235
- pass 2 (++): 0 found - 235 modified | TOTAL: 235
- pass 1 (+-): 281 found - 281 modified | TOTAL: 516
- pass 2 (+-): 0 found - 281 modified | TOTAL: 516
- pass 1 (--): 243 found - 243 modified | TOTAL: 759
- pass 2 (--): 0 found - 243 modified | TOTAL: 759
- pass 1 (-+): 247 found - 247 modified | TOTAL: 1006
- pass 2 (-+): 0 found - 247 modified | TOTAL: 1006
- Iteration Number : 2
- pass 1 (xy+): 5 found - 5 modified | TOTAL: 5
- pass 2 (xy+): 0 found - 5 modified | TOTAL: 5
- pass 1 (xy-): 6 found - 6 modified | TOTAL: 11
- pass 2 (xy-): 0 found - 6 modified | TOTAL: 11
- pass 1 (yz+): 4 found - 4 modified | TOTAL: 15
- pass 2 (yz+): 0 found - 4 modified | TOTAL: 15
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 17
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 17
- pass 1 (xz+): 4 found - 4 modified | TOTAL: 21
- pass 2 (xz+): 0 found - 4 modified | TOTAL: 21
- pass 1 (xz-): 5 found - 5 modified | TOTAL: 26
- pass 2 (xz-): 0 found - 5 modified | TOTAL: 26
- 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 (+++): 0 found - 0 modified | TOTAL: 3
- Iteration Number : 2
- pass 1 (++): 3 found - 3 modified | TOTAL: 3
- pass 2 (++): 0 found - 3 modified | TOTAL: 3
- pass 1 (+-): 1 found - 1 modified | TOTAL: 4
- pass 2 (+-): 0 found - 1 modified | TOTAL: 4
- pass 1 (--): 3 found - 3 modified | TOTAL: 7
- pass 2 (--): 0 found - 3 modified | TOTAL: 7
- pass 1 (-+): 1 found - 1 modified | TOTAL: 8
- pass 2 (-+): 0 found - 1 modified | TOTAL: 8
- Iteration Number : 3
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 2
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 3
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 3
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 4
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 4
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 5
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 5
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 1195 (out of 485218: 0.246281)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Sun Oct 8 04:06:03 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri
- mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
- logging cutting plane coordinates to ../scripts/ponscc.cut.log...
- INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
- using segmentation aseg.auto_noCCseg.mgz...
- reading input volume...done.
- searching for cutting planes...voxel to talairach voxel transform
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- voxel to talairach voxel transform
- 0.95970 -0.11366 -0.01385 17.30839;
- 0.11444 1.18235 0.23256 -75.74860;
- -0.01114 -0.23848 1.09834 12.30527;
- 0.00000 0.00000 0.00000 1.00000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1597 (min = 350, max = 1400), aspect = 0.56 (min = 0.10, max = 0.75)
- need search nearby
- using seed (124, 121, 151), TAL = (4.0, 23.0, 7.0)
- talairach voxel to voxel transform
- 1.03028 0.09750 -0.00766 -10.35275;
- -0.09761 0.80190 -0.17102 64.53651;
- -0.01074 0.17510 0.87325 2.70390;
- 0.00000 0.00000 0.00000 1.00000;
- segmentation indicates cc at (124, 121, 151) --> (4.0, 23.0, 7.0)
- done.
- writing output to filled.mgz...
- filling took 0.7 minutes
- talairach cc position changed to (4.00, 23.00, 7.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(22.00, 23.00, 7.00) SRC: (109.50, 125.40, 154.61)
- search lh wm seed point around talairach space (-14.00, 23.00, 7.00), SRC: (146.59, 121.88, 154.23)
- compute mri_fill using aseg
- Erasing Brain Stem and Cerebellum ...
- Define left and right masks using aseg:
- Building Voronoi diagram ...
- Using the Voronoi diagram to separate WM into two hemispheres ...
- Find the largest connected component for each hemisphere ...
- #--------------------------------------------
- #@# Tessellate lh Sun Oct 8 04:06:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 2 found - 2 modified | TOTAL: 2
- pass 2 (xy+): 0 found - 2 modified | TOTAL: 2
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 3
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 3
- pass 1 (yz+): 3 found - 3 modified | TOTAL: 6
- pass 2 (yz+): 0 found - 3 modified | TOTAL: 6
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 7
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 7
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 8
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 8
- pass 1 (xz-): 2 found - 2 modified | TOTAL: 10
- pass 2 (xz-): 0 found - 2 modified | TOTAL: 10
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 1 found - 1 modified | TOTAL: 1
- pass 2 (--): 0 found - 1 modified | TOTAL: 1
- pass 1 (-+): 1 found - 1 modified | TOTAL: 2
- pass 2 (-+): 0 found - 1 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+): 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 = 12 (out of 233604: 0.005137)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- slice 50: 370 vertices, 429 faces
- slice 60: 5508 vertices, 5711 faces
- slice 70: 14280 vertices, 14668 faces
- slice 80: 26295 vertices, 26722 faces
- slice 90: 38280 vertices, 38683 faces
- slice 100: 50218 vertices, 50664 faces
- slice 110: 62727 vertices, 63162 faces
- slice 120: 75916 vertices, 76394 faces
- slice 130: 88153 vertices, 88603 faces
- slice 140: 100213 vertices, 100639 faces
- slice 150: 110733 vertices, 111100 faces
- slice 160: 119768 vertices, 120068 faces
- slice 170: 128046 vertices, 128334 faces
- slice 180: 134337 vertices, 134536 faces
- slice 190: 138336 vertices, 138462 faces
- slice 200: 139346 vertices, 139388 faces
- slice 210: 139346 vertices, 139388 faces
- slice 220: 139346 vertices, 139388 faces
- slice 230: 139346 vertices, 139388 faces
- slice 240: 139346 vertices, 139388 faces
- slice 250: 139346 vertices, 139388 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...
- 139346 voxel in cpt #1: X=-42 [v=139346,e=418164,f=278776] located at (-32.566956, -12.473964, 6.639351)
- For the whole surface: X=-42 [v=139346,e=418164,f=278776]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Tessellate rh Sun Oct 8 04:06:55 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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+): 2 found - 2 modified | TOTAL: 2
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 2
- pass 1 (yz-): 3 found - 3 modified | TOTAL: 5
- pass 2 (yz-): 0 found - 3 modified | TOTAL: 5
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 7
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 7
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 7
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 1 found - 1 modified | TOTAL: 1
- pass 2 (--): 0 found - 1 modified | TOTAL: 1
- pass 1 (-+): 1 found - 1 modified | TOTAL: 2
- pass 2 (-+): 0 found - 1 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+): 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 = 9 (out of 232816: 0.003866)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
- $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- slice 50: 562 vertices, 618 faces
- slice 60: 6543 vertices, 6823 faces
- slice 70: 16841 vertices, 17262 faces
- slice 80: 29602 vertices, 29994 faces
- slice 90: 42492 vertices, 42932 faces
- slice 100: 54817 vertices, 55264 faces
- slice 110: 67460 vertices, 67890 faces
- slice 120: 79936 vertices, 80370 faces
- slice 130: 91495 vertices, 91909 faces
- slice 140: 103196 vertices, 103616 faces
- slice 150: 113148 vertices, 113498 faces
- slice 160: 122368 vertices, 122671 faces
- slice 170: 129723 vertices, 130012 faces
- slice 180: 135976 vertices, 136187 faces
- slice 190: 139987 vertices, 140140 faces
- slice 200: 140834 vertices, 140884 faces
- slice 210: 140834 vertices, 140884 faces
- slice 220: 140834 vertices, 140884 faces
- slice 230: 140834 vertices, 140884 faces
- slice 240: 140834 vertices, 140884 faces
- slice 250: 140834 vertices, 140884 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...
- 140834 voxel in cpt #1: X=-50 [v=140834,e=422652,f=281768] located at (28.968601, -14.518121, 1.524312)
- For the whole surface: X=-50 [v=140834,e=422652,f=281768]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Sun Oct 8 04:07:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- #--------------------------------------------
- #@# Smooth1 rh Sun Oct 8 04:07:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- Waiting for PID 10126 of (10126 10129) to complete...
- Waiting for PID 10129 of (10126 10129) 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 (10126 10129) completed and logs appended.
- #--------------------------------------------
- #@# Inflation1 lh Sun Oct 8 04:07:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- #--------------------------------------------
- #@# Inflation1 rh Sun Oct 8 04:07:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Waiting for PID 10182 of (10182 10186) to complete...
- Waiting for PID 10186 of (10182 10186) 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 = 44.1 mm, total surface area = 72260 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 1.0 minutes
-
step 000: RMS=0.157 (target=0.015)
step 005: RMS=0.118 (target=0.015)
step 010: RMS=0.088 (target=0.015)
step 015: RMS=0.073 (target=0.015)
step 020: RMS=0.062 (target=0.015)
step 025: RMS=0.053 (target=0.015)
step 030: RMS=0.047 (target=0.015)
step 035: RMS=0.043 (target=0.015)
step 040: RMS=0.039 (target=0.015)
step 045: RMS=0.036 (target=0.015)
step 050: RMS=0.035 (target=0.015)
step 055: RMS=0.033 (target=0.015)
step 060: RMS=0.032 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 60.537796
- mris_inflate stimesec 0.128980
- mris_inflate ru_maxrss 203972
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 29467
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 9824
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 3898
- mris_inflate ru_nivcsw 4125
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Not saving sulc
- Reading ../surf/rh.smoothwm.nofix
- avg radius = 44.5 mm, total surface area = 73001 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.8 minutes
-
step 000: RMS=0.158 (target=0.015)
step 005: RMS=0.118 (target=0.015)
step 010: RMS=0.087 (target=0.015)
step 015: RMS=0.073 (target=0.015)
step 020: RMS=0.063 (target=0.015)
step 025: RMS=0.054 (target=0.015)
step 030: RMS=0.047 (target=0.015)
step 035: RMS=0.043 (target=0.015)
step 040: RMS=0.040 (target=0.015)
step 045: RMS=0.037 (target=0.015)
step 050: RMS=0.036 (target=0.015)
step 055: RMS=0.035 (target=0.015)
step 060: RMS=0.033 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 48.431637
- mris_inflate stimesec 0.120981
- mris_inflate ru_maxrss 206112
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 29490
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 9928
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2724
- mris_inflate ru_nivcsw 4442
- PIDs (10182 10186) completed and logs appended.
- #--------------------------------------------
- #@# QSphere lh Sun Oct 8 04:08:08 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- #--------------------------------------------
- #@# QSphere rh Sun Oct 8 04:08:08 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- Waiting for PID 10252 of (10252 10256) to complete...
- Waiting for PID 10256 of (10252 10256) 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 0.99 +- 0.53 (0.00-->7.66) (max @ vno 52576 --> 53865)
- face area 0.03 +- 0.03 (-0.12-->1.03)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.332...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=175.518, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.260, avgs=0
- 010/300: dt: 0.9000, rms radial error=174.707, avgs=0
- 015/300: dt: 0.9000, rms radial error=173.981, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.155, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.272, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.357, avgs=0
- 035/300: dt: 0.9000, rms radial error=170.427, avgs=0
- 040/300: dt: 0.9000, rms radial error=169.488, avgs=0
- 045/300: dt: 0.9000, rms radial error=168.546, avgs=0
- 050/300: dt: 0.9000, rms radial error=167.604, avgs=0
- 055/300: dt: 0.9000, rms radial error=166.666, avgs=0
- 060/300: dt: 0.9000, rms radial error=165.730, avgs=0
- 065/300: dt: 0.9000, rms radial error=164.799, avgs=0
- 070/300: dt: 0.9000, rms radial error=163.872, avgs=0
- 075/300: dt: 0.9000, rms radial error=162.950, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.033, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.120, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.213, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.310, avgs=0
- 100/300: dt: 0.9000, rms radial error=158.413, avgs=0
- 105/300: dt: 0.9000, rms radial error=157.520, avgs=0
- 110/300: dt: 0.9000, rms radial error=156.632, avgs=0
- 115/300: dt: 0.9000, rms radial error=155.749, avgs=0
- 120/300: dt: 0.9000, rms radial error=154.871, avgs=0
- 125/300: dt: 0.9000, rms radial error=153.998, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.130, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.266, avgs=0
- 140/300: dt: 0.9000, rms radial error=151.408, avgs=0
- 145/300: dt: 0.9000, rms radial error=150.554, avgs=0
- 150/300: dt: 0.9000, rms radial error=149.705, avgs=0
- 155/300: dt: 0.9000, rms radial error=148.861, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.021, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.186, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.356, avgs=0
- 175/300: dt: 0.9000, rms radial error=145.530, avgs=0
- 180/300: dt: 0.9000, rms radial error=144.709, avgs=0
- 185/300: dt: 0.9000, rms radial error=143.892, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.080, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.272, avgs=0
- 200/300: dt: 0.9000, rms radial error=141.468, avgs=0
- 205/300: dt: 0.9000, rms radial error=140.670, avgs=0
- 210/300: dt: 0.9000, rms radial error=139.875, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.085, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.300, avgs=0
- 225/300: dt: 0.9000, rms radial error=137.519, avgs=0
- 230/300: dt: 0.9000, rms radial error=136.742, avgs=0
- 235/300: dt: 0.9000, rms radial error=135.970, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.202, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.438, avgs=0
- 250/300: dt: 0.9000, rms radial error=133.679, avgs=0
- 255/300: dt: 0.9000, rms radial error=132.924, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.173, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.427, avgs=0
- 270/300: dt: 0.9000, rms radial error=130.685, avgs=0
- 275/300: dt: 0.9000, rms radial error=129.946, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.212, avgs=0
- 285/300: dt: 0.9000, rms radial error=128.483, avgs=0
- 290/300: dt: 0.9000, rms radial error=127.757, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.035, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.318, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 15939.70
- 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 = 2504.53
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
- epoch 3 (K=160.0), pass 1, starting sse = 228.13
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.12/12 = 0.00974
- epoch 4 (K=640.0), pass 1, starting sse = 11.84
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.15/17 = 0.00894
- final distance error %23.18
- writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.08 hours
- mris_sphere utimesec 294.522225
- mris_sphere stimesec 0.233964
- mris_sphere ru_maxrss 204184
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 29518
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 9808
- mris_sphere ru_oublock 9848
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 9029
- mris_sphere ru_nivcsw 22293
- FSRUNTIME@ mris_sphere 0.0823 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 0.98 +- 0.54 (0.00-->7.50) (max @ vno 67255 --> 68430)
- face area 0.03 +- 0.03 (-0.17-->0.80)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.326...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=175.727, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.469, avgs=0
- 010/300: dt: 0.9000, rms radial error=174.916, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.191, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.365, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.482, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.568, avgs=0
- 035/300: dt: 0.9000, rms radial error=170.637, avgs=0
- 040/300: dt: 0.9000, rms radial error=169.697, avgs=0
- 045/300: dt: 0.9000, rms radial error=168.756, avgs=0
- 050/300: dt: 0.9000, rms radial error=167.815, avgs=0
- 055/300: dt: 0.9000, rms radial error=166.876, avgs=0
- 060/300: dt: 0.9000, rms radial error=165.941, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.010, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.084, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.162, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.245, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.333, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.426, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.524, avgs=0
- 100/300: dt: 0.9000, rms radial error=158.626, avgs=0
- 105/300: dt: 0.9000, rms radial error=157.734, avgs=0
- 110/300: dt: 0.9000, rms radial error=156.847, avgs=0
- 115/300: dt: 0.9000, rms radial error=155.964, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.086, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.213, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.345, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.481, avgs=0
- 140/300: dt: 0.9000, rms radial error=151.623, avgs=0
- 145/300: dt: 0.9000, rms radial error=150.768, avgs=0
- 150/300: dt: 0.9000, rms radial error=149.919, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.074, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.234, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.399, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.568, avgs=0
- 175/300: dt: 0.9000, rms radial error=145.742, avgs=0
- 180/300: dt: 0.9000, rms radial error=144.921, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.104, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.292, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.485, avgs=0
- 200/300: dt: 0.9000, rms radial error=141.681, avgs=0
- 205/300: dt: 0.9000, rms radial error=140.883, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.089, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.299, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.514, avgs=0
- 225/300: dt: 0.9000, rms radial error=137.733, avgs=0
- 230/300: dt: 0.9000, rms radial error=136.956, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.184, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.416, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.653, avgs=0
- 250/300: dt: 0.9000, rms radial error=133.893, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.138, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.387, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.641, avgs=0
- 270/300: dt: 0.9000, rms radial error=130.898, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.160, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.426, avgs=0
- 285/300: dt: 0.9000, rms radial error=128.696, avgs=0
- 290/300: dt: 0.9000, rms radial error=127.970, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.248, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.530, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 16228.14
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
- epoch 2 (K=40.0), pass 1, starting sse = 2598.14
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00004
- epoch 3 (K=160.0), pass 1, starting sse = 248.79
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.07/10 = 0.00720
- epoch 4 (K=640.0), pass 1, starting sse = 15.86
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.11/15 = 0.00749
- final distance error %25.01
- writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.09 hours
- mris_sphere utimesec 317.713700
- mris_sphere stimesec 0.273958
- mris_sphere ru_maxrss 206308
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 29537
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 9912
- mris_sphere ru_oublock 9952
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 8825
- mris_sphere ru_nivcsw 20885
- FSRUNTIME@ mris_sphere 0.0864 hours 1 threads
- PIDs (10252 10256) completed and logs appended.
- #--------------------------------------------
- #@# Fix Topology Copy lh Sun Oct 8 04:13:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- #--------------------------------------------
- #@# Fix Topology Copy rh Sun Oct 8 04:13:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- #@# Fix Topology lh Sun Oct 8 04:13:19 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051311 lh
- #@# Fix Topology rh Sun Oct 8 04:13:19 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051311 rh
- Waiting for PID 10482 of (10482 10485) to complete...
- Waiting for PID 10485 of (10482 10485) to complete...
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051311 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=-42 (nv=139346, nf=278776, ne=418164, g=22)
- 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...
- 2737 ambiguous faces found in tessellation
- segmenting defects...
