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- Sun Oct 8 00:08:31 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
- -subjid 0050379 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050379/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
- subjid 0050379
- 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-598 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: 65993848 54253916 11739932 1765224 0 50101184
- -/+ buffers/cache: 4152732 61841116
- 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:31-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-598 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: 2017/10/07-22:08:32-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-598 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: 2017/10/07-22:08:32-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-598 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: 2017/10/07-22:08:32-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-598 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: 2017/10/07-22:08:32-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-598 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: 2017/10/07-22:08:32-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-598 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: 2017/10/07-22:08:32-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-598 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-6.0.0/0050379
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050379/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/orig/001.mgz
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050379/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/orig/001.mgz
- $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
- reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050379/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-6.0.0/0050379/mri/orig/001.mgz...
- #--------------------------------------------
- #@# MotionCor Sun Oct 8 00:08:33 CEST 2017
- Found 1 runs
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/rawavg.mgz
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/orig.mgz --conform
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/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-6.0.0/0050379/mri/orig.mgz...
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Sun Oct 8 00:08:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/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-598 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
- Sun Oct 8 00:08:45 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.11567
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11567/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.11567/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.11567/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sun Oct 8 00:08:47 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.11567/nu0.mnc ./tmp.mri_nu_correct.mni.11567/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.11567/0/ -iterations 1000 -distance 50
- [ntraut@tars-598:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/] [2017-10-08 00:08:47] 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.11567/0/ ./tmp.mri_nu_correct.mni.11567/nu0.mnc ./tmp.mri_nu_correct.mni.11567/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 23
- CV of field change: 0.000977872
-
-
-
- mri_convert ./tmp.mri_nu_correct.mni.11567/nu1.mnc orig_nu.mgz --like orig.mgz --conform
- mri_convert.bin ./tmp.mri_nu_correct.mni.11567/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.11567/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...
-
-
- Sun Oct 8 00:09:41 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 Sun Oct 8 00:09:41 CEST 2017
- Ended at Sun Oct 8 00:10:15 CEST 2017
- talairach_avi done
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Sun Oct 8 00:10:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6271, pval=0.3663 >= 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-6.0.0/0050379/mri/transforms/talairach_avi.log
- tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/transforms/talairach_avi.log
- TalAviQA: 0.97588
- z-score: 0
- #--------------------------------------------
- #@# Nu Intensity Correction Sun Oct 8 00:10:17 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-6.0.0/0050379/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-598 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
- Sun Oct 8 00:10:17 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.12124
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12124/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.12124/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.12124/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sun Oct 8 00:10:19 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.12124/nu0.mnc ./tmp.mri_nu_correct.mni.12124/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12124/0/
- [ntraut@tars-598:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/] [2017-10-08 00:10:20] running:
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.12124/0/ ./tmp.mri_nu_correct.mni.12124/nu0.mnc ./tmp.mri_nu_correct.mni.12124/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 18
- CV of field change: 0.000971584
-
-
- --------------------------------------------------------
- Iteration 2 Sun Oct 8 00:11:01 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.12124/nu1.mnc ./tmp.mri_nu_correct.mni.12124/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.12124/1/
- [ntraut@tars-598:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/] [2017-10-08 00:11:01] 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.12124/1/ ./tmp.mri_nu_correct.mni.12124/nu1.mnc ./tmp.mri_nu_correct.mni.12124/nu2.imp
- 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: 11
- CV of field change: 0.000988857
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.12124/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12124/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-6.0.0/0050379/mri
- cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.12124/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12124/ones.mgz
- sysname Linux
- hostname tars-598
- machine x86_64
- user ntraut
- input ./tmp.mri_nu_correct.mni.12124/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.12124/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.12124/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12124/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12124/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.12124/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12124/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12124/input.mean.dat
- sysname Linux
- hostname tars-598
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.12124/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.12124/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12124/ones.mgz --i ./tmp.mri_nu_correct.mni.12124/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12124/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12124/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.12124/ones.mgz --i ./tmp.mri_nu_correct.mni.12124/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12124/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12124/output.mean.dat
- sysname Linux
- hostname tars-598
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.12124/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.12124/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.12124/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.12124/nu2.mnc ./tmp.mri_nu_correct.mni.12124/nu2.mnc mul 1.01559682291303652118
- Saving result to './tmp.mri_nu_correct.mni.12124/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.12124/nu2.mnc nu.mgz --like orig.mgz
- mri_convert.bin ./tmp.mri_nu_correct.mni.12124/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.12124/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -1)
- k_ras = (0, 1, 0)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 8 seconds.