- 27 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 27 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.7890 (-4.8945)
- -vertex loglikelihood: -6.8951 (-3.4475)
- -normal dot loglikelihood: -3.5819 (-3.5819)
- -quad curv loglikelihood: -6.5129 (-3.2565)
- Total Loglikelihood : -26.7789
- CORRECTING DEFECT 0 (vertices=17, convex hull=32, v0=58)
- After retessellation of defect 0 (v0=58), euler #=-24 (137664,412243,274555) : difference with theory (-24) = 0
- CORRECTING DEFECT 1 (vertices=5, convex hull=22, v0=9693)
- After retessellation of defect 1 (v0=9693), euler #=-23 (137664,412248,274561) : difference with theory (-23) = 0
- CORRECTING DEFECT 2 (vertices=82, convex hull=67, v0=16434)
- After retessellation of defect 2 (v0=16434), euler #=-22 (137678,412318,274618) : difference with theory (-22) = 0
- CORRECTING DEFECT 3 (vertices=40, convex hull=63, v0=23247)
- After retessellation of defect 3 (v0=23247), euler #=-21 (137701,412413,274691) : difference with theory (-21) = 0
- CORRECTING DEFECT 4 (vertices=22, convex hull=38, v0=26254)
- After retessellation of defect 4 (v0=26254), euler #=-20 (137710,412452,274722) : difference with theory (-20) = 0
- CORRECTING DEFECT 5 (vertices=107, convex hull=112, v0=31553)
- After retessellation of defect 5 (v0=31553), euler #=-19 (137755,412633,274859) : difference with theory (-19) = 0
- CORRECTING DEFECT 6 (vertices=43, convex hull=83, v0=52726)
- After retessellation of defect 6 (v0=52726), euler #=-18 (137767,412703,274918) : difference with theory (-18) = 0
- CORRECTING DEFECT 7 (vertices=329, convex hull=195, v0=56138)
- After retessellation of defect 7 (v0=56138), euler #=-17 (137874,413113,275222) : difference with theory (-17) = 0
- CORRECTING DEFECT 8 (vertices=36, convex hull=42, v0=57150)
- After retessellation of defect 8 (v0=57150), euler #=-16 (137886,413162,275260) : difference with theory (-16) = 0
- CORRECTING DEFECT 9 (vertices=31, convex hull=47, v0=69006)
- After retessellation of defect 9 (v0=69006), euler #=-15 (137900,413223,275308) : difference with theory (-15) = 0
- CORRECTING DEFECT 10 (vertices=35, convex hull=69, v0=69199)
- After retessellation of defect 10 (v0=69199), euler #=-14 (137917,413308,275377) : difference with theory (-14) = 0
- CORRECTING DEFECT 11 (vertices=31, convex hull=35, v0=72507)
- After retessellation of defect 11 (v0=72507), euler #=-13 (137928,413353,275412) : difference with theory (-13) = 0
- CORRECTING DEFECT 12 (vertices=122, convex hull=59, v0=74238)
- After retessellation of defect 12 (v0=74238), euler #=-12 (137945,413428,275471) : difference with theory (-12) = 0
- CORRECTING DEFECT 13 (vertices=69, convex hull=137, v0=81626)
- After retessellation of defect 13 (v0=81626), euler #=-11 (137959,413528,275558) : difference with theory (-11) = 0
- CORRECTING DEFECT 14 (vertices=171, convex hull=144, v0=85529)
- After retessellation of defect 14 (v0=85529), euler #=-10 (138033,413816,275773) : difference with theory (-10) = 0
- CORRECTING DEFECT 15 (vertices=49, convex hull=106, v0=87337)
- After retessellation of defect 15 (v0=87337), euler #=-9 (138055,413926,275862) : difference with theory (-9) = 0
- CORRECTING DEFECT 16 (vertices=39, convex hull=52, v0=92564)
- After retessellation of defect 16 (v0=92564), euler #=-8 (138077,414016,275931) : difference with theory (-8) = 0
- CORRECTING DEFECT 17 (vertices=23, convex hull=33, v0=93729)
- After retessellation of defect 17 (v0=93729), euler #=-7 (138083,414046,275956) : difference with theory (-7) = 0
- CORRECTING DEFECT 18 (vertices=24, convex hull=59, v0=93887)
- After retessellation of defect 18 (v0=93887), euler #=-6 (138095,414107,276006) : difference with theory (-6) = 0
- CORRECTING DEFECT 19 (vertices=69, convex hull=38, v0=95322)
- After retessellation of defect 19 (v0=95322), euler #=-5 (138105,414154,276044) : difference with theory (-5) = 0
- CORRECTING DEFECT 20 (vertices=56, convex hull=53, v0=99762)
- After retessellation of defect 20 (v0=99762), euler #=-4 (138117,414212,276091) : difference with theory (-4) = 0
- CORRECTING DEFECT 21 (vertices=13, convex hull=25, v0=101051)
- After retessellation of defect 21 (v0=101051), euler #=-3 (138119,414225,276103) : difference with theory (-3) = 0
- CORRECTING DEFECT 22 (vertices=106, convex hull=41, v0=102169)
- After retessellation of defect 22 (v0=102169), euler #=-2 (138128,414265,276135) : difference with theory (-2) = 0
- CORRECTING DEFECT 23 (vertices=7, convex hull=20, v0=111208)
- After retessellation of defect 23 (v0=111208), euler #=-1 (138130,414278,276147) : difference with theory (-1) = 0
- CORRECTING DEFECT 24 (vertices=23, convex hull=66, v0=130383)
- After retessellation of defect 24 (v0=130383), euler #=0 (138142,414343,276201) : difference with theory (0) = 0
- CORRECTING DEFECT 25 (vertices=95, convex hull=100, v0=132130)
- After retessellation of defect 25 (v0=132130), euler #=1 (138169,414470,276302) : difference with theory (1) = 0
- CORRECTING DEFECT 26 (vertices=37, convex hull=73, v0=135282)
- After retessellation of defect 26 (v0=135282), euler #=2 (138191,414567,276378) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.08-->8.79) (max @ vno 131208 --> 134668)
- 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 (0.08-->8.79) (max @ vno 131208 --> 134668)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 94 mutations (37.0%), 160 crossovers (63.0%), 100 vertices were eliminated
- building final representation...
- 1155 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=138191, nf=276378, ne=414567, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 16.8 minutes
- 0 defective edges
- removing intersecting faces
- 000: 193 intersecting
- mris_fix_topology utimesec 1010.039450
- mris_fix_topology stimesec 0.220966
- mris_fix_topology ru_maxrss 431784
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 54447
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 19616
- mris_fix_topology ru_oublock 13168
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 568
- mris_fix_topology ru_nivcsw 2139
- FSRUNTIME@ mris_fix_topology lh 0.2806 hours 1 threads
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051311 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=-50 (nv=140834, nf=281768, ne=422652, g=26)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 3420 ambiguous faces found in tessellation
- segmenting defects...
- 36 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 36 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.7348 (-4.8674)
- -vertex loglikelihood: -6.8606 (-3.4303)
- -normal dot loglikelihood: -3.6111 (-3.6111)
- -quad curv loglikelihood: -6.5602 (-3.2801)
- Total Loglikelihood : -26.7668
- CORRECTING DEFECT 0 (vertices=21, convex hull=41, v0=430)
- After retessellation of defect 0 (v0=430), euler #=-33 (138759,415426,276634) : difference with theory (-33) = 0
- CORRECTING DEFECT 1 (vertices=27, convex hull=54, v0=993)
- After retessellation of defect 1 (v0=993), euler #=-32 (138768,415474,276674) : difference with theory (-32) = 0
- CORRECTING DEFECT 2 (vertices=33, convex hull=78, v0=6713)
- After retessellation of defect 2 (v0=6713), euler #=-31 (138782,415551,276738) : difference with theory (-31) = 0
- CORRECTING DEFECT 3 (vertices=12, convex hull=25, v0=9798)
- After retessellation of defect 3 (v0=9798), euler #=-30 (138782,415557,276745) : difference with theory (-30) = 0
- CORRECTING DEFECT 4 (vertices=32, convex hull=69, v0=14733)
- After retessellation of defect 4 (v0=14733), euler #=-29 (138800,415637,276808) : difference with theory (-29) = 0
- CORRECTING DEFECT 5 (vertices=37, convex hull=67, v0=21556)
- After retessellation of defect 5 (v0=21556), euler #=-28 (138814,415706,276864) : difference with theory (-28) = 0
- CORRECTING DEFECT 6 (vertices=46, convex hull=56, v0=22998)
- After retessellation of defect 6 (v0=22998), euler #=-27 (138824,415756,276905) : difference with theory (-27) = 0
- CORRECTING DEFECT 7 (vertices=39, convex hull=79, v0=24789)
- After retessellation of defect 7 (v0=24789), euler #=-26 (138842,415843,276975) : difference with theory (-26) = 0
- CORRECTING DEFECT 8 (vertices=23, convex hull=58, v0=28469)
- After retessellation of defect 8 (v0=28469), euler #=-25 (138855,415906,277026) : difference with theory (-25) = 0
- CORRECTING DEFECT 9 (vertices=29, convex hull=72, v0=44609)
- After retessellation of defect 9 (v0=44609), euler #=-24 (138870,415978,277084) : difference with theory (-24) = 0
- CORRECTING DEFECT 10 (vertices=14, convex hull=61, v0=46348)
- After retessellation of defect 10 (v0=46348), euler #=-23 (138877,416020,277120) : difference with theory (-23) = 0
- CORRECTING DEFECT 11 (vertices=533, convex hull=230, v0=54413)
- After retessellation of defect 11 (v0=54413), euler #=-22 (139078,416742,277642) : difference with theory (-22) = 0
- CORRECTING DEFECT 12 (vertices=75, convex hull=114, v0=57254)
- After retessellation of defect 12 (v0=57254), euler #=-21 (139111,416891,277759) : difference with theory (-21) = 0
- CORRECTING DEFECT 13 (vertices=6, convex hull=29, v0=60947)
- After retessellation of defect 13 (v0=60947), euler #=-20 (139114,416907,277773) : difference with theory (-20) = 0
- CORRECTING DEFECT 14 (vertices=13, convex hull=23, v0=61982)
- After retessellation of defect 14 (v0=61982), euler #=-19 (139117,416923,277787) : difference with theory (-19) = 0
- CORRECTING DEFECT 15 (vertices=34, convex hull=56, v0=72095)
- After retessellation of defect 15 (v0=72095), euler #=-18 (139128,416977,277831) : difference with theory (-18) = 0
- CORRECTING DEFECT 16 (vertices=29, convex hull=74, v0=86194)
- After retessellation of defect 16 (v0=86194), euler #=-17 (139145,417060,277898) : difference with theory (-17) = 0
- CORRECTING DEFECT 17 (vertices=83, convex hull=35, v0=88125)
- After retessellation of defect 17 (v0=88125), euler #=-16 (139154,417101,277931) : difference with theory (-16) = 0
- CORRECTING DEFECT 18 (vertices=6, convex hull=31, v0=91299)
- After retessellation of defect 18 (v0=91299), euler #=-15 (139157,417119,277947) : difference with theory (-15) = 0
- CORRECTING DEFECT 19 (vertices=6, convex hull=18, v0=93459)
- After retessellation of defect 19 (v0=93459), euler #=-14 (139159,417131,277958) : difference with theory (-14) = 0
- CORRECTING DEFECT 20 (vertices=52, convex hull=63, v0=94693)
- After retessellation of defect 20 (v0=94693), euler #=-13 (139179,417218,278026) : difference with theory (-13) = 0
- CORRECTING DEFECT 21 (vertices=74, convex hull=29, v0=94740)
- After retessellation of defect 21 (v0=94740), euler #=-12 (139187,417255,278056) : difference with theory (-12) = 0
- CORRECTING DEFECT 22 (vertices=51, convex hull=60, v0=96926)
- After retessellation of defect 22 (v0=96926), euler #=-11 (139205,417331,278115) : difference with theory (-11) = 0
- CORRECTING DEFECT 23 (vertices=28, convex hull=64, v0=99171)
- After retessellation of defect 23 (v0=99171), euler #=-10 (139223,417407,278174) : difference with theory (-10) = 0
- CORRECTING DEFECT 24 (vertices=25, convex hull=31, v0=99326)
- After retessellation of defect 24 (v0=99326), euler #=-9 (139229,417435,278197) : difference with theory (-9) = 0
- CORRECTING DEFECT 25 (vertices=32, convex hull=25, v0=100457)
- After retessellation of defect 25 (v0=100457), euler #=-8 (139232,417455,278215) : difference with theory (-8) = 0
- CORRECTING DEFECT 26 (vertices=269, convex hull=67, v0=102839)
- After retessellation of defect 26 (v0=102839), euler #=-7 (139249,417533,278277) : difference with theory (-7) = 0
- CORRECTING DEFECT 27 (vertices=12, convex hull=27, v0=108088)
- After retessellation of defect 27 (v0=108088), euler #=-6 (139253,417554,278295) : difference with theory (-6) = 0
- CORRECTING DEFECT 28 (vertices=22, convex hull=47, v0=108235)
- After retessellation of defect 28 (v0=108235), euler #=-5 (139266,417607,278336) : difference with theory (-5) = 0
- CORRECTING DEFECT 29 (vertices=45, convex hull=92, v0=114956)
- After retessellation of defect 29 (v0=114956), euler #=-4 (139289,417714,278421) : difference with theory (-4) = 0
- CORRECTING DEFECT 30 (vertices=21, convex hull=29, v0=115595)
- After retessellation of defect 30 (v0=115595), euler #=-3 (139293,417733,278437) : difference with theory (-3) = 0
- CORRECTING DEFECT 31 (vertices=76, convex hull=76, v0=118470)
- After retessellation of defect 31 (v0=118470), euler #=-2 (139317,417840,278521) : difference with theory (-2) = 0
- CORRECTING DEFECT 32 (vertices=37, convex hull=68, v0=124542)
- After retessellation of defect 32 (v0=124542), euler #=-1 (139327,417897,278569) : difference with theory (-1) = 0
- CORRECTING DEFECT 33 (vertices=152, convex hull=41, v0=127554)
- After retessellation of defect 33 (v0=127554), euler #=0 (139339,417948,278609) : difference with theory (0) = 0
- CORRECTING DEFECT 34 (vertices=46, convex hull=88, v0=129681)
- After retessellation of defect 34 (v0=129681), euler #=1 (139354,418029,278676) : difference with theory (1) = 0
- CORRECTING DEFECT 35 (vertices=43, convex hull=75, v0=135169)
- After retessellation of defect 35 (v0=135169), euler #=2 (139374,418116,278744) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.09-->6.59) (max @ vno 60282 --> 139396)
- 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 (0.09-->6.59) (max @ vno 60282 --> 139396)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 112 mutations (33.9%), 218 crossovers (66.1%), 81 vertices were eliminated
- building final representation...
- 1460 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=139374, nf=278744, ne=418116, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 19.2 minutes
- 0 defective edges
- removing intersecting faces
- 000: 201 intersecting
- 001: 2 intersecting
- mris_fix_topology utimesec 1150.230138
- mris_fix_topology stimesec 0.253961
- mris_fix_topology ru_maxrss 435940
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 55422
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 0
- mris_fix_topology ru_oublock 13296
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 673
- mris_fix_topology ru_nivcsw 3223
- FSRUNTIME@ mris_fix_topology rh 0.3195 hours 1 threads
- PIDs (10482 10485) completed and logs appended.
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 138191 - 414567 + 276378 = 2 --> 0 holes
- F =2V-4: 276378 = 276382-4 (0)
- 2E=3F: 829134 = 829134 (0)
- total defect index = 0
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 139374 - 418116 + 278744 = 2 --> 0 holes
- F =2V-4: 278744 = 278748-4 (0)
- 2E=3F: 836232 = 836232 (0)
- total defect index = 0
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 66 intersecting
- 001: 3 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 28 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Sun Oct 8 04:32:42 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051311 lh
- #--------------------------------------------
- #@# Make White Surf rh Sun Oct 8 04:32:42 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051311 rh
- Waiting for PID 11131 of (11131 11134) to complete...
- Waiting for PID 11134 of (11131 11134) to complete...
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051311 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-6.0.0/0051311/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- 35848 bright wm thresholded.
- 156 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.orig...
- computing class statistics...
- border white: 240312 voxels (1.43%)
- border gray 287731 voxels (1.72%)
- WM (99.0): 98.1 +- 10.3 [70.0 --> 110.0]
- GM (60.0) : 61.5 +- 10.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 45.3 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 56.0 (was 85)
- setting MAX_CSF to 34.7 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 45.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 24.0 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.03-->2.90) (max @ vno 130587 --> 138144)
- face area 0.27 +- 0.12 (0.00-->2.04)
- mean absolute distance = 0.58 +- 0.65
- 3585 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=105+-7.0, GM=56+-7.0
- mean inside = 91.9, mean outside = 65.1
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- mean border=71.0, 116 (116) missing vertices, mean dist 0.3 [0.4 (%33.8)->0.7 (%66.2))]
- %76 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 0.91 +- 0.25 (0.09-->3.17) (max @ vno 72099 --> 72142)
- face area 0.27 +- 0.13 (0.00-->2.14)
- mean absolute distance = 0.27 +- 0.39
- 2967 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5828566.5, rms=14.101
- 001: dt: 0.5000, sse=3163324.8, rms=9.961 (29.358%)
- 002: dt: 0.5000, sse=2130821.8, rms=7.776 (21.939%)
- 003: dt: 0.5000, sse=1630200.8, rms=6.448 (17.076%)
- 004: dt: 0.5000, sse=1409752.6, rms=5.769 (10.522%)
- 005: dt: 0.5000, sse=1296108.9, rms=5.376 (6.813%)
- 006: dt: 0.5000, sse=1256569.2, rms=5.236 (2.610%)
- 007: dt: 0.5000, sse=1220788.2, rms=5.097 (2.652%)
- rms = 5.07, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=1212928.8, rms=5.068 (0.572%)
- 009: dt: 0.2500, sse=872511.0, rms=3.516 (30.632%)
- 010: dt: 0.2500, sse=799205.3, rms=3.094 (11.983%)
- rms = 3.06, time step reduction 2 of 3 to 0.125...
- 011: dt: 0.2500, sse=795160.0, rms=3.061 (1.065%)
- 012: dt: 0.1250, sse=708332.5, rms=2.423 (20.857%)
- 013: dt: 0.1250, sse=692640.4, rms=2.325 (4.057%)
- rms = 2.31, time step reduction 3 of 3 to 0.062...
- 014: dt: 0.1250, sse=690988.1, rms=2.308 (0.714%)
- positioning took 1.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=75.9, 106 (36) missing vertices, mean dist -0.2 [0.3 (%79.7)->0.2 (%20.3))]
- %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.24 (0.11-->3.27) (max @ vno 91467 --> 90257)
- face area 0.35 +- 0.16 (0.00-->2.79)
- mean absolute distance = 0.19 +- 0.28
- 2873 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1799238.1, rms=6.472
- 015: dt: 0.5000, sse=1271073.2, rms=4.682 (27.666%)
- rms = 5.10, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.2500, sse=971985.1, rms=3.260 (30.374%)
- 017: dt: 0.2500, sse=884295.2, rms=2.705 (17.017%)
- 018: dt: 0.2500, sse=841317.5, rms=2.384 (11.866%)
- rms = 2.42, time step reduction 2 of 3 to 0.125...
- 019: dt: 0.1250, sse=815062.8, rms=2.165 (9.189%)
- 020: dt: 0.1250, sse=779678.9, rms=1.825 (15.679%)
- 021: dt: 0.1250, sse=773294.4, rms=1.757 (3.747%)
- rms = 1.75, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=772957.4, rms=1.749 (0.465%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=78.6, 104 (35) missing vertices, mean dist -0.1 [0.2 (%72.0)->0.2 (%28.0))]
- %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.09-->3.38) (max @ vno 137832 --> 137848)
- face area 0.34 +- 0.16 (0.00-->2.80)
- mean absolute distance = 0.16 +- 0.25
- 2270 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1043450.6, rms=3.725
- rms = 4.70, time step reduction 1 of 3 to 0.250...
- 023: dt: 0.2500, sse=834889.4, rms=2.441 (34.472%)
- 024: dt: 0.2500, sse=777642.2, rms=1.911 (21.688%)
- rms = 1.92, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.1250, sse=762493.3, rms=1.766 (7.599%)
- 026: dt: 0.1250, sse=741858.1, rms=1.547 (12.429%)
- rms = 1.50, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=737703.9, rms=1.501 (2.935%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=79.4, 109 (34) missing vertices, mean dist -0.0 [0.2 (%55.7)->0.2 (%44.3))]
- %91 local maxima, % 4 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-6.0.0/0051311/surf/lh.white.preaparc...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=758994.1, rms=1.811
- rms = 3.12, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=710640.3, rms=1.199 (33.818%)
- 029: dt: 0.2500, sse=704772.4, rms=1.105 (7.813%)
- rms = 1.11, time step reduction 2 of 3 to 0.125...
- rms = 1.08, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=701658.6, rms=1.080 (2.291%)
- positioning took 0.5 minutes
- generating cortex label...
- 12 non-cortical segments detected
- only using segment with 7182 vertices
- erasing segment 1 (vno[0] = 76332)
- erasing segment 2 (vno[0] = 84616)
- erasing segment 3 (vno[0] = 88126)
- erasing segment 4 (vno[0] = 91531)
- erasing segment 5 (vno[0] = 94153)
- erasing segment 6 (vno[0] = 98135)
- erasing segment 7 (vno[0] = 98478)
- erasing segment 8 (vno[0] = 98489)
- erasing segment 9 (vno[0] = 104034)
- erasing segment 10 (vno[0] = 108007)
- erasing segment 11 (vno[0] = 137881)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.area
- vertex spacing 0.90 +- 0.25 (0.03-->3.35) (max @ vno 90257 --> 91467)
- face area 0.34 +- 0.15 (0.00-->2.83)
- refinement took 5.4 minutes
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051311 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-6.0.0/0051311/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- 35848 bright wm thresholded.
- 156 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.orig...
- computing class statistics...
- border white: 240312 voxels (1.43%)
- border gray 287731 voxels (1.72%)
- WM (99.0): 98.1 +- 10.3 [70.0 --> 110.0]
- GM (60.0) : 61.5 +- 10.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 58.0 (was 85)
- setting MAX_CSF to 36.7 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 47.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 26.0 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.04-->4.58) (max @ vno 138977 --> 139000)
- face area 0.27 +- 0.12 (0.00-->3.16)
- mean absolute distance = 0.58 +- 0.67
- 3762 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=105+-7.0, GM=58+-6.1
- mean inside = 92.0, mean outside = 65.8
- 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
- mean border=72.3, 52 (52) missing vertices, mean dist 0.3 [0.4 (%35.8)->0.7 (%64.2))]
- %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.25 (0.13-->5.76) (max @ vno 60282 --> 138977)
- face area 0.27 +- 0.13 (0.00-->5.56)
- mean absolute distance = 0.27 +- 0.40
- 2143 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5467821.0, rms=13.538
- 001: dt: 0.5000, sse=2945513.5, rms=9.482 (29.958%)
- 002: dt: 0.5000, sse=2017694.5, rms=7.449 (21.441%)
- 003: dt: 0.5000, sse=1586877.9, rms=6.253 (16.052%)
- 004: dt: 0.5000, sse=1388094.6, rms=5.630 (9.969%)
- 005: dt: 0.5000, sse=1274923.0, rms=5.248 (6.785%)
- 006: dt: 0.5000, sse=1235404.0, rms=5.112 (2.592%)
- 007: dt: 0.5000, sse=1206988.0, rms=4.978 (2.626%)
- rms = 4.95, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=1192553.5, rms=4.949 (0.578%)
- 009: dt: 0.2500, sse=855988.6, rms=3.381 (31.691%)
- 010: dt: 0.2500, sse=785341.0, rms=2.946 (12.850%)
- rms = 2.90, time step reduction 2 of 3 to 0.125...
- 011: dt: 0.2500, sse=776621.4, rms=2.902 (1.500%)
- 012: dt: 0.1250, sse=691380.2, rms=2.260 (22.122%)
- 013: dt: 0.1250, sse=679022.5, rms=2.158 (4.504%)
- rms = 2.14, time step reduction 3 of 3 to 0.062...
- 014: dt: 0.1250, sse=686921.1, rms=2.137 (0.979%)
- 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
- mean border=77.0, 57 (8) missing vertices, mean dist -0.2 [0.3 (%78.9)->0.2 (%21.1))]
- %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.08-->5.96) (max @ vno 60282 --> 138977)
- face area 0.34 +- 0.16 (0.00-->7.98)
- mean absolute distance = 0.18 +- 0.29
- 2133 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1726784.0, rms=6.185
- 015: dt: 0.5000, sse=1234674.0, rms=4.496 (27.310%)
- rms = 4.94, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.2500, sse=946672.4, rms=3.072 (31.683%)
- 017: dt: 0.2500, sse=868999.9, rms=2.543 (17.223%)
- 018: dt: 0.2500, sse=829932.0, rms=2.249 (11.534%)
- rms = 2.28, time step reduction 2 of 3 to 0.125...
- 019: dt: 0.1250, sse=806890.4, rms=2.041 (9.247%)
- 020: dt: 0.1250, sse=774507.4, rms=1.719 (15.774%)
- 021: dt: 0.1250, sse=768998.5, rms=1.659 (3.496%)
- rms = 1.66, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=768732.5, rms=1.656 (0.205%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 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 2 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
- mean border=79.7, 72 (2) missing vertices, mean dist -0.1 [0.2 (%71.6)->0.2 (%28.4))]
- %90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.09-->6.06) (max @ vno 60282 --> 138977)
- face area 0.34 +- 0.16 (0.00-->8.07)
- mean absolute distance = 0.16 +- 0.25
- 2187 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1019899.9, rms=3.560
- rms = 4.56, time step reduction 1 of 3 to 0.250...
- 023: dt: 0.2500, sse=823222.6, rms=2.297 (35.490%)
- 024: dt: 0.2500, sse=771493.2, rms=1.811 (21.135%)
- rms = 1.81, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.1250, sse=758685.1, rms=1.679 (7.281%)
- 026: dt: 0.1250, sse=741915.2, rms=1.480 (11.875%)
- rms = 1.44, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=739957.0, rms=1.438 (2.841%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 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
- mean border=80.4, 87 (2) missing vertices, mean dist -0.0 [0.2 (%54.6)->0.2 (%45.4))]
- %91 local maxima, % 5 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-6.0.0/0051311/surf/rh.white.preaparc...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=758699.2, rms=1.727
- rms = 2.97, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=712249.9, rms=1.147 (33.592%)
- 029: dt: 0.2500, sse=707332.9, rms=1.059 (7.654%)
- rms = 1.07, time step reduction 2 of 3 to 0.125...
- rms = 1.04, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=704595.3, rms=1.037 (2.037%)
- positioning took 0.5 minutes
- generating cortex label...
- 8 non-cortical segments detected
- only using segment with 7022 vertices
- erasing segment 1 (vno[0] = 96954)
- erasing segment 2 (vno[0] = 100245)
- erasing segment 3 (vno[0] = 100483)
- erasing segment 4 (vno[0] = 101478)
- erasing segment 5 (vno[0] = 101683)
- erasing segment 6 (vno[0] = 102458)
- erasing segment 7 (vno[0] = 139191)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.area
- vertex spacing 0.89 +- 0.25 (0.04-->6.08) (max @ vno 60282 --> 138977)
- face area 0.34 +- 0.16 (0.00-->7.95)
- refinement took 5.7 minutes
- PIDs (11131 11134) completed and logs appended.
- #--------------------------------------------
- #@# Smooth2 lh Sun Oct 8 04:38:21 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
- #--------------------------------------------
- #@# Smooth2 rh Sun Oct 8 04:38:21 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
- Waiting for PID 11352 of (11352 11355) to complete...
- Waiting for PID 11355 of (11352 11355) 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 (11352 11355) completed and logs appended.
- #--------------------------------------------
- #@# Inflation2 lh Sun Oct 8 04:38:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- #--------------------------------------------
- #@# Inflation2 rh Sun Oct 8 04:38:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Waiting for PID 11398 of (11398 11401) to complete...
- Waiting for PID 11401 of (11398 11401) to complete...
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- Reading ../surf/lh.smoothwm
- avg radius = 44.3 mm, total surface area = 83768 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.182 (target=0.015)
step 005: RMS=0.126 (target=0.015)
step 010: RMS=0.094 (target=0.015)
step 015: RMS=0.078 (target=0.015)
step 020: RMS=0.065 (target=0.015)
step 025: RMS=0.053 (target=0.015)
step 030: RMS=0.044 (target=0.015)
step 035: RMS=0.038 (target=0.015)
step 040: RMS=0.032 (target=0.015)
step 045: RMS=0.028 (target=0.015)
step 050: RMS=0.025 (target=0.015)
step 055: RMS=0.023 (target=0.015)
step 060: RMS=0.022 (target=0.015)
- inflation complete.
- inflation took 1.0 minutes
- mris_inflate utimesec 61.082714
- mris_inflate stimesec 0.108983
- mris_inflate ru_maxrss 202404
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 29715
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 10824
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 3526
- mris_inflate ru_nivcsw 3846
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Reading ../surf/rh.smoothwm
- avg radius = 44.7 mm, total surface area = 84391 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.183 (target=0.015)
step 005: RMS=0.126 (target=0.015)
step 010: RMS=0.094 (target=0.015)
step 015: RMS=0.078 (target=0.015)
step 020: RMS=0.065 (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=0.032 (target=0.015)
step 045: RMS=0.029 (target=0.015)
step 050: RMS=0.025 (target=0.015)
step 055: RMS=0.023 (target=0.015)
step 060: RMS=0.021 (target=0.015)
- inflation complete.
- inflation took 0.8 minutes
- mris_inflate utimesec 47.815730
- mris_inflate stimesec 0.094985
- mris_inflate ru_maxrss 204116
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 29635
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 10920
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2309
- mris_inflate ru_nivcsw 4203
- PIDs (11398 11401) completed and logs appended.
- #--------------------------------------------
- #@# Curv .H and .K lh Sun Oct 8 04:39:25 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf
- mris_curvature -w lh.white.preaparc
- rm -f lh.white.H
- ln -s lh.white.preaparc.H lh.white.H
- rm -f lh.white.K
- ln -s lh.white.preaparc.K lh.white.K
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
- #--------------------------------------------
- #@# Curv .H and .K rh Sun Oct 8 04:39:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf
- reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 11498 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- Waiting for PID 11501 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- Waiting for PID 11504 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- Waiting for PID 11507 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- Waiting for PID 11510 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- Waiting for PID 11513 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- Waiting for PID 11516 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- Waiting for PID 11519 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- Waiting for PID 11522 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- Waiting for PID 11525 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- Waiting for PID 11531 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- Waiting for PID 11534 of (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) to complete...
- mris_curvature -w lh.white.preaparc
- total integrated curvature = 3.249*4pi (40.828) --> -2 handles
- ICI = 156.9, FI = 2021.3, variation=30512.116
- 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
- 145 vertices thresholded to be in k1 ~ [-0.34 0.27], k2 ~ [-0.08 0.10]
- total integrated curvature = 0.519*4pi (6.527) --> 0 handles
- ICI = 1.5, FI = 8.2, variation=146.046
- 104 vertices thresholded to be in [-0.01 0.01]
- writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 122 vertices thresholded to be in [-0.12 0.14]
- done.
- writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.021
- done.
- mris_curvature -w rh.white.preaparc
- total integrated curvature = -2.483*4pi (-31.207) --> 3 handles
- ICI = 155.6, FI = 2059.7, variation=31019.524
- 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
- 206 vertices thresholded to be in k1 ~ [-0.19 0.23], k2 ~ [-0.10 0.07]
- total integrated curvature = 0.572*4pi (7.182) --> 0 handles
- ICI = 1.5, FI = 8.7, variation=152.789
- 120 vertices thresholded to be in [-0.01 0.01]
- writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 158 vertices thresholded to be in [-0.12 0.11]
- done.
- writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.021
- done.
- PIDs (11498 11501 11504 11507 11510 11513 11516 11519 11522 11525 11531 11534) completed and logs appended.
- #-----------------------------------------
- #@# Curvature Stats lh Sun Oct 8 04:40:53 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051311 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 [ 0051311/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 [ 243 ]
- Gb_filter = 0
- WARN: S lookup min: -0.461582
- WARN: S explicit min: 0.000000 vertex = 170
- #-----------------------------------------
- #@# Curvature Stats rh Sun Oct 8 04:40:59 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051311 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 [ 0051311/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 [ 257 ]
- Gb_filter = 0
- WARN: S lookup min: -0.100520
- WARN: S explicit min: 0.000000 vertex = 103
- #--------------------------------------------
- #@# Sphere lh Sun Oct 8 04:41:03 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- #--------------------------------------------
- #@# Sphere rh Sun Oct 8 04:41:04 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- Waiting for PID 11695 of (11695 11699) to complete...
- Waiting for PID 11699 of (11695 11699) to complete...
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0.307...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- singular matrix in quadratic form
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %18.70
- pass 1: epoch 2 of 3 starting distance error %18.70
- unfolding complete - removing small folds...
- starting distance error %18.66
- removing remaining folds...
- final distance error %18.68
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 124 negative triangles
- 199: dt=0.9900, 124 negative triangles
- 200: dt=0.9900, 39 negative triangles
- 201: dt=0.9900, 25 negative triangles
- 202: dt=0.9900, 16 negative triangles
- 203: dt=0.9900, 15 negative triangles
- 204: dt=0.9900, 18 negative triangles
- 205: dt=0.9900, 8 negative triangles
- 206: dt=0.9900, 7 negative triangles
- 207: dt=0.9900, 8 negative triangles
- 208: dt=0.9900, 5 negative triangles
- 209: dt=0.9900, 4 negative triangles
- 210: dt=0.9900, 2 negative triangles
- 211: dt=0.9900, 2 negative triangles
- 212: dt=0.9900, 1 negative triangles
- 213: dt=0.9900, 1 negative triangles
- 214: dt=0.9900, 3 negative triangles
- 215: dt=0.9900, 1 negative triangles
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 1.16 hours
- mris_sphere utimesec 4172.881625
- mris_sphere stimesec 1.909709
- mris_sphere ru_maxrss 284624
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 50398
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 9768
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 122416
- mris_sphere ru_nivcsw 347293
- FSRUNTIME@ mris_sphere 1.1595 hours 1 threads
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0.301...
- 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
- singular matrix in quadratic form
- singular matrix in quadratic form
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %18.70
- pass 1: epoch 2 of 3 starting distance error %18.69
- unfolding complete - removing small folds...
- starting distance error %18.63
- removing remaining folds...
- final distance error %18.65
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 89 negative triangles
- 220: dt=0.9900, 89 negative triangles
- 221: dt=0.9900, 23 negative triangles
- 222: dt=0.9900, 10 negative triangles
- 223: dt=0.9900, 14 negative triangles
- 224: dt=0.9900, 6 negative triangles
- 225: dt=0.9900, 6 negative triangles
- 226: dt=0.9900, 4 negative triangles
- 227: dt=0.9900, 4 negative triangles
- 228: dt=0.9900, 3 negative triangles
- 229: dt=0.9900, 2 negative triangles
- 230: dt=0.9900, 2 negative triangles
- 231: dt=0.9900, 2 negative triangles
- 232: dt=0.9900, 1 negative triangles
- 233: dt=0.9900, 1 negative triangles
- 234: dt=0.9900, 1 negative triangles
- 235: dt=0.9900, 1 negative triangles
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.19 hours
- mris_sphere utimesec 4384.874397
- mris_sphere stimesec 1.973699
- mris_sphere ru_maxrss 289184
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 50516
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 9848
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 137180
- mris_sphere ru_nivcsw 340264
- FSRUNTIME@ mris_sphere 1.1945 hours 1 threads
- PIDs (11695 11699) completed and logs appended.
- #--------------------------------------------
- #@# Surf Reg lh Sun Oct 8 05:52:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg
- #--------------------------------------------
- #@# Surf Reg rh Sun Oct 8 05:52:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 15619 of (15619 15622) to complete...
- Waiting for PID 15622 of (15619 15622) to complete...
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 5.700
- curvature mean = 0.023, std = 0.817
- curvature mean = 0.018, std = 0.868
- Starting MRISrigidBodyAlignGlobal()
- d=16.00 min @ (-4.00, -4.00, 0.00) sse = 227802.1, tmin=3.1244
- d=8.00 min @ (2.00, 2.00, 0.00) sse = 225854.3, tmin=4.2226
- d=4.00 min @ (-1.00, -1.00, 0.00) sse = 223141.5, tmin=5.3361
- d=1.00 min @ (0.25, 0.25, 0.00) sse = 223084.5, tmin=7.5552
- d=0.50 min @ (-0.12, -0.12, 0.00) sse = 223037.5, tmin=8.6392
- tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 8.64 min
- curvature mean = -0.001, std = 0.839
- curvature mean = 0.009, std = 0.945
- curvature mean = -0.002, std = 0.851
- curvature mean = 0.004, std = 0.977
- curvature mean = -0.002, std = 0.854
- curvature mean = 0.001, std = 0.990
- 2 Reading smoothwm
- curvature mean = -0.026, std = 0.315
- curvature mean = 0.039, std = 0.249
- curvature mean = 0.072, std = 0.313
- curvature mean = 0.035, std = 0.306
- curvature mean = 0.041, std = 0.497
- curvature mean = 0.034, std = 0.333
- curvature mean = 0.023, std = 0.638
- curvature mean = 0.034, std = 0.344
- curvature mean = 0.008, std = 0.756
- MRISregister() return, current seed 0
- -01: dt=0.0000, 15 negative triangles
- 111: dt=0.9900, 15 negative triangles
- expanding nbhd size to 1
- 112: dt=0.9900, 19 negative triangles
- 113: dt=0.9900, 13 negative triangles
- 114: dt=0.9900, 19 negative triangles
- 115: dt=0.9900, 21 negative triangles
- 116: dt=0.9900, 20 negative triangles
- 117: dt=0.9900, 20 negative triangles
- 118: dt=0.9900, 18 negative triangles
- 119: dt=0.9900, 15 negative triangles
- 120: dt=0.9900, 13 negative triangles
- 121: dt=0.9900, 8 negative triangles
- 122: dt=0.9900, 9 negative triangles
- 123: dt=0.9900, 6 negative triangles
- 124: dt=0.9900, 4 negative triangles
- 125: dt=0.9900, 2 negative triangles
- 126: dt=0.9900, 2 negative triangles
- writing registered surface to ../surf/lh.sphere.reg...
- registration took 1.56 hours
- mris_register utimesec 5606.586669
- mris_register stimesec 4.234356
- mris_register ru_maxrss 256680
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 36015
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 9728
- mris_register ru_oublock 9792
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 407330
- mris_register ru_nivcsw 269930
- FSRUNTIME@ mris_register 1.5585 hours 1 threads
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 5.713
- curvature mean = 0.027, std = 0.813
- curvature mean = 0.020, std = 0.866
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 0.00) sse = 249752.4, tmin=1.0370
- d=16.00 min @ (-4.00, 0.00, 0.00) sse = 226703.2, tmin=3.1728
- d=4.00 min @ (1.00, 1.00, 1.00) sse = 223628.5, tmin=5.3280
- d=2.00 min @ (0.00, 0.00, -0.50) sse = 222983.6, tmin=6.4211
- d=1.00 min @ (-0.25, 0.00, 0.00) sse = 222951.1, tmin=7.5114
- d=0.50 min @ (0.12, 0.00, 0.12) sse = 222924.3, tmin=8.5917
- tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 8.59 min
- curvature mean = -0.005, std = 0.828
- curvature mean = 0.009, std = 0.946
- curvature mean = -0.009, std = 0.837
- curvature mean = 0.004, std = 0.978
- curvature mean = -0.011, std = 0.839
- curvature mean = 0.001, std = 0.991
- 2 Reading smoothwm
- curvature mean = -0.026, std = 0.319
- curvature mean = 0.033, std = 0.240
- curvature mean = 0.075, std = 0.318
- curvature mean = 0.029, std = 0.297
- curvature mean = 0.040, std = 0.500
- curvature mean = 0.029, std = 0.322
- curvature mean = 0.023, std = 0.639
- curvature mean = 0.029, std = 0.334
- curvature mean = 0.008, std = 0.758
- MRISregister() return, current seed 0
- -01: dt=0.0000, 19 negative triangles
- 115: dt=0.9900, 19 negative triangles
- expanding nbhd size to 1
- 116: dt=0.9900, 27 negative triangles
- 117: dt=0.9900, 18 negative triangles
- 118: dt=0.9900, 12 negative triangles
- 119: dt=0.9900, 17 negative triangles
- 120: dt=0.9900, 18 negative triangles
- 121: dt=0.9900, 15 negative triangles
- 122: dt=0.9900, 7 negative triangles
- 123: dt=0.9900, 7 negative triangles
- 124: dt=0.9900, 15 negative triangles
- 125: dt=0.9900, 7 negative triangles
- 126: dt=0.9900, 9 negative triangles
- 127: dt=0.9900, 7 negative triangles
- 128: dt=0.9900, 4 negative triangles
- 129: dt=0.9900, 4 negative triangles
- 130: dt=0.9900, 2 negative triangles
- 131: dt=0.9900, 3 negative triangles
- 132: dt=0.9900, 1 negative triangles
- 133: dt=0.9900, 4 negative triangles
- writing registered surface to ../surf/rh.sphere.reg...
- registration took 1.57 hours
- mris_register utimesec 5649.931079
- mris_register stimesec 4.622297
- mris_register ru_maxrss 258224
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 36443
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 9880
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 404345
- mris_register ru_nivcsw 270991
- FSRUNTIME@ mris_register 1.5706 hours 1 threads
- PIDs (15619 15622) completed and logs appended.
- #--------------------------------------------
- #@# Jacobian white lh Sun Oct 8 07:26:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# Jacobian white rh Sun Oct 8 07:26:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- Waiting for PID 23687 of (23687 23690) to complete...
- Waiting for PID 23690 of (23687 23690) 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 (23687 23690) completed and logs appended.
- #--------------------------------------------
- #@# AvgCurv lh Sun Oct 8 07:27:00 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 07:27:00 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 23733 of (23733 23736) to complete...
- Waiting for PID 23736 of (23733 23736) 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 (23733 23736) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc lh Sun Oct 8 07:27:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 07:27:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 23783 of (23783 23786) to complete...
- Waiting for PID 23786 of (23783 23786) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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...
- 1033 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3032 changed, 138191 examined...
- 001: 716 changed, 12871 examined...
- 002: 169 changed, 4065 examined...
- 003: 64 changed, 1012 examined...
- 004: 24 changed, 393 examined...
- 005: 11 changed, 156 examined...
- 006: 6 changed, 65 examined...
- 007: 0 changed, 36 examined...
- 241 labels changed using aseg
- 000: 120 total segments, 78 labels (350 vertices) changed
- 001: 42 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 10 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1638 vertices marked for relabeling...