- mapping (10, 98) to ( 3, 110)
-
-
- Sun Oct 8 00:12:16 CEST 2017
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Sun Oct 8 00:12:18 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri
- mri_normalize -g 1 -mprage nu.mgz T1.mgz
- using max gradient = 1.000
- assuming input volume is MGH (Van der Kouwe) MP-RAGE
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.07366 -0.13470 -0.10551 -120.60033;
- 0.10699 1.01755 0.05988 -158.30618;
- 0.09698 0.04264 1.20020 -88.94356;
- 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 = 13
- Starting OpenSpline(): npoints = 13
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 110
- white matter peak found at 109
- gm peak at 70 (70), valley at 37 (37)
- csf peak at 36, setting threshold to 58
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 110
- white matter peak found at 110
- gm peak at 64 (64), valley at 31 (31)
- csf peak at 32, setting threshold to 53
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 3 seconds.
- #--------------------------------------------
- #@# Skull Stripping Sun Oct 8 00:14:22 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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=12.0
- skull bounding box = (42, 60, 18) --> (205, 200, 217)
- using (96, 107, 118) as brain centroid...
- mean wm in atlas = 108, using box (76,90,93) --> (116, 124,142) to find MRI wm
- before smoothing, mri peak at 108
- robust fit to distribution - 108 +- 5.6
- after smoothing, mri peak at 108, scaling input intensities by 1.000
- scaling channel 0 by 1
- initial log_p = -4.654
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.502006 @ (9.091, -9.091, -9.091)
- max log p = -4.422995 @ (-4.545, -13.636, 4.545)
- max log p = -4.409709 @ (2.273, 6.818, 2.273)
- max log p = -4.373405 @ (-1.136, -1.136, -1.136)
- max log p = -4.356010 @ (-0.568, -0.568, -0.568)
- max log p = -4.356010 @ (0.000, 0.000, 0.000)
- Found translation: (5.1, -17.6, -4.0): log p = -4.356
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.973, old_max_log_p =-4.356 (thresh=-4.4)
- 1.04098 -0.13885 0.15500 -2.91797;
- 0.15927 1.22567 0.02372 -67.97312;
- -0.11999 0.00000 1.07125 2.20564;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.973, old_max_log_p =-3.973 (thresh=-4.0)
- 1.04098 -0.13885 0.15500 -2.91797;
- 0.15927 1.22567 0.02372 -67.97312;
- -0.11999 0.00000 1.07125 2.20564;
- 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=-3.906, old_max_log_p =-3.973 (thresh=-4.0)
- 1.04966 -0.05856 0.15164 -12.14417;
- 0.10038 1.30141 -0.02527 -66.46988;
- -0.10646 0.03472 1.01238 0.12561;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.903, old_max_log_p =-3.906 (thresh=-3.9)
- 1.04834 -0.01478 0.18375 -22.44738;
- 0.06487 1.27817 -0.03072 -57.93505;
- -0.14339 0.03730 1.02576 2.67582;
- 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=-3.889, old_max_log_p =-3.903 (thresh=-3.9)
- 1.04924 -0.07878 0.15162 -9.02487;
- 0.11678 1.28035 -0.02284 -65.06382;
- -0.10888 0.03607 1.03003 -0.91482;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.880, old_max_log_p =-3.889 (thresh=-3.9)
- 1.05170 -0.07896 0.15197 -9.33870;
- 0.11719 1.28486 -0.02292 -65.79296;
- -0.10876 0.03602 1.02883 -0.78376;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.876, old_max_log_p =-3.880 (thresh=-3.9)
- 1.05170 -0.07896 0.15197 -9.33870;
- 0.11747 1.28787 -0.02298 -66.28039;
- -0.10876 0.03602 1.02883 -0.78376;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.874, old_max_log_p =-3.876 (thresh=-3.9)
- 1.05416 -0.07915 0.15233 -9.65327;
- 0.11788 1.29240 -0.02306 -67.01381;
- -0.10876 0.03602 1.02883 -0.78376;
- 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
- 1.05416 -0.07915 0.15233 -9.65327;
- 0.11788 1.29240 -0.02306 -67.01381;
- -0.10876 0.03602 1.02883 -0.78376;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3243
- Quasinewton: input matrix
- 1.05416 -0.07915 0.15233 -9.65327;
- 0.11788 1.29240 -0.02306 -67.01381;
- -0.10876 0.03602 1.02883 -0.78376;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.05416 -0.07915 0.15233 -9.65327;
- 0.11788 1.29240 -0.02306 -67.01381;
- -0.10876 0.03602 1.02883 -0.78376;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.874 (old=-4.654)
- transform before final EM align:
- 1.05416 -0.07915 0.15233 -9.65327;
- 0.11788 1.29240 -0.02306 -67.01381;
- -0.10876 0.03602 1.02883 -0.78376;
- 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
- 1.05416 -0.07915 0.15233 -9.65327;
- 0.11788 1.29240 -0.02306 -67.01381;
- -0.10876 0.03602 1.02883 -0.78376;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 364799
- Quasinewton: input matrix
- 1.05416 -0.07915 0.15233 -9.65327;
- 0.11788 1.29240 -0.02306 -67.01381;
- -0.10876 0.03602 1.02883 -0.78376;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 012: -log(p) = 4.3 tol 0.000000
- final transform:
- 1.05416 -0.07915 0.15233 -9.65327;
- 0.11788 1.29240 -0.02306 -67.01381;
- -0.10876 0.03602 1.02883 -0.78376;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach_with_skull.lta...
- mri_em_register utimesec 1942.437704
- mri_em_register stimesec 2.561610
- mri_em_register ru_maxrss 609824
- mri_em_register ru_ixrss 0
- mri_em_register ru_idrss 0
- mri_em_register ru_isrss 0
- mri_em_register ru_minflt 157571
- 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 181805
- mri_em_register ru_nivcsw 3372
- registration took 20 minutes and 8 seconds.
- mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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=122 y=132 z=117 r=66
- first estimation of the main basin volume: 1256475 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 16 found in the rest of the brain
- global maximum in x=105, y=115, z=85, 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=8743542683 voxels, voxel volume =1.000
- = 8743542683 mmm3 = 8743542.784 cm3
- done.
- PostAnalyze...Basin Prior
- 20 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=124,y=135, z=111, r=9457 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45403
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1097880403
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1122109038
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1124439786
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1068278978
- OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1076318694
- Problem with the least square interpolation in GM_MIN calculation.
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 4, 6, 36, 60
- after analyzing : 4, 26, 36, 34
- RIGHT_CER
- before analyzing : 3, 3, 21, 64
- after analyzing : 3, 17, 25, 28
- LEFT_CER
- before analyzing : 3, 3, 22, 66
- after analyzing : 3, 17, 25, 29
- RIGHT_BRAIN
- before analyzing : 4, 6, 35, 63
- after analyzing : 4, 25, 35, 34
- LEFT_BRAIN
- before analyzing : 4, 6, 36, 60
- after analyzing : 4, 26, 36, 34
- OTHER
- before analyzing : 3, 4, 60, 91
- after analyzing : 3, 41, 60, 53
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...59 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.009
- curvature mean = 70.765, std = 7.981
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 6.16, sigma = 9.46
- after rotation: sse = 6.16, sigma = 9.46
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 6.63, its var is 8.74
- before Erosion-Dilatation 3.65% of inacurate vertices
- after Erosion-Dilatation 5.39% 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...26 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1603057 voxels, voxel volume = 1.000 mm3
- = 1603057 mmm3 = 1603.057 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- mri_watershed utimesec 21.436741
- mri_watershed stimesec 0.436933
- mri_watershed ru_maxrss 818276
- mri_watershed ru_ixrss 0
- mri_watershed ru_idrss 0
- mri_watershed ru_isrss 0
- mri_watershed ru_minflt 211533
- mri_watershed ru_majflt 0
- mri_watershed ru_nswap 0
- mri_watershed ru_inblock 4680
- mri_watershed ru_oublock 2560
- mri_watershed ru_msgsnd 0
- mri_watershed ru_msgrcv 0
- mri_watershed ru_nsignals 0
- mri_watershed ru_nvcsw 3118
- mri_watershed ru_nivcsw 87
- mri_watershed done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Sun Oct 8 00:34:51 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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=22.0
- skull bounding box = (56, 78, 29) --> (191, 185, 204)
- using (101, 114, 117) as brain centroid...