- 1638 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 15 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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...
- 1353 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2925 changed, 139374 examined...
- 001: 722 changed, 12530 examined...
- 002: 138 changed, 3960 examined...
- 003: 47 changed, 832 examined...
- 004: 26 changed, 286 examined...
- 005: 9 changed, 154 examined...
- 006: 3 changed, 54 examined...
- 007: 3 changed, 18 examined...
- 008: 1 changed, 18 examined...
- 009: 1 changed, 7 examined...
- 010: 0 changed, 7 examined...
- 122 labels changed using aseg
- 000: 101 total segments, 64 labels (310 vertices) changed
- 001: 38 total segments, 1 labels (1 vertices) changed
- 002: 37 total segments, 0 labels (0 vertices) changed
- 8 filter iterations complete (10 requested, 0 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1320 vertices marked for relabeling...
- 1320 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 15 seconds.
- PIDs (23783 23786) completed and logs appended.
- #--------------------------------------------
- #@# Make Pial Surf lh Sun Oct 8 07:27:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051311 lh
- #--------------------------------------------
- #@# Make Pial Surf rh Sun Oct 8 07:27:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051311 rh
- Waiting for PID 23846 of (23846 23849) to complete...
- Waiting for PID 23849 of (23846 23849) to complete...
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051311 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-6.0.0/0051311/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- 35848 bright wm thresholded.
- 156 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.orig...
- computing class statistics...
- border white: 240312 voxels (1.43%)
- border gray 287731 voxels (1.72%)
- WM (99.0): 98.1 +- 10.3 [70.0 --> 110.0]
- GM (60.0) : 61.5 +- 10.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 45.3 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 56.0 (was 85)
- setting MAX_CSF to 34.7 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 45.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 24.0 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105+-7.0, GM=56+-7.0
- mean inside = 91.9, mean outside = 65.1
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.25 (0.03-->3.35) (max @ vno 90257 --> 91467)
- face area 0.33 +- 0.15 (0.00-->2.81)
- mean absolute distance = 0.49 +- 0.62
- 2437 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 83 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 1 with 3 points - only 0.00% unknown
- deleting segment 3 with 19 points - only 0.00% unknown
- deleting segment 5 with 17 points - only 0.00% unknown
- deleting segment 6 with 11 points - only 0.00% unknown
- deleting segment 7 with 166 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 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 8 points - only 0.00% unknown
- deleting segment 11 with 27 points - only 0.00% unknown
- deleting segment 13 with 6 points - only 0.00% unknown
- deleting segment 14 with 5 points - only 0.00% unknown
- deleting segment 15 with 15 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 16 with 1 points - only 0.00% unknown
- deleting segment 17 with 7 points - only 0.00% unknown
- deleting segment 18 with 19 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 19 with 2 points - only 0.00% unknown
- deleting segment 20 with 19 points - only 0.00% unknown
- mean border=70.5, 113 (112) missing vertices, mean dist 0.4 [0.6 (%10.4)->0.5 (%89.6))]
- %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.11-->3.58) (max @ vno 137832 --> 137848)
- face area 0.33 +- 0.16 (0.00-->2.58)
- mean absolute distance = 0.28 +- 0.40
- 2414 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3755122.5, rms=10.794
- 001: dt: 0.5000, sse=1720844.8, rms=6.294 (41.697%)
- 002: dt: 0.5000, sse=1358764.8, rms=5.124 (18.583%)
- 003: dt: 0.5000, sse=1314777.1, rms=4.971 (2.987%)
- 004: dt: 0.5000, sse=1252582.4, rms=4.735 (4.745%)
- rms = 4.84, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.2500, sse=949344.0, rms=3.266 (31.025%)
- 006: dt: 0.2500, sse=877987.2, rms=2.809 (13.996%)
- 007: dt: 0.2500, sse=841022.6, rms=2.544 (9.443%)
- rms = 2.55, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.1250, sse=820443.2, rms=2.386 (6.187%)
- 009: dt: 0.1250, sse=795615.6, rms=2.152 (9.837%)
- rms = 2.11, time step reduction 3 of 3 to 0.062...
- 010: dt: 0.1250, sse=789494.6, rms=2.105 (2.156%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 64 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 17 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 29 points - only 0.00% unknown
- deleting segment 6 with 47 points - only 0.00% unknown
- deleting segment 7 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 11 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- mean border=75.6, 127 (45) missing vertices, mean dist -0.2 [0.3 (%81.2)->0.2 (%18.8))]
- %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.25 (0.07-->3.74) (max @ vno 103892 --> 102841)
- face area 0.35 +- 0.17 (0.00-->2.92)
- mean absolute distance = 0.19 +- 0.28
- 2959 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1829541.1, rms=6.500
- 011: dt: 0.5000, sse=1274621.9, rms=4.612 (29.043%)
- rms = 4.99, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.2500, sse=978680.4, rms=3.181 (31.019%)
- 013: dt: 0.2500, sse=888229.3, rms=2.577 (19.006%)
- 014: dt: 0.2500, sse=843763.6, rms=2.248 (12.752%)
- rms = 2.30, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.1250, sse=818631.8, rms=2.023 (10.024%)
- 016: dt: 0.1250, sse=785208.8, rms=1.676 (17.151%)
- 017: dt: 0.1250, sse=779556.1, rms=1.607 (4.131%)
- rms = 1.61, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=779488.3, rms=1.606 (0.043%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 63 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 16 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 5 points - only 0.00% unknown
- deleting segment 5 with 42 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 38 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- deleting segment 12 with 5 points - only 0.00% unknown
- deleting segment 13 with 14 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 14 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- deleting segment 16 with 9 points - only 0.00% unknown
- mean border=78.4, 122 (42) missing vertices, mean dist -0.1 [0.2 (%72.6)->0.2 (%27.4))]
- %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.07-->3.84) (max @ vno 103892 --> 102841)
- face area 0.34 +- 0.16 (0.00-->2.91)
- mean absolute distance = 0.16 +- 0.25
- 2168 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1055452.4, rms=3.723
- rms = 4.64, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=844207.4, rms=2.417 (35.075%)
- 020: dt: 0.2500, sse=781465.7, rms=1.848 (23.528%)
- rms = 1.84, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=781604.3, rms=1.838 (0.528%)
- 022: dt: 0.1250, sse=745635.4, rms=1.448 (21.246%)
- 023: dt: 0.1250, sse=741126.8, rms=1.395 (3.653%)
- rms = 1.40, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=741352.9, rms=1.405 (-0.695%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 69 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 16 points - only 0.00% unknown
- deleting segment 3 with 9 points - only 0.00% unknown
- deleting segment 4 with 5 points - only 0.00% unknown
- deleting segment 5 with 55 points - only 0.00% unknown
- deleting segment 6 with 42 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 9 with 6 points - only 0.00% unknown
- deleting segment 10 with 10 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- deleting segment 12 with 5 points - only 0.00% unknown
- deleting segment 13 with 15 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- deleting segment 15 with 12 points - only 0.00% unknown
- mean border=79.3, 119 (39) missing vertices, mean dist -0.0 [0.2 (%56.3)->0.2 (%43.7))]
- %91 local maxima, % 4 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-6.0.0/0051311/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=765083.0, rms=1.774
- rms = 3.17, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=714790.0, rms=1.123 (36.713%)
- 026: dt: 0.2500, sse=712543.6, rms=1.049 (6.567%)
- rms = 1.07, time step reduction 2 of 3 to 0.125...
- rms = 1.02, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=708560.7, rms=1.023 (2.540%)
- positioning took 0.5 minutes
- generating cortex label...
- 11 non-cortical segments detected
- only using segment with 7168 vertices
- erasing segment 1 (vno[0] = 76332)
- erasing segment 2 (vno[0] = 84616)
- erasing segment 3 (vno[0] = 91531)
- erasing segment 4 (vno[0] = 94153)
- erasing segment 5 (vno[0] = 98442)
- erasing segment 6 (vno[0] = 98478)
- erasing segment 7 (vno[0] = 98489)
- erasing segment 8 (vno[0] = 98786)
- erasing segment 9 (vno[0] = 104034)
- erasing segment 10 (vno[0] = 108007)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.area
- vertex spacing 0.90 +- 0.26 (0.03-->3.82) (max @ vno 102841 --> 103892)
- face area 0.34 +- 0.16 (0.00-->2.94)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=43.8, 95 (95) missing vertices, mean dist 1.6 [1.1 (%0.0)->2.8 (%100.0))]
- % 9 local maxima, %45 large gradients and %42 min vals, 220 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=35400876.0, rms=36.216
- 001: dt: 0.0500, sse=30142642.0, rms=33.361 (7.881%)
- 002: dt: 0.0500, sse=26413566.0, rms=31.179 (6.541%)
- 003: dt: 0.0500, sse=23615460.0, rms=29.435 (5.593%)
- 004: dt: 0.0500, sse=21416034.0, rms=27.989 (4.915%)
- 005: dt: 0.0500, sse=19622606.0, rms=26.751 (4.422%)
- 006: dt: 0.0500, sse=18119448.0, rms=25.667 (4.050%)
- 007: dt: 0.0500, sse=16831526.0, rms=24.701 (3.764%)
- 008: dt: 0.0500, sse=15711696.0, rms=23.829 (3.530%)
- 009: dt: 0.0500, sse=14724296.0, rms=23.033 (3.341%)
- 010: dt: 0.0500, sse=13846595.0, rms=22.301 (3.177%)
- positioning took 1.0 minutes
- mean border=43.7, 76 (48) missing vertices, mean dist 1.3 [0.5 (%0.1)->2.3 (%99.9))]
- %10 local maxima, %45 large gradients and %41 min vals, 218 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=14543182.0, rms=22.888
- 011: dt: 0.0500, sse=13754083.0, rms=22.227 (2.887%)
- 012: dt: 0.0500, sse=13043432.0, rms=21.615 (2.756%)
- 013: dt: 0.0500, sse=12399521.0, rms=21.044 (2.639%)
- 014: dt: 0.0500, sse=11814524.0, rms=20.512 (2.528%)
- 015: dt: 0.0500, sse=11282697.0, rms=20.016 (2.418%)
- 016: dt: 0.0500, sse=10798164.0, rms=19.553 (2.313%)
- 017: dt: 0.0500, sse=10355857.0, rms=19.121 (2.212%)
- 018: dt: 0.0500, sse=9950833.0, rms=18.716 (2.118%)
- 019: dt: 0.0500, sse=9579313.0, rms=18.336 (2.027%)
- 020: dt: 0.0500, sse=9237729.0, rms=17.980 (1.941%)
- positioning took 1.0 minutes
- mean border=43.6, 85 (34) missing vertices, mean dist 1.1 [0.1 (%0.7)->2.0 (%99.3))]
- %10 local maxima, %44 large gradients and %41 min vals, 208 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=9338763.0, rms=18.093
- 021: dt: 0.0500, sse=9018147.0, rms=17.755 (1.871%)
- 022: dt: 0.0500, sse=8721436.0, rms=17.436 (1.798%)
- 023: dt: 0.0500, sse=8445248.0, rms=17.133 (1.735%)
- 024: dt: 0.0500, sse=8188415.0, rms=16.847 (1.671%)
- 025: dt: 0.0500, sse=7948759.5, rms=16.575 (1.613%)
- 026: dt: 0.0500, sse=7723675.5, rms=16.315 (1.565%)
- 027: dt: 0.0500, sse=7510516.5, rms=16.066 (1.530%)
- 028: dt: 0.0500, sse=7307269.5, rms=15.824 (1.505%)
- 029: dt: 0.0500, sse=7112988.0, rms=15.589 (1.483%)
- 030: dt: 0.0500, sse=6926479.0, rms=15.360 (1.468%)
- positioning took 0.9 minutes
- mean border=43.5, 112 (30) missing vertices, mean dist 0.9 [0.1 (%4.9)->1.7 (%95.1))]
- %10 local maxima, %44 large gradients and %41 min vals, 166 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=6972207.5, rms=15.419
- 031: dt: 0.5000, sse=5598785.5, rms=13.625 (11.640%)
- 032: dt: 0.5000, sse=4584189.0, rms=12.123 (11.021%)
- 033: dt: 0.5000, sse=3793819.2, rms=10.811 (10.822%)
- 034: dt: 0.5000, sse=3181480.2, rms=9.667 (10.578%)
- 035: dt: 0.5000, sse=2730441.5, rms=8.729 (9.705%)
- 036: dt: 0.5000, sse=2366877.2, rms=7.889 (9.629%)
- 037: dt: 0.5000, sse=2089727.8, rms=7.184 (8.930%)
- 038: dt: 0.5000, sse=1870660.0, rms=6.573 (8.510%)
- 039: dt: 0.5000, sse=1730285.9, rms=6.149 (6.445%)
- 040: dt: 0.5000, sse=1625369.5, rms=5.812 (5.489%)
- 041: dt: 0.5000, sse=1570804.9, rms=5.628 (3.152%)
- 042: dt: 0.5000, sse=1521996.8, rms=5.458 (3.024%)
- 043: dt: 0.5000, sse=1496413.9, rms=5.368 (1.657%)
- 044: dt: 0.5000, sse=1465133.0, rms=5.254 (2.122%)
- rms = 5.23, time step reduction 1 of 3 to 0.250...
- 045: dt: 0.5000, sse=1459227.6, rms=5.232 (0.425%)
- 046: dt: 0.2500, sse=1347008.4, rms=4.757 (9.069%)
- 047: dt: 0.2500, sse=1311001.9, rms=4.612 (3.048%)
- rms = 4.62, time step reduction 2 of 3 to 0.125...
- rms = 4.57, time step reduction 3 of 3 to 0.062...
- 048: dt: 0.1250, sse=1302025.4, rms=4.572 (0.879%)
- positioning took 2.5 minutes
- mean border=42.2, 2417 (15) missing vertices, mean dist 0.1 [0.2 (%47.2)->0.6 (%52.8))]
- %20 local maxima, %36 large gradients and %39 min vals, 100 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=1629398.2, rms=5.002
- 049: dt: 0.5000, sse=1534525.8, rms=4.632 (7.395%)
- 050: dt: 0.5000, sse=1497675.2, rms=4.513 (2.571%)
- rms = 4.57, time step reduction 1 of 3 to 0.250...
- 051: dt: 0.2500, sse=1371910.9, rms=3.893 (13.723%)
- 052: dt: 0.2500, sse=1337024.2, rms=3.697 (5.052%)
- rms = 3.65, time step reduction 2 of 3 to 0.125...
- 053: dt: 0.2500, sse=1328096.1, rms=3.649 (1.284%)
- 054: dt: 0.1250, sse=1298250.0, rms=3.477 (4.719%)
- rms = 3.44, time step reduction 3 of 3 to 0.062...
- 055: dt: 0.1250, sse=1291071.1, rms=3.438 (1.108%)
- positioning took 1.3 minutes
- mean border=41.4, 2512 (11) missing vertices, mean dist 0.1 [0.2 (%48.1)->0.4 (%51.9))]
- %35 local maxima, %21 large gradients and %38 min vals, 99 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=1355480.8, rms=3.741
- rms = 4.21, time step reduction 1 of 3 to 0.250...
- 056: dt: 0.2500, sse=1316513.9, rms=3.529 (5.675%)
- 057: dt: 0.2500, sse=1304796.2, rms=3.469 (1.695%)
- rms = 3.46, time step reduction 2 of 3 to 0.125...
- 058: dt: 0.2500, sse=1302105.6, rms=3.463 (0.171%)
- 059: dt: 0.1250, sse=1281792.0, rms=3.343 (3.473%)
- rms = 3.31, time step reduction 3 of 3 to 0.062...
- 060: dt: 0.1250, sse=1275961.2, rms=3.312 (0.910%)
- positioning took 1.0 minutes
- mean border=40.8, 4618 (10) missing vertices, mean dist 0.0 [0.2 (%50.1)->0.3 (%49.9))]
- %37 local maxima, %18 large gradients and %37 min vals, 110 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-6.0.0/0051311/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1298095.1, rms=3.415
- rms = 3.82, time step reduction 1 of 3 to 0.250...
- 061: dt: 0.2500, sse=1279861.1, rms=3.307 (3.139%)
- rms = 3.26, time step reduction 2 of 3 to 0.125...
- 062: dt: 0.2500, sse=1268734.1, rms=3.260 (1.423%)
- 063: dt: 0.1250, sse=1258230.9, rms=3.193 (2.059%)
- rms = 3.16, time step reduction 3 of 3 to 0.062...
- 064: dt: 0.1250, sse=1252270.2, rms=3.164 (0.930%)
- positioning took 0.9 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.area.pial
- vertex spacing 1.04 +- 0.46 (0.09-->6.78) (max @ vno 92738 --> 91562)
- face area 0.42 +- 0.34 (0.00-->5.97)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 138191 vertices processed
- 25000 of 138191 vertices processed
- 50000 of 138191 vertices processed
- 75000 of 138191 vertices processed
- 100000 of 138191 vertices processed
- 125000 of 138191 vertices processed
- 0 of 138191 vertices processed
- 25000 of 138191 vertices processed
- 50000 of 138191 vertices processed
- 75000 of 138191 vertices processed
- 100000 of 138191 vertices processed
- 125000 of 138191 vertices processed
- thickness calculation complete, 143:745 truncations.
- 28741 vertices at 0 distance
- 95024 vertices at 1 distance
- 87752 vertices at 2 distance
- 37377 vertices at 3 distance
- 11270 vertices at 4 distance
- 3122 vertices at 5 distance
- 922 vertices at 6 distance
- 311 vertices at 7 distance
- 122 vertices at 8 distance
- 61 vertices at 9 distance
- 60 vertices at 10 distance
- 43 vertices at 11 distance
- 33 vertices at 12 distance
- 25 vertices at 13 distance
- 20 vertices at 14 distance
- 24 vertices at 15 distance
- 22 vertices at 16 distance
- 21 vertices at 17 distance
- 15 vertices at 18 distance
- 15 vertices at 19 distance
- 10 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.thickness
- positioning took 15.8 minutes
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051311 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-6.0.0/0051311/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- 35848 bright wm thresholded.
- 156 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.orig...
- computing class statistics...
- border white: 240312 voxels (1.43%)
- border gray 287731 voxels (1.72%)
- WM (99.0): 98.1 +- 10.3 [70.0 --> 110.0]
- GM (60.0) : 61.5 +- 10.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 58.0 (was 85)
- setting MAX_CSF to 36.7 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 47.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 26.0 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105+-7.0, GM=58+-6.1
- mean inside = 92.0, mean outside = 65.8
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.04-->6.08) (max @ vno 60282 --> 138977)
- face area 0.33 +- 0.16 (0.00-->7.91)
- mean absolute distance = 0.48 +- 0.63
- 2484 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 9 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 3 with 8 points - only 0.00% unknown
- deleting segment 4 with 7 points - only 0.00% unknown
- deleting segment 5 with 181 points - only 0.00% unknown
- deleting segment 6 with 8 points - only 0.00% unknown
- deleting segment 7 with 12 points - only 0.00% unknown
- deleting segment 8 with 34 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 points - only 0.00% unknown
- mean border=71.9, 71 (71) missing vertices, mean dist 0.3 [0.6 (%11.3)->0.5 (%88.7))]
- %70 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.08-->6.18) (max @ vno 60282 --> 138977)
- face area 0.33 +- 0.16 (0.00-->7.21)
- mean absolute distance = 0.28 +- 0.39
- 1995 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3506080.5, rms=10.292
- 001: dt: 0.5000, sse=1637130.2, rms=5.947 (42.215%)
- 002: dt: 0.5000, sse=1305644.6, rms=4.883 (17.894%)
- rms = 4.83, time step reduction 1 of 3 to 0.250...
- 003: dt: 0.5000, sse=1289566.8, rms=4.833 (1.024%)
- 004: dt: 0.2500, sse=900513.7, rms=2.920 (39.584%)
- 005: dt: 0.2500, sse=852226.1, rms=2.594 (11.165%)
- 006: dt: 0.2500, sse=841431.1, rms=2.505 (3.426%)
- rms = 2.47, time step reduction 2 of 3 to 0.125...
- 007: dt: 0.2500, sse=838076.6, rms=2.466 (1.569%)
- 008: dt: 0.1250, sse=788703.8, rms=2.061 (16.399%)
- 009: dt: 0.1250, sse=783273.6, rms=1.987 (3.614%)
- rms = 1.97, time step reduction 3 of 3 to 0.062...
- 010: dt: 0.1250, sse=780424.3, rms=1.974 (0.665%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 9 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 4 with 48 points - only 0.00% unknown
- deleting segment 5 with 61 points - only 0.00% unknown
- deleting segment 6 with 8 points - only 0.00% unknown
- deleting segment 7 with 5 points - only 0.00% unknown
- deleting segment 9 with 6 points - only 0.00% unknown
- deleting segment 10 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 11 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- mean border=76.8, 70 (13) missing vertices, mean dist -0.2 [0.3 (%80.5)->0.2 (%19.5))]
- %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.12-->6.34) (max @ vno 60282 --> 138977)
- face area 0.35 +- 0.17 (0.00-->8.36)
- mean absolute distance = 0.19 +- 0.29
- 2215 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1736477.6, rms=6.191
- 011: dt: 0.5000, sse=1224823.8, rms=4.380 (29.249%)
- rms = 4.85, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.2500, sse=942636.1, rms=2.937 (32.940%)
- 013: dt: 0.2500, sse=864538.9, rms=2.383 (18.875%)
- 014: dt: 0.2500, sse=830967.2, rms=2.099 (11.912%)
- rms = 2.14, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.1250, sse=815277.8, rms=1.886 (10.134%)
- 016: dt: 0.1250, sse=778571.7, rms=1.558 (17.378%)
- 017: dt: 0.1250, sse=773968.8, rms=1.506 (3.381%)
- rms = 1.51, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=774367.0, rms=1.514 (-0.546%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 11 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 66 points - only 0.00% unknown
- deleting segment 4 with 64 points - only 0.00% unknown
- deleting segment 5 with 9 points - only 0.00% unknown
- deleting segment 6 with 15 points - only 0.00% unknown
- deleting segment 7 with 18 points - only 0.00% unknown
- deleting segment 8 with 11 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 10 with 8 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- mean border=79.5, 81 (9) missing vertices, mean dist -0.1 [0.2 (%72.2)->0.2 (%27.8))]
- %90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.04-->6.49) (max @ vno 60282 --> 138977)
- face area 0.34 +- 0.17 (0.00-->8.51)
- mean absolute distance = 0.16 +- 0.25
- 2171 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1030806.9, rms=3.559
- rms = 4.52, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=831310.8, rms=2.276 (36.065%)
- 020: dt: 0.2500, sse=778198.8, rms=1.744 (23.345%)
- rms = 1.73, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=773353.0, rms=1.732 (0.710%)
- 022: dt: 0.1250, sse=744248.8, rms=1.383 (20.166%)
- rms = 1.33, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=741281.4, rms=1.334 (3.503%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 11 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 7 points - only 0.00% unknown
- deleting segment 3 with 82 points - only 0.00% unknown
- deleting segment 4 with 64 points - only 0.00% unknown
- deleting segment 5 with 9 points - only 0.00% unknown
- deleting segment 6 with 17 points - only 0.00% unknown
- deleting segment 7 with 34 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 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 10 with 3 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 11 with 4 points - only 0.00% unknown
- mean border=80.2, 75 (6) missing vertices, mean dist -0.0 [0.2 (%55.4)->0.2 (%44.6))]
- %91 local maxima, % 5 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-6.0.0/0051311/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=762835.1, rms=1.693
- rms = 3.04, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=716406.3, rms=1.070 (36.794%)
- 025: dt: 0.2500, sse=720953.5, rms=1.004 (6.194%)
- rms = 1.02, time step reduction 2 of 3 to 0.125...
- rms = 0.98, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=712810.8, rms=0.979 (2.487%)
- positioning took 0.5 minutes
- generating cortex label...
- 7 non-cortical segments detected
- only using segment with 6998 vertices
- erasing segment 1 (vno[0] = 100245)
- erasing segment 2 (vno[0] = 100483)
- erasing segment 3 (vno[0] = 101478)
- erasing segment 4 (vno[0] = 101683)
- erasing segment 5 (vno[0] = 102458)
- erasing segment 6 (vno[0] = 106694)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.area
- vertex spacing 0.90 +- 0.26 (0.02-->6.50) (max @ vno 60282 --> 138977)
- face area 0.34 +- 0.16 (0.00-->8.45)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=45.7, 68 (68) missing vertices, mean dist 1.6 [0.7 (%0.0)->2.8 (%100.0))]
- %11 local maxima, %45 large gradients and %40 min vals, 252 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=33686880.0, rms=35.163
- 001: dt: 0.0500, sse=28598608.0, rms=32.340 (8.029%)
- 002: dt: 0.0500, sse=24998718.0, rms=30.183 (6.669%)
- 003: dt: 0.0500, sse=22307940.0, rms=28.464 (5.695%)
- 004: dt: 0.0500, sse=20196632.0, rms=27.039 (5.007%)
- 005: dt: 0.0500, sse=18481422.0, rms=25.823 (4.496%)
- 006: dt: 0.0500, sse=17047234.0, rms=24.761 (4.114%)
- 007: dt: 0.0500, sse=15822758.0, rms=23.817 (3.815%)
- 008: dt: 0.0500, sse=14760817.0, rms=22.966 (3.572%)
- 009: dt: 0.0500, sse=13828668.0, rms=22.192 (3.369%)
- 010: dt: 0.0500, sse=13001732.0, rms=21.483 (3.198%)
- positioning took 1.0 minutes
- mean border=45.6, 62 (30) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.3 (%100.0))]
- %12 local maxima, %45 large gradients and %40 min vals, 284 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=13753555.0, rms=22.134
- 011: dt: 0.0500, sse=13011137.0, rms=21.496 (2.881%)
- 012: dt: 0.0500, sse=12343652.0, rms=20.906 (2.745%)
- 013: dt: 0.0500, sse=11739548.0, rms=20.357 (2.625%)
- 014: dt: 0.0500, sse=11190804.0, rms=19.846 (2.514%)
- 015: dt: 0.0500, sse=10692594.0, rms=19.369 (2.400%)
- 016: dt: 0.0500, sse=10238159.0, rms=18.924 (2.298%)
- 017: dt: 0.0500, sse=9823011.0, rms=18.508 (2.198%)
- 018: dt: 0.0500, sse=9443201.0, rms=18.119 (2.102%)
- 019: dt: 0.0500, sse=9094914.0, rms=17.755 (2.011%)
- 020: dt: 0.0500, sse=8774104.0, rms=17.412 (1.929%)
- positioning took 1.0 minutes
- mean border=45.5, 70 (22) missing vertices, mean dist 1.1 [0.1 (%0.7)->2.0 (%99.3))]
- %12 local maxima, %45 large gradients and %39 min vals, 266 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=8848638.0, rms=17.501
- 021: dt: 0.0500, sse=8547564.0, rms=17.175 (1.863%)
- 022: dt: 0.0500, sse=8269377.5, rms=16.868 (1.787%)
- 023: dt: 0.0500, sse=8009411.5, rms=16.576 (1.731%)
- 024: dt: 0.0500, sse=7767427.0, rms=16.299 (1.669%)
- 025: dt: 0.0500, sse=7541563.5, rms=16.037 (1.611%)
- 026: dt: 0.0500, sse=7329277.5, rms=15.786 (1.565%)
- 027: dt: 0.0500, sse=7127478.5, rms=15.543 (1.535%)
- 028: dt: 0.0500, sse=6934666.0, rms=15.308 (1.514%)
- 029: dt: 0.0500, sse=6749800.0, rms=15.079 (1.497%)
- 030: dt: 0.0500, sse=6571519.5, rms=14.855 (1.488%)
- positioning took 1.0 minutes
- mean border=45.4, 94 (17) missing vertices, mean dist 1.0 [0.1 (%5.2)->1.7 (%94.8))]
- %12 local maxima, %44 large gradients and %39 min vals, 242 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=6635909.0, rms=14.938
- 031: dt: 0.5000, sse=5311811.5, rms=13.164 (11.876%)
- 032: dt: 0.5000, sse=4357166.5, rms=11.713 (11.025%)
- 033: dt: 0.5000, sse=3644997.2, rms=10.501 (10.346%)
- 034: dt: 0.5000, sse=3093473.2, rms=9.450 (10.012%)
- 035: dt: 0.5000, sse=2674150.0, rms=8.564 (9.375%)
- 036: dt: 0.5000, sse=2334165.0, rms=7.769 (9.280%)
- 037: dt: 0.5000, sse=2068139.1, rms=7.087 (8.785%)
- 038: dt: 0.5000, sse=1857737.1, rms=6.496 (8.337%)
- 039: dt: 0.5000, sse=1712160.9, rms=6.055 (6.793%)
- 040: dt: 0.5000, sse=1605909.4, rms=5.710 (5.696%)
- 041: dt: 0.5000, sse=1540755.8, rms=5.490 (3.851%)
- 042: dt: 0.5000, sse=1492366.5, rms=5.318 (3.129%)
- 043: dt: 0.5000, sse=1463870.8, rms=5.215 (1.941%)
- 044: dt: 0.5000, sse=1441382.5, rms=5.132 (1.597%)
- 045: dt: 0.5000, sse=1426086.8, rms=5.075 (1.097%)
- rms = 5.04, time step reduction 1 of 3 to 0.250...
- 046: dt: 0.5000, sse=1416135.0, rms=5.035 (0.785%)
- 047: dt: 0.2500, sse=1308482.0, rms=4.564 (9.371%)
- 048: dt: 0.2500, sse=1272248.1, rms=4.411 (3.334%)
- rms = 4.41, time step reduction 2 of 3 to 0.125...
- 049: dt: 0.2500, sse=1273089.4, rms=4.411 (0.010%)
- 050: dt: 0.1250, sse=1252802.1, rms=4.317 (2.129%)
- rms = 4.30, time step reduction 3 of 3 to 0.062...
- 051: dt: 0.1250, sse=1250073.1, rms=4.305 (0.288%)
- positioning took 2.9 minutes
- mean border=44.0, 2227 (5) missing vertices, mean dist 0.1 [0.2 (%45.5)->0.6 (%54.5))]
- %23 local maxima, %35 large gradients and %36 min vals, 129 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=1593886.6, rms=4.846
- 052: dt: 0.5000, sse=1497191.9, rms=4.467 (7.823%)
- 053: dt: 0.5000, sse=1466858.5, rms=4.372 (2.119%)
- rms = 4.41, time step reduction 1 of 3 to 0.250...
- 054: dt: 0.2500, sse=1339865.2, rms=3.729 (14.697%)
- 055: dt: 0.2500, sse=1301667.6, rms=3.508 (5.944%)
- rms = 3.46, time step reduction 2 of 3 to 0.125...
- 056: dt: 0.2500, sse=1294036.9, rms=3.465 (1.222%)
- 057: dt: 0.1250, sse=1264678.0, rms=3.288 (5.097%)
- rms = 3.25, time step reduction 3 of 3 to 0.062...
- 058: dt: 0.1250, sse=1257964.2, rms=3.251 (1.146%)
- positioning took 1.3 minutes
- mean border=43.0, 2351 (5) missing vertices, mean dist 0.1 [0.2 (%44.7)->0.4 (%55.3))]
- %38 local maxima, %21 large gradients and %35 min vals, 137 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=1336434.6, rms=3.646
- rms = 4.08, time step reduction 1 of 3 to 0.250...
- 059: dt: 0.2500, sse=1290467.0, rms=3.389 (7.028%)
- 060: dt: 0.2500, sse=1274165.2, rms=3.300 (2.648%)
- rms = 3.29, time step reduction 2 of 3 to 0.125...
- 061: dt: 0.2500, sse=1270490.0, rms=3.289 (0.332%)
- 062: dt: 0.1250, sse=1252317.0, rms=3.175 (3.454%)
- rms = 3.15, time step reduction 3 of 3 to 0.062...
- 063: dt: 0.1250, sse=1247989.9, rms=3.152 (0.728%)
- positioning took 1.0 minutes
- mean border=42.4, 4370 (5) missing vertices, mean dist 0.0 [0.2 (%48.3)->0.3 (%51.7))]
- %40 local maxima, %18 large gradients and %35 min vals, 134 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-6.0.0/0051311/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=1269251.2, rms=3.261
- rms = 3.71, time step reduction 1 of 3 to 0.250...
- 064: dt: 0.2500, sse=1250575.6, rms=3.147 (3.489%)
- rms = 3.11, time step reduction 2 of 3 to 0.125...
- 065: dt: 0.2500, sse=1241583.0, rms=3.110 (1.186%)
- 066: dt: 0.1250, sse=1231497.6, rms=3.043 (2.143%)
- rms = 3.02, time step reduction 3 of 3 to 0.062...
- 067: dt: 0.1250, sse=1226325.2, rms=3.017 (0.855%)
- positioning took 0.9 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.area.pial
- vertex spacing 1.03 +- 0.46 (0.03-->9.26) (max @ vno 139072 --> 65119)
- face area 0.42 +- 0.34 (0.00-->6.53)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 139374 vertices processed
- 25000 of 139374 vertices processed
- 50000 of 139374 vertices processed
- 75000 of 139374 vertices processed
- 100000 of 139374 vertices processed
- 125000 of 139374 vertices processed
- 0 of 139374 vertices processed
- 25000 of 139374 vertices processed
- 50000 of 139374 vertices processed
- 75000 of 139374 vertices processed
- 100000 of 139374 vertices processed
- 125000 of 139374 vertices processed
- thickness calculation complete, 221:675 truncations.
- 28637 vertices at 0 distance
- 93291 vertices at 1 distance
- 88975 vertices at 2 distance
- 38766 vertices at 3 distance
- 11881 vertices at 4 distance
- 3540 vertices at 5 distance
- 1139 vertices at 6 distance
- 347 vertices at 7 distance
- 151 vertices at 8 distance
- 95 vertices at 9 distance
- 52 vertices at 10 distance
- 21 vertices at 11 distance
- 26 vertices at 12 distance
- 35 vertices at 13 distance
- 31 vertices at 14 distance
- 28 vertices at 15 distance
- 26 vertices at 16 distance
- 31 vertices at 17 distance
- 17 vertices at 18 distance
- 15 vertices at 19 distance
- 26 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.thickness
- positioning took 15.9 minutes
- PIDs (23846 23849) completed and logs appended.
- #--------------------------------------------
- #@# Surf Volume lh Sun Oct 8 07:43:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label
- Total face volume 271164
- Total vertex volume 267919 (mask=0)
- #@# 0051311 lh 267919
-
- vertexvol Done
- #--------------------------------------------
- #@# Surf Volume rh Sun Oct 8 07:43:15 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label
- Total face volume 271597
- Total vertex volume 268028 (mask=0)
- #@# 0051311 rh 268028
-
- vertexvol Done
- #--------------------------------------------
- #@# Cortical ribbon mask Sun Oct 8 07:43:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311
- 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 = 238
- writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/ribbon.mgz
- mris_volmask took 17.72 minutes
- writing ribbon files
- #-----------------------------------------
- #@# Parcellation Stats lh Sun Oct 8 08:01:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 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 0051311 lh pial
- #-----------------------------------------
- #@# Parcellation Stats rh Sun Oct 8 08:01:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 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 0051311 rh pial
- Waiting for PID 25410 of (25410 25413 25416 25419) to complete...
- Waiting for PID 25413 of (25410 25413 25416 25419) to complete...
- Waiting for PID 25416 of (25410 25413 25416 25419) to complete...