- mean wm in atlas = 107, using box (84,101,95) --> (117, 127,138) to find MRI wm
- before smoothing, mri peak at 109
- robust fit to distribution - 108 +- 5.4
- after smoothing, mri peak at 108, scaling input intensities by 0.991
- scaling channel 0 by 0.990741
- initial log_p = -4.310
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.107468 @ (9.091, -9.091, -9.091)
- max log p = -3.902416 @ (-4.545, -4.545, 4.545)
- max log p = -3.876136 @ (-2.273, -6.818, -2.273)
- max log p = -3.852951 @ (1.136, 1.136, 3.409)
- max log p = -3.832984 @ (0.568, 0.568, -0.568)
- max log p = -3.832984 @ (0.000, 0.000, 0.000)
- Found translation: (4.0, -18.8, -4.0): log p = -3.833
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.693, old_max_log_p =-3.833 (thresh=-3.8)
- 1.07722 0.04261 0.13553 -26.21490;
- 0.03964 1.13938 -0.03378 -39.15936;
- -0.12608 0.03378 0.99144 7.77287;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.680, old_max_log_p =-3.693 (thresh=-3.7)
- 1.07722 0.04261 0.13553 -26.21490;
- 0.02284 1.13404 0.09592 -50.55250;
- -0.13017 -0.11523 0.98737 29.29026;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.680, old_max_log_p =-3.680 (thresh=-3.7)
- 1.07722 0.04261 0.13553 -26.21490;
- 0.02284 1.13404 0.09592 -50.55250;
- -0.13017 -0.11523 0.98737 29.29026;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.494, old_max_log_p =-3.680 (thresh=-3.7)
- 1.00777 -0.03329 0.16370 -12.45218;
- 0.11475 1.20281 -0.05774 -50.83788;
- -0.15852 0.07106 0.98497 3.81771;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.492, old_max_log_p =-3.494 (thresh=-3.5)
- 1.03527 -0.03596 0.10070 -8.36155;
- 0.10950 1.20449 -0.02548 -54.07191;
- -0.09773 0.02997 1.01358 -1.42624;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.456, old_max_log_p =-3.492 (thresh=-3.5)
- 1.02730 -0.06445 0.13437 -6.87401;
- 0.13737 1.20684 -0.03877 -56.82555;
- -0.12900 0.05074 1.00568 1.95310;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.445, old_max_log_p =-3.456 (thresh=-3.5)
- 1.02714 -0.07481 0.12652 -5.04157;
- 0.14683 1.20581 -0.04596 -57.05316;
- -0.11933 0.06001 1.00522 -0.91836;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.441, old_max_log_p =-3.445 (thresh=-3.4)
- 1.02955 -0.07498 0.12682 -5.35043;
- 0.14683 1.20581 -0.04596 -57.05316;
- -0.11919 0.05994 1.00404 -0.79372;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.441, old_max_log_p =-3.441 (thresh=-3.4)
- 1.02955 -0.07498 0.12682 -5.35043;
- 0.14683 1.20581 -0.04596 -57.05316;
- -0.11919 0.05994 1.00404 -0.79372;
- 0.00000 0.00000 0.00000 1.00000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 2830 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.02955 -0.07498 0.12682 -5.35043;
- 0.14683 1.20581 -0.04596 -57.05316;
- -0.11919 0.05994 1.00404 -0.79372;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2830
- Quasinewton: input matrix
- 1.02955 -0.07498 0.12682 -5.35043;
- 0.14683 1.20581 -0.04596 -57.05316;
- -0.11919 0.05994 1.00404 -0.79372;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.02955 -0.07498 0.12682 -5.35043;
- 0.14683 1.20581 -0.04596 -57.05316;
- -0.11919 0.05994 1.00404 -0.79372;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.441 (old=-4.310)
- transform before final EM align:
- 1.02955 -0.07498 0.12682 -5.35043;
- 0.14683 1.20581 -0.04596 -57.05316;
- -0.11919 0.05994 1.00404 -0.79372;
- 0.00000 0.00000 0.00000 1.00000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 315557 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.02955 -0.07498 0.12682 -5.35043;
- 0.14683 1.20581 -0.04596 -57.05316;
- -0.11919 0.05994 1.00404 -0.79372;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 315557
- Quasinewton: input matrix
- 1.02955 -0.07498 0.12682 -5.35043;
- 0.14683 1.20581 -0.04596 -57.05316;
- -0.11919 0.05994 1.00404 -0.79372;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 013: -log(p) = 3.9 tol 0.000000
- final transform:
- 1.02955 -0.07498 0.12682 -5.35043;
- 0.14683 1.20581 -0.04596 -57.05316;
- -0.11919 0.05994 1.00404 -0.79372;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach.lta...
- mri_em_register utimesec 1513.682885
- mri_em_register stimesec 2.052687
- 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 158983
- 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 131
- mri_em_register ru_nivcsw 2667
- registration took 12 minutes and 54 seconds.
- #--------------------------------------
- #@# CA Normalize Sun Oct 8 00:47:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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=22.0
- skull bounding box = (56, 78, 29) --> (191, 185, 204)
- using (101, 114, 117) as brain centroid...
- mean wm in atlas = 107, using box (84,101,95) --> (117, 127,138) to find MRI wm
- before smoothing, mri peak at 109
- robust fit to distribution - 108 +- 5.4
- after smoothing, mri peak at 108, scaling input intensities by 0.991
- scaling channel 0 by 0.990741
- using 246344 sample points...
- INFO: compute sample coordinates transform
- 1.02955 -0.07498 0.12682 -5.35043;
- 0.14683 1.20581 -0.04596 -57.05316;
- -0.11919 0.05994 1.00404 -0.79372;
- 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 (119, 77, 34) --> (190, 176, 201)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
- 0 of 2012 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 80, 32) --> (128, 184, 198)
- Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0
- 0 of 2061 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (130, 149, 55) --> (178, 181, 110)
- Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0
- 0 of 133 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (88, 149, 50) --> (131, 186, 107)
- Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0
- 0 of 37 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (110, 143, 87) --> (144, 201, 121)
- Brain_Stem: limiting intensities to 93.0 --> 132.0
- 0 of 92 (0.0%) samples deleted
- using 4335 total control points for intensity normalization...
- bias field = 0.980 +- 0.064
- 6 of 4335 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (119, 77, 34) --> (190, 176, 201)
- Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
- 0 of 2273 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 80, 32) --> (128, 184, 198)
- Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
- 0 of 2399 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (130, 149, 55) --> (178, 181, 110)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 2 of 182 (1.1%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (88, 149, 50) --> (131, 186, 107)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 5 of 100 (5.0%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (110, 143, 87) --> (144, 201, 121)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 14 of 172 (8.1%) samples deleted
- using 5126 total control points for intensity normalization...
- bias field = 1.028 +- 0.058
- 7 of 5052 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (119, 77, 34) --> (190, 176, 201)
- Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0
- 0 of 2282 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 80, 32) --> (128, 184, 198)
- Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 1 of 2413 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (130, 149, 55) --> (178, 181, 110)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 68 of 224 (30.4%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (88, 149, 50) --> (131, 186, 107)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 56 of 122 (45.9%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (110, 143, 87) --> (144, 201, 121)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 114 of 237 (48.1%) samples deleted
- using 5278 total control points for intensity normalization...
- bias field = 1.027 +- 0.051
- 16 of 4941 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 1 minutes and 39 seconds.