- Waiting for PID 25419 of (25410 25413 25416 25419) 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 0051311 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271164
- Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 1751 1185 3061 2.548 0.430 0.122 0.032 28 2.5 bankssts
- 615 414 1115 2.693 0.484 0.100 0.013 5 0.3 caudalanteriorcingulate
- 3360 2263 6758 2.677 0.425 0.114 0.021 36 2.9 caudalmiddlefrontal
- 2359 1525 3329 1.972 0.452 0.147 0.038 40 3.4 cuneus
- 483 317 1829 3.805 0.728 0.106 0.027 4 0.4 entorhinal
- 4170 2848 9692 2.932 0.572 0.127 0.027 57 4.7 fusiform
- 7437 5191 16241 2.646 0.535 0.130 0.027 129 9.1 inferiorparietal
- 3777 2605 9676 2.914 0.662 0.140 0.037 66 5.3 inferiortemporal
- 1789 1162 3163 2.452 0.941 0.125 0.028 27 1.9 isthmuscingulate
- 9160 5981 15375 2.353 0.490 0.136 0.029 142 10.6 lateraloccipital
- 3810 2644 8905 2.923 0.591 0.134 0.033 52 5.1 lateralorbitofrontal
- 4541 3113 7617 2.283 0.564 0.140 0.032 68 6.1 lingual
- 2613 1775 5365 2.702 0.607 0.120 0.028 38 3.0 medialorbitofrontal
- 4473 3129 11900 2.903 0.636 0.134 0.031 84 6.0 middletemporal
- 998 641 1860 2.523 0.603 0.081 0.015 6 0.5 parahippocampal
- 2160 1366 4160 2.785 0.450 0.100 0.019 17 1.5 paracentral
- 2528 1754 5524 2.719 0.444 0.117 0.026 31 2.6 parsopercularis
- 960 647 2352 2.725 0.542 0.156 0.048 21 1.9 parsorbitalis
- 1914 1355 4178 2.660 0.427 0.138 0.035 40 2.5 parstriangularis
- 1921 1319 2059 1.793 0.411 0.140 0.033 28 2.5 pericalcarine
- 7804 5159 13868 2.319 0.574 0.121 0.024 105 7.5 postcentral
- 1716 1140 3778 2.886 0.628 0.116 0.023 21 1.7 posteriorcingulate
- 8302 5589 17097 2.717 0.497 0.101 0.018 73 5.8 precentral
- 7201 4907 14122 2.569 0.544 0.126 0.026 106 7.5 precuneus
- 1266 821 2799 2.857 0.525 0.118 0.023 18 1.1 rostralanteriorcingulate
- 7239 4949 14379 2.504 0.533 0.143 0.039 155 11.6 rostralmiddlefrontal
- 11100 7625 25452 2.825 0.534 0.124 0.026 139 11.5 superiorfrontal
- 9031 5916 16043 2.470 0.464 0.124 0.023 123 8.5 superiorparietal
- 6076 4070 14232 2.905 0.619 0.106 0.021 66 5.4 superiortemporal
- 4606 3160 9826 2.784 0.532 0.129 0.025 78 5.1 supramarginal
- 456 293 1112 2.687 0.526 0.155 0.042 13 0.9 frontalpole
- 669 466 2453 3.637 0.631 0.144 0.040 12 1.1 temporalpole
- 688 419 1283 2.602 0.343 0.105 0.018 7 0.4 transversetemporal
- 3465 2333 7241 3.092 0.687 0.126 0.033 55 4.3 insula
- mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0051311 lh pial
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271164
- Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 1751 1188 3061 2.548 0.430 0.135 0.037 38 3.0 bankssts
- 615 503 1115 2.693 0.484 0.151 0.037 10 1.1 caudalanteriorcingulate
- 3360 2700 6758 2.677 0.425 0.142 0.033 52 4.9 caudalmiddlefrontal
- 2359 1919 3329 1.972 0.452 0.146 0.035 35 3.5 cuneus
- 483 646 1829 3.805 0.728 0.213 0.050 7 1.1 entorhinal
- 4170 3811 9692 2.932 0.572 0.166 0.043 70 8.2 fusiform
- 7437 6973 16241 2.646 0.535 0.164 0.038 117 12.9 inferiorparietal
- 3777 3799 9676 2.914 0.662 0.195 0.056 194 10.2 inferiortemporal
- 1789 1468 3163 2.452 0.941 0.163 0.045 33 3.7 isthmuscingulate
- 9160 7264 15375 2.353 0.490 0.140 0.034 140 13.5 lateraloccipital
- 3810 3364 8905 2.923 0.591 0.169 0.044 72 7.6 lateralorbitofrontal
- 4541 3764 7617 2.283 0.564 0.151 0.045 84 8.4 lingual
- 2613 2267 5365 2.702 0.607 0.163 0.040 49 4.7 medialorbitofrontal
- 4473 4852 11900 2.903 0.636 0.182 0.037 65 8.0 middletemporal
- 998 867 1860 2.523 0.603 0.138 0.032 7 1.5 parahippocampal
- 2160 1617 4160 2.785 0.450 0.126 0.027 30 2.5 paracentral
- 2528 2245 5524 2.719 0.444 0.154 0.032 31 3.7 parsopercularis
- 960 999 2352 2.725 0.542 0.210 0.048 15 2.1 parsorbitalis
- 1914 1761 4178 2.660 0.427 0.175 0.038 30 3.5 parstriangularis
- 1921 1062 2059 1.793 0.411 0.117 0.037 40 3.2 pericalcarine
- 7804 6627 13868 2.319 0.574 0.139 0.028 92 9.1 postcentral
- 1716 1467 3778 2.886 0.628 0.164 0.041 55 3.1 posteriorcingulate
- 8302 6720 17097 2.717 0.497 0.123 0.024 94 8.7 precentral
- 7201 5943 14122 2.569 0.544 0.149 0.036 111 11.5 precuneus
- 1266 1155 2799 2.857 0.525 0.156 0.036 18 2.0 rostralanteriorcingulate
- 7239 6410 14379 2.504 0.533 0.177 0.044 131 14.9 rostralmiddlefrontal
- 11100 9930 25452 2.825 0.534 0.148 0.033 158 15.7 superiorfrontal
- 9031 7007 16043 2.470 0.464 0.141 0.033 133 13.0 superiorparietal
- 6076 5426 14232 2.905 0.619 0.148 0.031 78 8.8 superiortemporal
- 4606 3730 9826 2.784 0.532 0.148 0.036 66 7.1 supramarginal
- 456 544 1112 2.687 0.526 0.238 0.050 6 1.3 frontalpole
- 669 907 2453 3.637 0.631 0.202 0.040 12 1.2 temporalpole
- 688 579 1283 2.602 0.343 0.127 0.033 4 1.0 transversetemporal
- 3465 2282 7241 3.092 0.687 0.143 0.044 75 5.6 insula
- mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051311 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271597
- Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 1636 1131 3064 2.684 0.433 0.120 0.022 22 1.3 bankssts
- 1049 722 2374 2.903 0.544 0.114 0.016 11 0.7 caudalanteriorcingulate
- 2734 1864 5384 2.678 0.413 0.115 0.021 29 2.2 caudalmiddlefrontal
- 2752 1773 4203 2.089 0.526 0.146 0.044 48 4.7 cuneus
- 585 388 1929 3.454 0.684 0.137 0.046 8 1.0 entorhinal
- 4177 2779 9760 3.018 0.575 0.129 0.028 62 4.9 fusiform
- 8872 6055 18999 2.727 0.482 0.131 0.026 141 9.5 inferiorparietal
- 3945 2608 9248 2.929 0.651 0.123 0.030 66 4.9 inferiortemporal
- 1746 1124 3194 2.434 0.930 0.119 0.028 26 1.9 isthmuscingulate
- 8556 5549 14547 2.366 0.515 0.132 0.030 130 9.6 lateraloccipital
- 3538 2426 7704 2.792 0.593 0.138 0.036 60 4.8 lateralorbitofrontal
- 4594 3070 8635 2.418 0.652 0.141 0.036 75 6.9 lingual
- 2614 1866 5771 2.629 0.590 0.129 0.032 45 3.2 medialorbitofrontal
- 4846 3276 12295 3.066 0.594 0.123 0.025 78 4.8 middletemporal
- 843 583 1743 2.702 0.529 0.097 0.018 7 0.4 parahippocampal
- 2404 1541 4347 2.609 0.438 0.104 0.020 19 1.9 paracentral
- 2133 1474 4705 2.777 0.464 0.120 0.024 28 2.1 parsopercularis
- 1107 775 2733 2.851 0.595 0.153 0.042 22 2.0 parsorbitalis
- 2620 1814 5349 2.566 0.428 0.139 0.030 60 3.0 parstriangularis
- 2399 1592 2624 1.864 0.431 0.133 0.031 33 3.0 pericalcarine
- 5894 3887 9629 2.194 0.550 0.113 0.021 69 4.8 postcentral
- 2260 1506 4724 2.677 0.850 0.129 0.029 35 2.4 posteriorcingulate
- 7711 5141 15317 2.678 0.472 0.110 0.020 75 6.3 precentral
- 6871 4594 13690 2.645 0.520 0.120 0.026 94 7.3 precuneus
- 996 682 2234 2.911 0.439 0.142 0.038 25 1.4 rostralanteriorcingulate
- 7823 5334 15522 2.466 0.559 0.139 0.037 161 11.6 rostralmiddlefrontal
- 11518 7865 25748 2.793 0.539 0.120 0.026 143 11.3 superiorfrontal
- 9407 6253 16577 2.425 0.420 0.123 0.024 138 8.7 superiorparietal
- 5854 3968 13019 2.857 0.524 0.110 0.021 69 5.2 superiortemporal
- 5353 3604 10994 2.743 0.460 0.120 0.023 75 5.0 supramarginal
- 469 311 1231 2.743 0.521 0.171 0.056 17 1.3 frontalpole
- 542 384 2482 4.018 0.659 0.143 0.044 11 1.1 temporalpole
- 567 338 1069 2.611 0.303 0.111 0.018 8 0.3 transversetemporal
- 3239 2204 7153 3.142 0.707 0.127 0.031 44 4.0 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 0051311 rh pial
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271597
- Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 1636 1127 3064 2.684 0.433 0.132 0.035 26 2.2 bankssts
- 1049 918 2374 2.903 0.544 0.152 0.032 24 1.3 caudalanteriorcingulate
- 2734 2074 5384 2.678 0.413 0.131 0.027 36 3.4 caudalmiddlefrontal
- 2752 2254 4203 2.089 0.526 0.154 0.041 45 5.0 cuneus
- 585 691 1929 3.454 0.684 0.174 0.042 7 1.1 entorhinal
- 4177 3622 9760 3.018 0.575 0.161 0.042 92 8.6 fusiform
- 8872 7617 18999 2.727 0.482 0.156 0.038 142 14.6 inferiorparietal
- 3945 3608 9248 2.929 0.651 0.164 0.041 66 7.7 inferiortemporal
- 1746 1382 3194 2.434 0.930 0.156 0.044 32 3.2 isthmuscingulate
- 8556 6770 14547 2.366 0.515 0.140 0.036 151 13.4 lateraloccipital
- 3538 3103 7704 2.792 0.593 0.178 0.073 91 14.6 lateralorbitofrontal
- 4594 4094 8635 2.418 0.652 0.163 0.044 85 8.9 lingual
- 2614 2471 5771 2.629 0.590 0.164 0.040 39 4.6 medialorbitofrontal
- 4846 4711 12295 3.066 0.594 0.161 0.035 64 7.9 middletemporal
- 843 709 1743 2.702 0.529 0.144 0.034 17 1.4 parahippocampal
- 2404 1763 4347 2.609 0.438 0.122 0.028 28 2.8 paracentral
- 2133 1868 4705 2.777 0.464 0.151 0.032 28 3.1 parsopercularis
- 1107 1142 2733 2.851 0.595 0.203 0.050 24 2.6 parsorbitalis
- 2620 2348 5349 2.566 0.428 0.165 0.037 36 4.2 parstriangularis
- 2399 1311 2624 1.864 0.431 0.104 0.027 47 2.5 pericalcarine
- 5894 4880 9629 2.194 0.550 0.133 0.026 60 6.6 postcentral
- 2260 1936 4724 2.677 0.850 0.158 0.038 36 4.0 posteriorcingulate
- 7711 6026 15317 2.678 0.472 0.123 0.024 95 8.1 precentral
- 6871 5643 13690 2.645 0.520 0.144 0.034 101 10.4 precuneus
- 996 903 2234 2.911 0.439 0.171 0.046 22 1.9 rostralanteriorcingulate
- 7823 7057 15522 2.466 0.559 0.184 0.047 144 17.3 rostralmiddlefrontal
- 11518 10018 25748 2.793 0.539 0.147 0.032 158 16.1 superiorfrontal
- 9407 7406 16577 2.425 0.420 0.141 0.032 139 12.9 superiorparietal
- 5854 5090 13019 2.857 0.524 0.140 0.030 76 7.9 superiortemporal
- 5353 4225 10994 2.743 0.460 0.135 0.031 72 7.0 supramarginal
- 469 571 1231 2.743 0.521 0.224 0.047 6 1.1 frontalpole
- 542 832 2482 4.018 0.659 0.208 0.033 7 0.8 temporalpole
- 567 468 1069 2.611 0.303 0.123 0.024 3 0.6 transversetemporal
- 3239 2090 7153 3.142 0.707 0.132 0.038 115 5.5 insula
- PIDs (25410 25413 25416 25419) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 2 lh Sun Oct 8 08:02:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 08:02:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 25513 of (25513 25516) to complete...
- Waiting for PID 25516 of (25513 25516) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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...
- 34 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9319 changed, 138191 examined...
- 001: 2212 changed, 36062 examined...
- 002: 623 changed, 11496 examined...
- 003: 242 changed, 3509 examined...
- 004: 106 changed, 1341 examined...
- 005: 64 changed, 632 examined...
- 006: 37 changed, 335 examined...
- 007: 19 changed, 220 examined...
- 008: 12 changed, 101 examined...
- 009: 1 changed, 57 examined...
- 010: 0 changed, 6 examined...
- 10 labels changed using aseg
- 000: 295 total segments, 206 labels (2377 vertices) changed
- 001: 101 total segments, 12 labels (94 vertices) changed
- 002: 92 total segments, 3 labels (18 vertices) changed
- 003: 89 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 32 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1044 vertices marked for relabeling...
- 1044 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 0051311 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...
- 6 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9217 changed, 139374 examined...
- 001: 2143 changed, 36317 examined...
- 002: 624 changed, 11383 examined...
- 003: 261 changed, 3577 examined...
- 004: 117 changed, 1456 examined...
- 005: 65 changed, 695 examined...
- 006: 27 changed, 356 examined...
- 007: 10 changed, 159 examined...
- 008: 3 changed, 60 examined...
- 009: 2 changed, 20 examined...
- 010: 2 changed, 14 examined...
- 011: 3 changed, 10 examined...
- 012: 3 changed, 13 examined...
- 013: 0 changed, 9 examined...
- 0 labels changed using aseg
- 000: 279 total segments, 194 labels (2874 vertices) changed
- 001: 93 total segments, 8 labels (59 vertices) changed
- 002: 85 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 25 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1069 vertices marked for relabeling...
- 1069 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 0 minutes and 21 seconds.
- PIDs (25513 25516) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Sun Oct 8 08:02:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 lh white
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Sun Oct 8 08:02:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 rh white
- Waiting for PID 25563 of (25563 25566) to complete...
- Waiting for PID 25566 of (25563 25566) 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 0051311 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271164
- Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 1263 829 2154 2.276 0.493 0.140 0.040 29 2.0 G&S_frontomargin
- 2451 1629 4911 2.550 0.561 0.133 0.026 41 2.5 G&S_occipital_inf
- 1703 1077 3542 2.618 0.523 0.114 0.021 18 1.4 G&S_paracentral
- 1806 1201 3902 2.692 0.405 0.123 0.023 25 1.7 G&S_subcentral
- 827 565 2197 2.727 0.485 0.177 0.058 22 2.3 G&S_transv_frontopol
- 2230 1503 4686 2.865 0.447 0.121 0.024 25 2.2 G&S_cingul-Ant
- 1145 811 2105 2.653 0.365 0.108 0.013 9 0.7 G&S_cingul-Mid-Ant
- 1175 790 2489 2.893 0.458 0.106 0.022 9 1.1 G&S_cingul-Mid-Post
- 785 534 2326 3.263 0.528 0.164 0.040 17 1.3 G_cingul-Post-dorsal
- 332 216 813 2.826 0.840 0.144 0.039 8 0.4 G_cingul-Post-ventral
- 2386 1522 3634 1.980 0.576 0.154 0.041 50 3.6 G_cuneus
- 1523 1022 4137 3.006 0.398 0.122 0.029 28 1.6 G_front_inf-Opercular
- 477 317 1165 2.691 0.397 0.184 0.067 23 1.1 G_front_inf-Orbital
- 967 689 2606 2.821 0.418 0.154 0.042 21 1.8 G_front_inf-Triangul
- 4351 2962 10755 2.756 0.518 0.149 0.040 112 6.8 G_front_middle
- 7372 4984 19235 2.973 0.537 0.132 0.029 119 8.2 G_front_sup
- 732 504 1794 3.232 0.757 0.138 0.036 16 0.9 G_Ins_lg&S_cent_ins
- 763 520 2445 3.518 0.761 0.133 0.040 21 1.1 G_insular_short
- 2756 1858 6558 2.626 0.518 0.155 0.037 72 4.5 G_occipital_middle
- 1628 1058 3080 2.484 0.493 0.139 0.032 23 2.0 G_occipital_sup
- 1899 1246 5199 3.155 0.508 0.140 0.032 35 2.4 G_oc-temp_lat-fusifor
- 3262 2154 5761 2.217 0.604 0.153 0.040 63 5.3 G_oc-temp_med-Lingual
- 1159 732 3111 3.115 0.889 0.103 0.025 11 1.2 G_oc-temp_med-Parahip
- 2427 1682 7066 3.042 0.631 0.148 0.042 47 4.2 G_orbital
- 2349 1667 6392 2.849 0.601 0.148 0.033 55 3.3 G_pariet_inf-Angular
- 2375 1595 6397 2.999 0.543 0.142 0.031 55 3.1 G_pariet_inf-Supramar
- 3074 1976 6207 2.511 0.446 0.116 0.022 48 2.8 G_parietal_sup
- 3143 2025 6496 2.479 0.564 0.129 0.030 53 3.6 G_postcentral
- 2897 1955 7482 2.909 0.450 0.108 0.020 34 2.3 G_precentral
- 3857 2642 8730 2.539 0.554 0.133 0.031 77 4.5 G_precuneus
- 764 517 1961 2.716 0.591 0.133 0.034 18 1.2 G_rectus
- 518 305 936 2.963 0.678 0.112 0.042 8 0.7 G_subcallosal
- 521 304 1104 2.732 0.291 0.106 0.019 6 0.3 G_temp_sup-G_T_transv
- 1991 1345 6326 3.155 0.603 0.144 0.034 44 2.7 G_temp_sup-Lateral
- 906 618 2652 3.339 0.658 0.093 0.025 6 1.0 G_temp_sup-Plan_polar
- 805 566 1781 2.684 0.488 0.074 0.011 3 0.2 G_temp_sup-Plan_tempo
- 2163 1485 6427 3.014 0.658 0.154 0.044 50 3.7 G_temporal_inf
- 2385 1688 7733 3.094 0.647 0.146 0.037 60 3.8 G_temporal_middle
- 430 288 721 2.412 0.383 0.139 0.033 8 0.5 Lat_Fis-ant-Horizont
- 388 280 593 2.353 0.320 0.099 0.017 2 0.2 Lat_Fis-ant-Vertical
- 1111 728 1419 2.430 0.315 0.111 0.019 11 0.9 Lat_Fis-post
- 2084 1325 3106 2.110 0.483 0.141 0.033 37 2.5 Pole_occipital
- 1390 949 4656 3.317 0.770 0.141 0.037 27 2.0 Pole_temporal
- 2273 1590 2777 2.138 0.656 0.135 0.029 25 3.0 S_calcarine
- 3839 2597 4943 2.112 0.521 0.094 0.017 21 2.6 S_central
- 1377 940 2133 2.505 0.435 0.084 0.011 5 0.6 S_cingul-Marginalis
- 615 403 1040 3.153 0.561 0.096 0.017 3 0.4 S_circular_insula_ant
- 1262 840 1809 2.632 0.534 0.082 0.014 4 0.8 S_circular_insula_inf
- 1710 1157 2590 2.734 0.361 0.104 0.018 8 1.3 S_circular_insula_sup
- 624 429 1284 2.884 0.653 0.136 0.038 9 0.9 S_collat_transv_ant
- 444 296 610 2.399 0.483 0.126 0.024 4 0.4 S_collat_transv_post
- 1730 1215 2755 2.393 0.381 0.114 0.020 12 1.6 S_front_inf
- 1559 1082 2377 2.313 0.360 0.122 0.026 19 1.7 S_front_middle
- 2776 1938 4647 2.488 0.379 0.100 0.017 14 2.1 S_front_sup
- 184 135 401 2.552 0.389 0.086 0.016 1 0.1 S_interm_prim-Jensen
- 3413 2291 5301 2.442 0.424 0.120 0.020 41 2.9 S_intrapariet&P_trans
- 1294 873 1673 2.186 0.324 0.108 0.021 7 1.2 S_oc_middle&Lunatus
- 1878 1277 2795 2.441 0.443 0.127 0.023 19 1.9 S_oc_sup&transversal
- 938 624 1242 2.545 0.359 0.127 0.022 8 0.9 S_occipital_ant
- 739 519 1280 2.786 0.450 0.121 0.026 5 0.8 S_oc-temp_lat
- 2313 1626 3567 2.465 0.423 0.104 0.017 13 1.7 S_oc-temp_med&Lingual
- 316 219 460 2.455 0.374 0.120 0.022 4 0.3 S_orbital_lateral
- 570 429 909 2.402 0.405 0.117 0.019 4 0.3 S_orbital_med-olfact
- 1264 876 2590 2.757 0.542 0.129 0.031 13 1.7 S_orbital-H_Shaped
- 2553 1704 4399 2.610 0.512 0.122 0.022 29 2.2 S_parieto_occipital
- 1308 807 1364 1.963 0.778 0.100 0.017 16 0.8 S_pericallosal
- 3038 2070 4544 2.398 0.448 0.125 0.021 33 2.8 S_postcentral
- 1794 1221 2961 2.612 0.452 0.093 0.017 10 1.2 S_precentral-inf-part
- 1700 1122 2661 2.581 0.442 0.099 0.017 11 1.2 S_precentral-sup-part
- 845 603 1571 2.722 0.693 0.126 0.026 10 0.8 S_suborbital
- 1207 808 1739 2.481 0.462 0.119 0.022 8 1.1 S_subparietal
- 1105 778 1801 2.510 0.515 0.116 0.021 8 1.0 S_temporal_inf
- 6811 4675 12345 2.625 0.474 0.112 0.023 79 6.9 S_temporal_sup
- 414 289 559 2.346 0.265 0.107 0.014 2 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 0051311 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271597
- Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 917 635 1703 2.402 0.576 0.150 0.046 19 1.7 G&S_frontomargin
- 1511 941 3262 2.752 0.618 0.112 0.021 20 1.2 G&S_occipital_inf
- 1550 964 2933 2.459 0.423 0.119 0.025 19 1.5 G&S_paracentral
- 1165 773 2516 2.692 0.452 0.136 0.031 19 1.4 G&S_subcentral
- 1363 921 3258 2.668 0.461 0.155 0.044 36 2.5 G&S_transv_frontopol
- 2871 1990 5579 2.619 0.515 0.119 0.027 44 2.9 G&S_cingul-Ant
- 1311 900 2812 2.826 0.507 0.104 0.017 10 0.8 G&S_cingul-Mid-Ant
- 1674 1120 3362 2.855 0.493 0.129 0.030 21 1.9 G&S_cingul-Mid-Post
- 680 443 2062 3.200 0.555 0.157 0.044 16 1.2 G_cingul-Post-dorsal
- 333 221 936 3.027 0.657 0.161 0.039 8 0.5 G_cingul-Post-ventral
- 2635 1682 4034 2.020 0.572 0.152 0.049 52 5.0 G_cuneus
- 1620 1085 4167 2.868 0.442 0.134 0.032 32 2.1 G_front_inf-Opercular
- 494 335 961 2.535 0.463 0.143 0.033 10 0.6 G_front_inf-Orbital
- 1081 751 2779 2.750 0.378 0.174 0.047 47 1.9 G_front_inf-Triangul
- 3519 2386 9083 2.747 0.515 0.150 0.043 98 5.9 G_front_middle
- 7837 5296 20147 2.933 0.533 0.129 0.031 125 8.8 G_front_sup
- 646 458 1891 3.495 0.705 0.139 0.037 15 0.8 G_Ins_lg&S_cent_ins
- 722 480 2230 3.558 0.733 0.139 0.039 15 1.2 G_insular_short
- 2544 1693 6121 2.679 0.456 0.137 0.032 53 3.1 G_occipital_middle
- 2006 1306 4029 2.545 0.598 0.142 0.033 36 2.5 G_occipital_sup
- 2029 1287 5644 3.198 0.573 0.144 0.036 45 2.9 G_oc-temp_lat-fusifor
- 2950 1926 6419 2.572 0.645 0.151 0.040 56 4.7 G_oc-temp_med-Lingual
- 1056 694 3060 3.184 0.714 0.127 0.040 14 1.4 G_oc-temp_med-Parahip
- 2391 1691 6846 2.979 0.535 0.155 0.045 58 4.1 G_orbital
- 3370 2322 9421 2.896 0.527 0.147 0.033 83 4.4 G_pariet_inf-Angular
- 2548 1688 6128 2.879 0.474 0.135 0.028 48 3.1 G_pariet_inf-Supramar
- 3301 2174 6579 2.478 0.369 0.130 0.027 64 3.6 G_parietal_sup
- 2059 1323 3918 2.268 0.522 0.128 0.024 34 2.1 G_postcentral
- 2709 1820 7137 2.899 0.413 0.111 0.019 35 2.0 G_precentral
- 3314 2181 7982 2.729 0.503 0.130 0.031 64 4.0 G_precuneus
- 811 612 2667 2.930 0.584 0.157 0.053 22 1.6 G_rectus
- 176 120 400 3.490 0.500 0.131 0.048 3 0.4 G_subcallosal
- 400 233 891 2.739 0.344 0.117 0.020 7 0.2 G_temp_sup-G_T_transv
- 2171 1433 5986 3.125 0.530 0.139 0.033 41 2.7 G_temp_sup-Lateral
- 764 544 1989 2.924 0.880 0.117 0.037 15 1.3 G_temp_sup-Plan_polar
- 895 602 1867 2.778 0.365 0.082 0.011 4 0.4 G_temp_sup-Plan_tempo
- 2092 1354 5588 3.068 0.672 0.132 0.033 38 2.9 G_temporal_inf
- 2925 1969 8926 3.262 0.546 0.140 0.030 61 3.5 G_temporal_middle
- 509 345 840 2.490 0.403 0.117 0.017 5 0.4 Lat_Fis-ant-Horizont
- 399 295 620 2.278 0.292 0.092 0.012 2 0.1 Lat_Fis-ant-Vertical
- 1370 905 1977 2.669 0.321 0.111 0.020 10 1.1 Lat_Fis-post
- 3703 2366 5215 2.050 0.472 0.146 0.038 64 5.4 Pole_occipital
- 1509 1041 5095 3.394 0.744 0.139 0.038 33 2.4 Pole_temporal
- 2654 1808 3332 2.160 0.613 0.136 0.033 38 3.9 S_calcarine
- 3347 2243 4052 2.074 0.533 0.102 0.017 21 2.5 S_central
- 1644 1122 2514 2.444 0.528 0.091 0.013 7 0.9 S_cingul-Marginalis
- 605 396 894 2.786 0.405 0.092 0.017 2 0.4 S_circular_insula_ant
- 1215 807 1778 2.609 0.496 0.074 0.011 4 0.6 S_circular_insula_inf
- 1454 989 2386 2.841 0.431 0.112 0.020 9 1.3 S_circular_insula_sup
- 1033 672 1987 2.858 0.555 0.109 0.024 17 1.1 S_collat_transv_ant
- 553 375 687 2.127 0.315 0.122 0.018 5 0.4 S_collat_transv_post
- 1808 1240 2788 2.390 0.439 0.108 0.018 17 1.4 S_front_inf
- 1834 1273 2823 2.159 0.478 0.123 0.026 19 2.1 S_front_middle
- 2825 1942 4416 2.435 0.373 0.104 0.018 19 2.1 S_front_sup
- 616 431 872 2.505 0.309 0.109 0.014 4 0.4 S_interm_prim-Jensen
- 4130 2781 6022 2.353 0.368 0.101 0.015 31 2.4 S_intrapariet&P_trans
- 1123 781 1446 2.192 0.310 0.103 0.017 6 0.8 S_oc_middle&Lunatus
- 1555 1045 2238 2.482 0.392 0.145 0.030 21 1.9 S_oc_sup&transversal
- 846 569 1201 2.432 0.308 0.093 0.016 5 0.4 S_occipital_ant
- 740 519 1389 2.743 0.537 0.098 0.017 5 0.4 S_oc-temp_lat
- 1917 1367 3033 2.548 0.374 0.104 0.016 11 1.3 S_oc-temp_med&Lingual
- 395 277 674 2.437 0.474 0.126 0.023 3 0.4 S_orbital_lateral
- 633 447 1008 2.576 0.578 0.112 0.020 5 0.5 S_orbital_med-olfact
- 1352 916 2742 2.828 0.608 0.134 0.032 15 1.8 S_orbital-H_Shaped
- 2258 1502 3465 2.563 0.457 0.111 0.022 17 2.1 S_parieto_occipital
- 1893 1200 1863 1.999 0.842 0.102 0.017 19 1.1 S_pericallosal
- 2242 1522 3340 2.305 0.398 0.105 0.018 20 1.4 S_postcentral
- 1776 1223 2961 2.659 0.456 0.107 0.015 12 1.1 S_precentral-inf-part
- 1406 932 2128 2.576 0.375 0.103 0.016 10 0.9 S_precentral-sup-part
- 394 268 505 2.342 0.443 0.124 0.020 3 0.3 S_suborbital
- 1366 960 2474 2.528 0.495 0.112 0.019 12 1.1 S_subparietal
- 992 700 1533 2.663 0.478 0.123 0.020 8 1.0 S_temporal_inf
- 6924 4733 12072 2.689 0.447 0.111 0.019 69 5.2 S_temporal_sup
- 202 148 342 2.751 0.473 0.121 0.016 1 0.2 S_temporal_transverse
- PIDs (25563 25566) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 3 lh Sun Oct 8 08:03:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 08:03:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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 25631 of (25631 25634) to complete...