- #--------------------------------------
- #@# CA Reg Sun Oct 8 00:49:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri
- mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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) = 1.28 (predicted orig area = 6.3)
- 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=0.814, neg=0, invalid=762
- 0001: dt=202.483487, rms=0.759 (6.760%), neg=0, invalid=762
- 0002: dt=183.641791, rms=0.742 (2.275%), neg=0, invalid=762
- 0003: dt=174.993007, rms=0.733 (1.225%), neg=0, invalid=762
- 0004: dt=221.952000, rms=0.727 (0.811%), neg=0, invalid=762
- 0005: dt=150.634146, rms=0.723 (0.554%), neg=0, invalid=762
- 0006: dt=295.936000, rms=0.719 (0.531%), neg=0, invalid=762
- 0007: dt=129.472000, rms=0.716 (0.391%), neg=0, invalid=762
- 0008: dt=517.888000, rms=0.712 (0.533%), neg=0, invalid=762
- 0009: dt=129.472000, rms=0.709 (0.441%), neg=0, invalid=762
- 0010: dt=369.920000, rms=0.707 (0.261%), neg=0, invalid=762
- 0011: dt=129.472000, rms=0.705 (0.327%), neg=0, invalid=762
- 0012: dt=369.920000, rms=0.703 (0.243%), neg=0, invalid=762
- 0013: dt=369.920000, rms=0.703 (-0.429%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.704, neg=0, invalid=762
- 0014: dt=129.472000, rms=0.701 (0.337%), neg=0, invalid=762
- 0015: dt=517.888000, rms=0.699 (0.383%), neg=0, invalid=762
- 0016: dt=295.936000, rms=0.698 (0.164%), neg=0, invalid=762
- 0017: dt=295.936000, rms=0.697 (0.104%), neg=0, invalid=762
- 0018: dt=295.936000, rms=0.695 (0.344%), neg=0, invalid=762
- 0019: dt=295.936000, rms=0.693 (0.252%), neg=0, invalid=762
- 0020: dt=295.936000, rms=0.690 (0.380%), neg=0, invalid=762
- 0021: dt=295.936000, rms=0.688 (0.325%), neg=0, invalid=762
- 0022: dt=295.936000, rms=0.686 (0.259%), neg=0, invalid=762
- 0023: dt=295.936000, rms=0.684 (0.337%), neg=0, invalid=762
- 0024: dt=295.936000, rms=0.682 (0.231%), neg=0, invalid=762
- 0025: dt=295.936000, rms=0.681 (0.202%), neg=0, invalid=762
- 0026: dt=295.936000, rms=0.679 (0.219%), neg=0, invalid=762
- 0027: dt=295.936000, rms=0.678 (0.142%), neg=0, invalid=762
- 0028: dt=295.936000, rms=0.677 (0.193%), neg=0, invalid=762
- 0029: dt=295.936000, rms=0.676 (0.191%), neg=0, invalid=762
- 0030: dt=295.936000, rms=0.675 (0.096%), neg=0, invalid=762
- 0031: dt=295.936000, rms=0.674 (0.134%), neg=0, invalid=762
- 0032: dt=295.936000, rms=0.673 (0.136%), neg=0, invalid=762
- 0033: dt=295.936000, rms=0.673 (0.101%), neg=0, invalid=762
- 0034: dt=295.936000, rms=0.672 (0.118%), neg=0, invalid=762
- 0035: dt=295.936000, rms=0.671 (0.115%), neg=0, invalid=762
- 0036: dt=129.472000, rms=0.671 (0.028%), neg=0, invalid=762
- 0037: dt=129.472000, rms=0.671 (0.000%), neg=0, invalid=762
- 0038: dt=129.472000, rms=0.671 (0.019%), neg=0, invalid=762
- 0039: dt=129.472000, rms=0.671 (0.035%), neg=0, invalid=762
- 0040: dt=129.472000, rms=0.670 (0.030%), neg=0, invalid=762
- 0041: dt=129.472000, rms=0.670 (0.027%), neg=0, invalid=762
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.676, neg=0, invalid=762
- 0042: dt=118.774775, rms=0.671 (0.742%), neg=0, invalid=762
- 0043: dt=145.152000, rms=0.665 (0.807%), neg=0, invalid=762
- 0044: dt=83.555556, rms=0.663 (0.401%), neg=0, invalid=762
- 0045: dt=87.445545, rms=0.660 (0.473%), neg=0, invalid=762
- 0046: dt=68.363636, rms=0.658 (0.267%), neg=0, invalid=762
- 0047: dt=145.152000, rms=0.655 (0.482%), neg=0, invalid=762
- 0048: dt=36.288000, rms=0.654 (0.165%), neg=0, invalid=762
- 0049: dt=36.288000, rms=0.653 (0.089%), neg=0, invalid=762
- 0050: dt=36.288000, rms=0.652 (0.173%), neg=0, invalid=762
- 0051: dt=36.288000, rms=0.650 (0.241%), neg=0, invalid=762
- 0052: dt=36.288000, rms=0.648 (0.304%), neg=0, invalid=762
- 0053: dt=36.288000, rms=0.646 (0.326%), neg=0, invalid=762
- 0054: dt=36.288000, rms=0.644 (0.338%), neg=0, invalid=762
- 0055: dt=36.288000, rms=0.642 (0.318%), neg=0, invalid=762
- 0056: dt=36.288000, rms=0.640 (0.297%), neg=0, invalid=762
- 0057: dt=36.288000, rms=0.638 (0.281%), neg=0, invalid=762
- 0058: dt=36.288000, rms=0.636 (0.277%), neg=0, invalid=762
- 0059: dt=36.288000, rms=0.635 (0.262%), neg=0, invalid=762
- 0060: dt=36.288000, rms=0.633 (0.238%), neg=0, invalid=762
- 0061: dt=36.288000, rms=0.632 (0.211%), neg=0, invalid=762
- 0062: dt=36.288000, rms=0.631 (0.192%), neg=0, invalid=762
- 0063: dt=36.288000, rms=0.630 (0.177%), neg=0, invalid=762
- 0064: dt=36.288000, rms=0.629 (0.165%), neg=0, invalid=762
- 0065: dt=36.288000, rms=0.628 (0.151%), neg=0, invalid=762
- 0066: dt=36.288000, rms=0.627 (0.146%), neg=0, invalid=762
- 0067: dt=36.288000, rms=0.626 (0.130%), neg=0, invalid=762
- 0068: dt=36.288000, rms=0.625 (0.106%), neg=0, invalid=762
- 0069: dt=36.288000, rms=0.625 (0.098%), neg=0, invalid=762
- 0070: dt=497.664000, rms=0.624 (0.122%), neg=0, invalid=762
- 0071: dt=20.736000, rms=0.624 (0.017%), neg=0, invalid=762
- 0072: dt=20.736000, rms=0.624 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.624, neg=0, invalid=762
- 0073: dt=103.680000, rms=0.623 (0.266%), neg=0, invalid=762
- 0074: dt=124.416000, rms=0.622 (0.134%), neg=0, invalid=762
- 0075: dt=124.416000, rms=0.622 (-0.094%), neg=0, invalid=762
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.645, neg=0, invalid=762
- 0076: dt=8.000000, rms=0.644 (0.152%), neg=0, invalid=762
- 0077: dt=2.800000, rms=0.644 (0.013%), neg=0, invalid=762
- 0078: dt=2.800000, rms=0.644 (0.002%), neg=0, invalid=762
- 0079: dt=2.800000, rms=0.644 (-0.025%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.644, neg=0, invalid=762
- 0080: dt=0.700000, rms=0.644 (0.080%), neg=0, invalid=762
- 0081: dt=0.500000, rms=0.644 (-0.003%), neg=0, invalid=762
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.702, neg=0, invalid=762
- 0082: dt=6.000000, rms=0.686 (2.283%), neg=0, invalid=762
- 0083: dt=3.333333, rms=0.685 (0.096%), neg=0, invalid=762
- 0084: dt=3.333333, rms=0.685 (-0.028%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.685, neg=0, invalid=762
- 0085: dt=0.000000, rms=0.685 (0.056%), neg=0, invalid=762
- 0086: dt=0.000000, rms=0.685 (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=0.742, neg=0, invalid=762
- 0087: dt=0.768000, rms=0.740 (0.254%), neg=0, invalid=762
- 0088: dt=1.792000, rms=0.737 (0.366%), neg=0, invalid=762
- 0089: dt=2.189655, rms=0.734 (0.431%), neg=0, invalid=762
- 0090: dt=0.448000, rms=0.734 (0.023%), neg=0, invalid=762
- 0091: dt=0.448000, rms=0.734 (0.020%), neg=0, invalid=762
- 0092: dt=0.448000, rms=0.733 (0.030%), neg=0, invalid=762
- 0093: dt=0.448000, rms=0.733 (0.024%), neg=0, invalid=762
- 0094: dt=0.448000, rms=0.733 (0.001%), neg=0, invalid=762
- 0095: dt=3.072000, rms=0.733 (0.096%), neg=0, invalid=762
- 0096: dt=0.080000, rms=0.733 (0.002%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.733, neg=0, invalid=762