- Waiting for PID 25634 of (25631 25634) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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...
- 1170 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2023 changed, 138191 examined...
- 001: 460 changed, 9343 examined...
- 002: 135 changed, 2654 examined...
- 003: 56 changed, 802 examined...
- 004: 39 changed, 336 examined...
- 005: 28 changed, 221 examined...
- 006: 16 changed, 160 examined...
- 007: 16 changed, 108 examined...
- 008: 11 changed, 86 examined...
- 009: 12 changed, 74 examined...
- 010: 10 changed, 66 examined...
- 011: 7 changed, 68 examined...
- 012: 3 changed, 41 examined...
- 013: 3 changed, 24 examined...
- 014: 1 changed, 20 examined...
- 015: 1 changed, 7 examined...
- 016: 0 changed, 7 examined...
- 306 labels changed using aseg
- 000: 63 total segments, 30 labels (259 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 8 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 764 vertices marked for relabeling...
- 764 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas.annot...
- classification took 0 minutes and 16 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051311 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...
- 1004 labels changed using aseg
- relabeling using gibbs priors...
- 000: 1989 changed, 139374 examined...
- 001: 433 changed, 9394 examined...
- 002: 117 changed, 2511 examined...
- 003: 37 changed, 721 examined...
- 004: 14 changed, 206 examined...
- 005: 7 changed, 90 examined...
- 006: 3 changed, 45 examined...
- 007: 3 changed, 18 examined...
- 008: 1 changed, 20 examined...
- 009: 1 changed, 7 examined...
- 010: 1 changed, 7 examined...
- 011: 0 changed, 7 examined...
- 107 labels changed using aseg
- 000: 54 total segments, 21 labels (145 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 1 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 961 vertices marked for relabeling...
- 961 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas.annot...
- classification took 0 minutes and 18 seconds.
- PIDs (25631 25634) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Sun Oct 8 08:03:51 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 lh white
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Sun Oct 8 08:03:51 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 rh white
- Waiting for PID 25677 of (25677 25680) to complete...
- Waiting for PID 25680 of (25677 25680) 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 0051311 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271164
- Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 1253 872 2743 2.864 0.459 0.117 0.019 15 0.9 caudalanteriorcingulate
- 3505 2366 6926 2.662 0.420 0.114 0.021 37 3.0 caudalmiddlefrontal
- 3230 2096 5010 2.134 0.551 0.143 0.035 52 4.3 cuneus
- 443 288 1718 3.869 0.681 0.109 0.029 4 0.5 entorhinal
- 3966 2710 9141 2.930 0.555 0.127 0.027 54 4.4 fusiform
- 7263 5067 15800 2.650 0.539 0.129 0.027 121 8.9 inferiorparietal
- 3798 2615 9795 2.951 0.670 0.138 0.037 64 5.5 inferiortemporal
- 1793 1166 3224 2.486 0.933 0.127 0.028 27 1.9 isthmuscingulate
- 9120 5968 15449 2.355 0.485 0.137 0.029 142 10.6 lateraloccipital
- 4146 2857 9742 2.878 0.638 0.142 0.039 73 6.7 lateralorbitofrontal
- 4711 3209 7846 2.271 0.563 0.139 0.032 71 6.3 lingual
- 2229 1520 4827 2.721 0.618 0.125 0.031 38 2.9 medialorbitofrontal
- 6173 4283 15321 2.851 0.591 0.134 0.032 120 8.3 middletemporal
- 1036 661 1922 2.509 0.613 0.081 0.015 6 0.6 parahippocampal
- 2567 1632 5200 2.826 0.460 0.100 0.020 20 1.8 paracentral
- 2389 1646 5236 2.753 0.425 0.116 0.025 30 2.3 parsopercularis
- 1110 748 2405 2.759 0.564 0.144 0.037 17 1.6 parsorbitalis
- 2158 1524 4605 2.617 0.436 0.138 0.034 46 2.9 parstriangularis
- 1882 1290 1997 1.790 0.419 0.141 0.033 28 2.5 pericalcarine
- 8692 5775 15560 2.342 0.566 0.121 0.024 115 8.2 postcentral
- 1861 1239 3914 2.830 0.657 0.116 0.023 22 1.8 posteriorcingulate
- 8173 5497 16834 2.720 0.495 0.101 0.018 71 5.8 precentral
- 7188 4905 14299 2.560 0.542 0.128 0.027 112 7.6 precuneus
- 1650 1084 3616 2.872 0.545 0.118 0.023 22 1.5 rostralanteriorcingulate
- 5073 3454 10249 2.544 0.546 0.142 0.037 102 7.8 rostralmiddlefrontal
- 12121 8310 26972 2.742 0.541 0.127 0.028 172 14.1 superiorfrontal
- 7154 4677 12279 2.442 0.452 0.120 0.022 93 6.6 superiorparietal
- 7788 5250 18313 2.906 0.656 0.111 0.024 90 7.6 superiortemporal
- 4346 2961 9175 2.789 0.538 0.131 0.025 75 4.9 supramarginal
- 705 426 1293 2.583 0.351 0.105 0.018 7 0.4 transversetemporal
- 2940 2001 6511 3.147 0.667 0.119 0.028 44 3.1 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 0051311 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 271597
- Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 1097 759 2521 2.886 0.558 0.116 0.016 12 0.7 caudalanteriorcingulate
- 2853 1956 5694 2.683 0.413 0.116 0.022 30 2.4 caudalmiddlefrontal
- 3274 2120 5178 2.147 0.573 0.138 0.040 49 5.0 cuneus
- 540 353 1791 3.470 0.668 0.134 0.045 7 0.9 entorhinal
- 3925 2610 9120 3.004 0.573 0.128 0.028 59 4.5 fusiform
- 8787 6011 18784 2.726 0.487 0.131 0.027 143 9.2 inferiorparietal
- 4222 2801 9970 2.951 0.649 0.123 0.030 69 5.3 inferiortemporal
- 1698 1098 3135 2.461 0.911 0.121 0.029 26 1.9 isthmuscingulate
- 8718 5653 14894 2.367 0.513 0.134 0.030 135 10.1 lateraloccipital
- 3768 2623 8466 2.802 0.618 0.146 0.040 73 5.8 lateralorbitofrontal
- 4575 3054 8578 2.413 0.653 0.139 0.036 74 6.8 lingual
- 1781 1295 4327 2.719 0.616 0.134 0.035 31 2.4 medialorbitofrontal
- 5964 4050 14540 3.022 0.583 0.124 0.024 95 5.8 middletemporal
- 883 624 1845 2.688 0.510 0.102 0.018 7 0.4 parahippocampal
- 2513 1610 4598 2.627 0.444 0.105 0.021 21 2.0 paracentral
- 2413 1675 5168 2.727 0.471 0.121 0.025 34 2.3 parsopercularis
- 953 642 2105 2.700 0.596 0.128 0.030 13 1.2 parsorbitalis
- 2613 1805 5394 2.594 0.421 0.139 0.030 58 3.1 parstriangularis
- 2322 1532 2546 1.876 0.429 0.134 0.031 32 2.9 pericalcarine
- 6551 4319 10684 2.204 0.544 0.114 0.021 77 5.5 postcentral
- 2375 1572 4780 2.648 0.860 0.128 0.029 35 2.7 posteriorcingulate
- 7359 4890 14722 2.681 0.470 0.110 0.020 72 6.1 precentral
- 7017 4717 14163 2.640 0.526 0.122 0.026 100 7.6 precuneus
- 1237 838 2547 2.866 0.475 0.140 0.037 29 1.7 rostralanteriorcingulate
- 5407 3686 10844 2.458 0.554 0.140 0.037 117 8.3 rostralmiddlefrontal
- 14618 9968 32009 2.734 0.546 0.123 0.028 205 15.6 superiorfrontal
- 7884 5244 13745 2.418 0.394 0.122 0.024 116 7.1 superiorparietal
- 7630 5168 17585 2.881 0.639 0.117 0.024 101 7.9 superiortemporal
- 5049 3389 10318 2.752 0.437 0.116 0.022 63 4.5 supramarginal
- 568 335 1072 2.614 0.304 0.112 0.018 8 0.3 transversetemporal
- 3068 2095 6905 3.181 0.678 0.123 0.029 39 3.5 insula
- PIDs (25677 25680) completed and logs appended.
- #-----------------------------------------
- #@# WM/GM Contrast lh Sun Oct 8 08:04:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- pctsurfcon --s 0051311 --lh-only
- #-----------------------------------------
- #@# WM/GM Contrast rh Sun Oct 8 08:04:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts
- pctsurfcon --s 0051311 --rh-only
- Waiting for PID 25793 of (25793 25804) to complete...
- Waiting for PID 25804 of (25793 25804) to complete...
- pctsurfcon --s 0051311 --lh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts/pctsurfcon.log
- Sun Oct 8 08:04:34 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-6.0.0/0051311/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-904 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-6.0.0/0051311/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.wm.mgh --regheader 0051311 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = lh
- ProjDist = -1
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- INFO: changing type to float
- Done loading volume
- Computing registration from header.
- Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00001;
- 0.00000 0.00000 1.00000 0.00002;
- 0.00000 -1.00000 0.00000 -0.00002;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 69144
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.wm.mgh
- Dim: 138191 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.gm.mgh --projfrac 0.3 --regheader 0051311 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = lh
- ProjFrac = 0.3
- thickness = thickness
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- INFO: changing type to float
- Done loading volume
- Computing registration from header.
- Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00001;
- 0.00000 0.00000 1.00000 0.00002;
- 0.00000 -1.00000 0.00000 -0.00002;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 85842
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.gm.mgh
- Dim: 138191 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25793/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/lh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.w-g.pct.mgh --annot 0051311 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/lh.w-g.pct.mgh --annot 0051311 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-904
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/lh.w-g.pct.mgh
- Vertex Area is 0.673771 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 0051311 --rh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/scripts/pctsurfcon.log
- Sun Oct 8 08:04:34 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-6.0.0/0051311/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-904 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-6.0.0/0051311/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.wm.mgh --regheader 0051311 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = rh
- ProjDist = -1
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- INFO: changing type to float
- Done loading volume
- Computing registration from header.
- Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00001;
- 0.00000 0.00000 1.00000 0.00002;
- 0.00000 -1.00000 0.00000 -0.00002;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 69378
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.wm.mgh
- Dim: 139374 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.gm.mgh --projfrac 0.3 --regheader 0051311 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = rh
- ProjFrac = 0.3
- thickness = thickness
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- INFO: changing type to float
- Done loading volume
- Computing registration from header.
- Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00001;
- 0.00000 0.00000 1.00000 0.00002;
- 0.00000 -1.00000 0.00000 -0.00002;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 86485
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.gm.mgh
- Dim: 139374 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/tmp.pctsurfcon.25804/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.w-g.pct.mgh --annot 0051311 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.w-g.pct.mgh --annot 0051311 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-904
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.w-g.pct.mgh
- Vertex Area is 0.671675 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 (25793 25804) completed and logs appended.
- #-----------------------------------------
- #@# Relabel Hypointensities Sun Oct 8 08:04:43 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri
- mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
- reading input surface ../surf/lh.white...
- relabeling lh hypointensities...
- 806 voxels changed to hypointensity...
- reading input surface ../surf/rh.white...
- relabeling rh hypointensities...
- 631 voxels changed to hypointensity...
- 1586 hypointense voxels neighboring cortex changed
- #-----------------------------------------
- #@# AParc-to-ASeg aparc Sun Oct 8 08:05:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311
- mri_aparc2aseg --s 0051311 --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 08:05:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311
- mri_aparc2aseg --s 0051311 --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 08:05:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311
- mri_aparc2aseg --s 0051311 --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 25959 of (25959 25962 25965) to complete...
- Waiting for PID 25962 of (25959 25962 25965) to complete...
- Waiting for PID 25965 of (25959 25962 25965) to complete...
- mri_aparc2aseg --s 0051311 --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 0051311
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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-6.0.0/0051311/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 6.09
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 108
- rescaling Left_Cerebral_Cortex from 61 --> 49
- rescaling Left_Lateral_Ventricle from 13 --> 6
- rescaling Left_Inf_Lat_Vent from 34 --> 25
- rescaling Left_Cerebellum_White_Matter from 86 --> 90
- rescaling Left_Cerebellum_Cortex from 60 --> 51
- rescaling Left_Thalamus from 94 --> 89
- rescaling Left_Thalamus_Proper from 84 --> 86
- rescaling Left_Caudate from 75 --> 61
- rescaling Left_Putamen from 80 --> 69
- rescaling Left_Pallidum from 98 --> 92
- rescaling Third_Ventricle from 25 --> 12
- rescaling Fourth_Ventricle from 22 --> 10
- rescaling Brain_Stem from 81 --> 83
- rescaling Left_Hippocampus from 57 --> 53
- rescaling Left_Amygdala from 56 --> 55
- rescaling CSF from 32 --> 19
- rescaling Left_Accumbens_area from 62 --> 55
- rescaling Left_VentralDC from 87 --> 88
- rescaling Right_Cerebral_White_Matter from 105 --> 107
- rescaling Right_Cerebral_Cortex from 58 --> 51
- rescaling Right_Lateral_Ventricle from 13 --> 8
- rescaling Right_Inf_Lat_Vent from 25 --> 24
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 53
- rescaling Right_Thalamus_Proper from 85 --> 81
- rescaling Right_Caudate from 62 --> 63
- rescaling Right_Putamen from 80 --> 73
- rescaling Right_Pallidum from 97 --> 91
- rescaling Right_Hippocampus from 53 --> 57
- rescaling Right_Amygdala from 55 --> 60
- rescaling Right_Accumbens_area from 65 --> 62
- rescaling Right_VentralDC from 86 --> 96
- rescaling Fifth_Ventricle from 40 --> 16
- rescaling WM_hypointensities from 78 --> 81
- 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 = 532369
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 165 changed.
- pass 2: 6 changed.
- pass 3: 1 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aparc+aseg.mgz
- mri_aparc2aseg --s 0051311 --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 0051311
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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-6.0.0/0051311/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 6.09
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 108
- rescaling Left_Cerebral_Cortex from 61 --> 49
- rescaling Left_Lateral_Ventricle from 13 --> 6
- rescaling Left_Inf_Lat_Vent from 34 --> 25
- rescaling Left_Cerebellum_White_Matter from 86 --> 90
- rescaling Left_Cerebellum_Cortex from 60 --> 51
- rescaling Left_Thalamus from 94 --> 89
- rescaling Left_Thalamus_Proper from 84 --> 86
- rescaling Left_Caudate from 75 --> 61
- rescaling Left_Putamen from 80 --> 69
- rescaling Left_Pallidum from 98 --> 92
- rescaling Third_Ventricle from 25 --> 12
- rescaling Fourth_Ventricle from 22 --> 10
- rescaling Brain_Stem from 81 --> 83
- rescaling Left_Hippocampus from 57 --> 53
- rescaling Left_Amygdala from 56 --> 55
- rescaling CSF from 32 --> 19
- rescaling Left_Accumbens_area from 62 --> 55
- rescaling Left_VentralDC from 87 --> 88
- rescaling Right_Cerebral_White_Matter from 105 --> 107
- rescaling Right_Cerebral_Cortex from 58 --> 51
- rescaling Right_Lateral_Ventricle from 13 --> 8
- rescaling Right_Inf_Lat_Vent from 25 --> 24
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 53
- rescaling Right_Thalamus_Proper from 85 --> 81
- rescaling Right_Caudate from 62 --> 63
- rescaling Right_Putamen from 80 --> 73
- rescaling Right_Pallidum from 97 --> 91
- rescaling Right_Hippocampus from 53 --> 57
- rescaling Right_Amygdala from 55 --> 60
- rescaling Right_Accumbens_area from 65 --> 62
- rescaling Right_VentralDC from 86 --> 96
- rescaling Fifth_Ventricle from 40 --> 16
- rescaling WM_hypointensities from 78 --> 81
- 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 = 532442
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 165 changed.
- pass 2: 6 changed.
- pass 3: 1 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/aparc.a2009s+aseg.mgz
- mri_aparc2aseg --s 0051311 --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 0051311
- outvol mri/aparc.DKTatlas+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/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-6.0.0/0051311/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 6.09
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 108
- rescaling Left_Cerebral_Cortex from 61 --> 49
- rescaling Left_Lateral_Ventricle from 13 --> 6
- rescaling Left_Inf_Lat_Vent from 34 --> 25
- rescaling Left_Cerebellum_White_Matter from 86 --> 90
- rescaling Left_Cerebellum_Cortex from 60 --> 51
- rescaling Left_Thalamus from 94 --> 89
- rescaling Left_Thalamus_Proper from 84 --> 86
- rescaling Left_Caudate from 75 --> 61
- rescaling Left_Putamen from 80 --> 69
- rescaling Left_Pallidum from 98 --> 92
- rescaling Third_Ventricle from 25 --> 12
- rescaling Fourth_Ventricle from 22 --> 10
- rescaling Brain_Stem from 81 --> 83
- rescaling Left_Hippocampus from 57 --> 53
- rescaling Left_Amygdala from 56 --> 55
- rescaling CSF from 32 --> 19
- rescaling Left_Accumbens_area from 62 --> 55
- rescaling Left_VentralDC from 87 --> 88
- rescaling Right_Cerebral_White_Matter from 105 --> 107
- rescaling Right_Cerebral_Cortex from 58 --> 51
- rescaling Right_Lateral_Ventricle from 13 --> 8
- rescaling Right_Inf_Lat_Vent from 25 --> 24
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 53
- rescaling Right_Thalamus_Proper from 85 --> 81
- rescaling Right_Caudate from 62 --> 63
- rescaling Right_Putamen from 80 --> 73
- rescaling Right_Pallidum from 97 --> 91
- rescaling Right_Hippocampus from 53 --> 57
- rescaling Right_Amygdala from 55 --> 60
- rescaling Right_Accumbens_area from 65 --> 62
- rescaling Right_VentralDC from 86 --> 96
- rescaling Fifth_Ventricle from 40 --> 16
- rescaling WM_hypointensities from 78 --> 81
- 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 = 532442
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 165 changed.
- pass 2: 6 changed.
- pass 3: 1 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
- PIDs (25959 25962 25965) completed and logs appended.
- #-----------------------------------------
- #@# APas-to-ASeg Sun Oct 8 08:13:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri
- apas2aseg --i aparc+aseg.mgz --o aseg.mgz
- Sun Oct 8 08:13:23 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-6.0.0/0051311/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-904 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-6.0.0/0051311/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-904
- 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 08:13:23 CEST 2017
- Ended at Sun Oct 8 08:13:30 CEST 2017
- Apas2aseg-Run-Time-Sec 7
-
- apas2aseg Done
- #--------------------------------------------
- #@# ASeg Stats Sun Oct 8 08:13:30 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311
- 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 0051311
- $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 0051311
- sysname Linux
- hostname tars-904
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1336087 mm^3 (det: 1.458067 )
- Computing euler number
- orig.nofix lheno = -42, rheno = -50
- orig.nofix lhholes = 22, rhholes = 26
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 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 08:17:12 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311
- mri_aparc2aseg --s 0051311 --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 0051311
- 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-6.0.0/0051311/mri/aparc+aseg.mgz
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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-6.0.0/0051311/mri/ribbon.mgz
- Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/ribbon.mgz
- Ripping vertices labeled as unkown
- Ripped 7753 vertices from left hemi
- Ripped 7720 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-6.0.0/0051311/mri/aseg.mgz
- Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 = 928308
- Used brute-force search on 677 voxels
- Fixing Parahip LH WM
- Found 11 clusters
- 0 k 2.000000
- 1 k 6.000000
- 2 k 1.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 6.000000
- 7 k 1067.000000
- 8 k 1.000000
- 9 k 5.000000
- 10 k 27.000000
- Fixing Parahip RH WM
- Found 10 clusters
- 0 k 3.000000
- 1 k 2.000000
- 2 k 2.000000
- 3 k 1180.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 2.000000
- 8 k 1.000000
- 9 k 2.000000
- 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 0051311 --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 0051311 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname tars-904
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1336087 mm^3 (det: 1.458067 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 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-6.0.0/0051311/label
- #--------------------------------------------
- #@# BA_exvivo Labels lh Sun Oct 8 08:28:06 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 26789 of (26789 26795 26801 26807 26813) to complete...
- Waiting for PID 26795 of (26789 26795 26801 26807 26813) to complete...
- Waiting for PID 26801 of (26789 26795 26801 26807 26813) to complete...
- Waiting for PID 26807 of (26789 26795 26801 26807 26813) to complete...
- Waiting for PID 26813 of (26789 26795 26801 26807 26813) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 545
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.label 4674
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 763
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.label 8672
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 282
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.label 4359
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 479
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.label 6462
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 404
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.label 6188
- mri_label2label: Done
- PIDs (26789 26795 26801 26807 26813) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 26865 of (26865 26871 26877 26883) to complete...
- Waiting for PID 26871 of (26865 26871 26877 26883) to complete...
- Waiting for PID 26877 of (26865 26871 26877 26883) to complete...
- Waiting for PID 26883 of (26865 26871 26877 26883) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 267
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.label 4337
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 1517
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.label 15106
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 425
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.label 4606
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 412
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.label 3834
- mri_label2label: Done
- PIDs (26865 26871 26877 26883) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 26923 of (26923 26929 26935 26941 26947) to complete...
- Waiting for PID 26929 of (26923 26929 26935 26941 26947) to complete...
- Waiting for PID 26935 of (26923 26929 26935 26941 26947) to complete...
- Waiting for PID 26941 of (26923 26929 26935 26941 26947) to complete...
- Waiting for PID 26947 of (26923 26929 26935 26941 26947) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 1399
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.label 6040
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 3162
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.label 11276
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 790
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.label 2808
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 35
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.label 1325
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 33
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.label 1232
- mri_label2label: Done
- PIDs (26923 26929 26935 26941 26947) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 27009 of (27009 27015 27020 27024 27032) to complete...
- Waiting for PID 27015 of (27009 27015 27020 27024 27032) to complete...
- Waiting for PID 27020 of (27009 27015 27020 27024 27032) to complete...
- Waiting for PID 27024 of (27009 27015 27020 27024 27032) to complete...
- Waiting for PID 27032 of (27009 27015 27020 27024 27032) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 124
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.thresh.label 1138
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 413
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.thresh.label 2505
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 92
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.thresh.label 1596
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 212
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.thresh.label 2208
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 134
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.thresh.label 2453
- mri_label2label: Done
- PIDs (27009 27015 27020 27024 27032) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 27072 of (27072 27078 27084 27089) to complete...
- Waiting for PID 27078 of (27072 27078 27084 27089) to complete...
- Waiting for PID 27084 of (27072 27078 27084 27089) to complete...
- Waiting for PID 27089 of (27072 27078 27084 27089) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 99
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.thresh.label 1648
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 814
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.thresh.label 7849
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 200
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.thresh.label 2112
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 180
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.thresh.label 1331
- mri_label2label: Done
- PIDs (27072 27078 27084 27089) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 27147 of (27147 27153 27156 27163 27170) to complete...
- Waiting for PID 27153 of (27147 27153 27156 27163 27170) to complete...
- Waiting for PID 27156 of (27147 27153 27156 27163 27170) to complete...
- Waiting for PID 27163 of (27147 27153 27156 27163 27170) to complete...
- Waiting for PID 27170 of (27147 27153 27156 27163 27170) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 916
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.thresh.label 4321
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 1383
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.thresh.label 4717
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 208
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.thresh.label 721
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 10
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.thresh.label 480
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 138191
- Number of reverse mapping hits = 14
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.thresh.label 464
- mri_label2label: Done
- PIDs (27147 27153 27156 27163 27170) completed and logs appended.
- mris_label2annot --s 0051311 --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-6.0.0/0051311/label
- cmdline mris_label2annot --s 0051311 --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-904
- machine x86_64
- user ntraut
- subject 0051311
- 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-6.0.0/0051311/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 93652 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/lh.BA_exvivo.annot
- mris_label2annot --s 0051311 --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-6.0.0/0051311/label
- cmdline mris_label2annot --s 0051311 --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-904
- machine x86_64
- user ntraut
- subject 0051311
- 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-6.0.0/0051311/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 111380 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 271164
- Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 1359 848 2892 2.519 0.443 0.148 0.035 28 1.9 BA1_exvivo
- 4436 2954 8118 2.541 0.485 0.127 0.024 62 4.3 BA2_exvivo
- 1288 849 1347 1.977 0.396 0.114 0.023 9 1.2 BA3a_exvivo
- 2751 1886 4243 2.003 0.573 0.109 0.020 27 2.2 BA3b_exvivo
- 1672 1059 3872 2.923 0.437 0.095 0.019 13 1.1 BA4a_exvivo
- 1417 961 2444 2.607 0.369 0.083 0.014 6 0.8 BA4p_exvivo
- 10522 7138 24107 2.816 0.528 0.112 0.021 107 8.7 BA6_exvivo
- 2530 1728 5876 2.849 0.440 0.106 0.023 31 2.1 BA44_exvivo
- 2611 1857 5691 2.584 0.468 0.144 0.036 56 3.9 BA45_exvivo
- 3463 2344 4446 1.867 0.467 0.134 0.035 49 4.9 V1_exvivo
- 8849 5756 14003 2.220 0.532 0.148 0.035 151 12.0 V2_exvivo
- 2612 1785 4972 2.524 0.462 0.131 0.024 44 2.4 MT_exvivo
- 497 309 1630 3.451 0.810 0.101 0.026 5 0.4 perirhinal_exvivo
- 532 373 1288 3.032 0.927 0.099 0.025 4 0.5 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 0051311 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 271164
- Total vertex volume 267919 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 860 541 1866 2.548 0.468 0.135 0.032 14 1.0 BA1_exvivo
- 2180 1474 4139 2.533 0.451 0.128 0.026 32 2.3 BA2_exvivo
- 1081 715 1066 1.925 0.387 0.117 0.024 8 1.0 BA3a_exvivo
- 1802 1229 2285 1.786 0.384 0.099 0.017 15 1.3 BA3b_exvivo
- 1650 1063 3791 2.888 0.447 0.087 0.016 10 1.0 BA4a_exvivo
- 1163 792 1943 2.567 0.382 0.091 0.016 7 0.7 BA4p_exvivo
- 6044 4117 14226 2.838 0.537 0.112 0.021 62 5.0 BA6_exvivo
- 1646 1111 3813 2.829 0.430 0.111 0.025 25 1.5 BA44_exvivo
- 1111 797 2824 2.752 0.444 0.158 0.042 22 2.0 BA45_exvivo
- 3703 2523 4978 1.892 0.482 0.135 0.035 52 5.2 V1_exvivo
- 4353 2812 6372 2.099 0.498 0.158 0.039 87 6.7 V2_exvivo
- 691 485 1469 2.615 0.488 0.141 0.025 11 0.7 MT_exvivo
- 248 152 941 3.810 0.688 0.101 0.017 2 0.2 perirhinal_exvivo
- 279 192 680 3.108 0.750 0.082 0.022 1 0.2 entorhinal_exvivo
- #--------------------------------------------
- #@# BA_exvivo Labels rh Sun Oct 8 08:31:37 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 27297 of (27297 27303 27309 27315 27321) to complete...
- Waiting for PID 27303 of (27297 27303 27309 27315 27321) to complete...
- Waiting for PID 27309 of (27297 27303 27309 27315 27321) to complete...
- Waiting for PID 27315 of (27297 27303 27309 27315 27321) to complete...
- Waiting for PID 27321 of (27297 27303 27309 27315 27321) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 252
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.label 4214
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 295
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.label 6982
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 176
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.label 4156
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 297
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.label 4819
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 332
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.label 6079
- mri_label2label: Done
- PIDs (27297 27303 27309 27315 27321) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 27368 of (27368 27374 27380 27383) to complete...
- Waiting for PID 27374 of (27368 27374 27380 27383) to complete...
- Waiting for PID 27380 of (27368 27374 27380 27383) to complete...
- Waiting for PID 27383 of (27368 27374 27380 27383) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 172
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.label 4645
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 1174
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.label 13430
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 792
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.label 7704
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 1029
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.label 6384
- mri_label2label: Done
- PIDs (27368 27374 27380 27383) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 27438 of (27438 27444 27449 27456 27461) to complete...
- Waiting for PID 27444 of (27438 27444 27449 27456 27461) to complete...
- Waiting for PID 27449 of (27438 27444 27449 27456 27461) to complete...
- Waiting for PID 27456 of (27438 27444 27449 27456 27461) to complete...
- Waiting for PID 27461 of (27438 27444 27449 27456 27461) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 1813
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.label 6540
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 3395
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.label 11411
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 511
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.label 2443
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 52
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.label 1090
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 14
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.label 766
- mri_label2label: Done
- PIDs (27438 27444 27449 27456 27461) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 27507 of (27507 27513 27519 27524 27531) to complete...
- Waiting for PID 27513 of (27507 27513 27519 27524 27531) to complete...
- Waiting for PID 27519 of (27507 27513 27519 27524 27531) to complete...
- Waiting for PID 27524 of (27507 27513 27519 27524 27531) to complete...
- Waiting for PID 27531 of (27507 27513 27519 27524 27531) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 62
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.thresh.label 938
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 51
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.thresh.label 2739
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 56
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.thresh.label 1754
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 165
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.thresh.label 2348
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 61
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.thresh.label 1449
- mri_label2label: Done
- PIDs (27507 27513 27519 27524 27531) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 27578 of (27578 27584 27589 27596) to complete...
- Waiting for PID 27584 of (27578 27584 27589 27596) to complete...
- Waiting for PID 27589 of (27578 27584 27589 27596) to complete...
- Waiting for PID 27596 of (27578 27584 27589 27596) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 75
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.thresh.label 1564
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 585
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.thresh.label 7544
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 221
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.thresh.label 1233
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 239
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.thresh.label 1417
- mri_label2label: Done
- PIDs (27578 27584 27589 27596) 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 0051311 --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 0051311 --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 0051311 --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 0051311 --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 0051311 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 27643 of (27643 27649 27655 27661 27667) to complete...
- Waiting for PID 27649 of (27643 27649 27655 27661 27667) to complete...
- Waiting for PID 27655 of (27643 27649 27655 27661 27667) to complete...
- Waiting for PID 27661 of (27643 27649 27655 27661 27667) to complete...
- Waiting for PID 27667 of (27643 27649 27655 27661 27667) 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 1183
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.thresh.label 4415
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 1457
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.thresh.label 4894
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 87
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.thresh.label 355
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 28
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.thresh.label 722
- 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 0051311 --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 = 0051311
- 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-6.0.0/0051311/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 139374
- Number of reverse mapping hits = 1
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.thresh.label 292
- mri_label2label: Done
- PIDs (27643 27649 27655 27661 27667) completed and logs appended.
- mris_label2annot --s 0051311 --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-6.0.0/0051311/label
- cmdline mris_label2annot --s 0051311 --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-904
- machine x86_64
- user ntraut
- subject 0051311
- 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-6.0.0/0051311/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 96535 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/label/rh.BA_exvivo.annot
- mris_label2annot --s 0051311 --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-6.0.0/0051311/label
- cmdline mris_label2annot --s 0051311 --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-904
- machine x86_64
- user ntraut
- subject 0051311
- 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-6.0.0/0051311/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 115381 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/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 0051311 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 271597
- Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 943 558 1945 2.454 0.392 0.154 0.029 18 1.2 BA1_exvivo
- 2810 1918 5068 2.363 0.428 0.110 0.020 34 2.1 BA2_exvivo
- 1153 777 1142 1.930 0.428 0.130 0.029 11 1.2 BA3a_exvivo
- 2110 1400 2811 1.852 0.467 0.099 0.017 17 1.4 BA3b_exvivo
- 1507 971 3285 2.786 0.360 0.094 0.019 11 1.1 BA4a_exvivo
- 1360 878 2219 2.553 0.382 0.098 0.017 10 1.0 BA4p_exvivo
- 8745 5947 19970 2.832 0.497 0.114 0.021 94 7.1 BA6_exvivo
- 3788 2607 7914 2.734 0.467 0.117 0.023 43 3.6 BA44_exvivo
- 4327 2977 9011 2.582 0.480 0.140 0.032 94 5.6 BA45_exvivo
- 4179 2726 5777 1.963 0.532 0.134 0.039 64 6.5 V1_exvivo
- 8928 5820 14519 2.269 0.583 0.149 0.039 159 13.7 V2_exvivo
- 2198 1478 3590 2.450 0.373 0.099 0.017 17 1.5 MT_exvivo
- 530 326 1724 3.407 0.653 0.120 0.031 5 0.6 perirhinal_exvivo
- 261 203 624 2.933 0.607 0.081 0.015 1 0.1 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 0051311 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051311/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 271597
- Total vertex volume 268028 (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) = 1336087 mm^3 (det: 1.458067 )
- lhCtxGM: 266714.963 266344.000 diff= 371.0 pctdiff= 0.139
- rhCtxGM: 266823.692 266257.000 diff= 566.7 pctdiff= 0.212
- lhCtxWM: 198961.453 198666.500 diff= 295.0 pctdiff= 0.148
- rhCtxWM: 197948.874 198501.500 diff= -552.6 pctdiff=-0.279
- SubCortGMVol 58840.000
- SupraTentVol 1008796.981 (1005342.000) diff=3454.981 pctdiff=0.342
- SupraTentVolNotVent 992172.981 (988718.000) diff=3454.981 pctdiff=0.348
- BrainSegVol 1148897.000 (1146357.000) diff=2540.000 pctdiff=0.221
- BrainSegVolNotVent 1128868.000 (1129419.981) diff=-551.981 pctdiff=-0.049
- BrainSegVolNotVent 1128868.000
- CerebellumVol 140022.000
- VentChorVol 16624.000
- 3rd4th5thCSF 3405.000
- CSFVol 865.000, OptChiasmVol 128.000
- MaskVol 1478177.000
- 600 346 1191 2.411 0.390 0.142 0.024 10 0.6 BA1_exvivo
- 1553 1054 2922 2.423 0.406 0.106 0.019 17 1.1 BA2_exvivo
- 1046 699 953 1.922 0.396 0.129 0.027 9 1.2 BA3a_exvivo
- 1682 1154 1969 1.710 0.381 0.091 0.013 10 0.9 BA3b_exvivo
- 920 569 2139 2.859 0.372 0.106 0.026 9 0.8 BA4a_exvivo
- 1074 740 1773 2.546 0.411 0.092 0.015 6 0.7 BA4p_exvivo
- 5483 3734 12985 2.850 0.507 0.117 0.022 65 4.6 BA6_exvivo
- 1039 708 2505 2.836 0.464 0.141 0.032 20 1.4 BA44_exvivo
- 1200 859 2780 2.597 0.395 0.148 0.037 31 1.6 BA45_exvivo
- 4009 2600 5260 1.940 0.513 0.132 0.038 58 6.2 V1_exvivo
- 4560 2997 7329 2.161 0.579 0.159 0.044 89 7.8 V2_exvivo
- 333 214 672 2.451 0.314 0.110 0.016 5 0.2 MT_exvivo
- 316 193 1023 3.335 0.650 0.120 0.023 3 0.3 perirhinal_exvivo
- 178 142 471 3.061 0.564 0.088 0.014 1 0.1 entorhinal_exvivo
- Started at Sat Oct 7 23:29:49 CEST 2017
- Ended at Sun Oct 8 08:35:00 CEST 2017
- #@#%# recon-all-run-time-hours 9.086
- recon-all -s 0051311 finished without error at Sun Oct 8 08:35:00 CEST 2017
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