- 0097: dt=1.024000, rms=0.732 (0.166%), neg=0, invalid=762
- 0098: dt=0.000000, rms=0.732 (-0.001%), 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=0.700, neg=0, invalid=762
- 0099: dt=0.835465, rms=0.681 (2.648%), neg=0, invalid=762
- 0100: dt=0.080000, rms=0.681 (0.129%), neg=0, invalid=762
- 0101: dt=0.080000, rms=0.681 (-0.087%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.681, neg=0, invalid=762
- 0102: dt=0.028000, rms=0.680 (0.086%), neg=0, invalid=762
- 0103: dt=0.006000, rms=0.680 (0.000%), neg=0, invalid=762
- 0104: dt=0.006000, rms=0.680 (-0.000%), neg=0, invalid=762
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.10027 (20)
- mri peak = 0.07903 (15)
- Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (512 voxels, overlap=0.480)
- Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (512 voxels, peak = 16), gca=16.3
- gca peak = 0.15565 (16)
- mri peak = 0.06551 (18)
- Right_Lateral_Ventricle (43): linear fit = 1.16 x + 0.0 (479 voxels, overlap=0.668)
- Right_Lateral_Ventricle (43): linear fit = 1.16 x + 0.0 (479 voxels, peak = 19), gca=18.6
- gca peak = 0.26829 (96)
- mri peak = 0.09891 (91)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (869 voxels, overlap=1.005)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (869 voxels, peak = 92), gca=91.7
- gca peak = 0.20183 (93)
- mri peak = 0.06250 (86)
- Left_Pallidum (13): linear fit = 0.92 x + 0.0 (771 voxels, overlap=1.023)
- Left_Pallidum (13): linear fit = 0.92 x + 0.0 (771 voxels, peak = 85), gca=85.1
- gca peak = 0.21683 (55)
- mri peak = 0.06995 (63)
- Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (878 voxels, overlap=0.716)
- Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (878 voxels, peak = 62), gca=62.4
- gca peak = 0.30730 (58)
- mri peak = 0.07338 (63)
- Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (852 voxels, overlap=0.975)
- Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (852 voxels, peak = 64), gca=63.5
- gca peak = 0.11430 (101)
- mri peak = 0.09810 (103)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (56567 voxels, overlap=0.687)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (56567 voxels, peak = 106), gca=105.5
- gca peak = 0.12076 (102)
- mri peak = 0.10229 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54894 voxels, overlap=0.587)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54894 voxels, peak = 107), gca=106.6
- gca peak = 0.14995 (59)
- mri peak = 0.03704 (65)
- Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (23565 voxels, overlap=0.846)
- Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (23565 voxels, peak = 65), gca=64.6
- gca peak = 0.15082 (58)
- mri peak = 0.03987 (62)
- Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22276 voxels, overlap=0.919)
- Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22276 voxels, peak = 64), gca=63.5
- gca peak = 0.14161 (67)
- mri peak = 0.07614 (68)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (556 voxels, overlap=0.991)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (556 voxels, peak = 67), gca=67.0
- gca peak = 0.15243 (71)
- mri peak = 0.06316 (74)
- Left_Caudate (11): linear fit = 1.03 x + 0.0 (908 voxels, overlap=0.989)
- Left_Caudate (11): linear fit = 1.03 x + 0.0 (908 voxels, peak = 73), gca=73.5
- gca peak = 0.13336 (57)
- mri peak = 0.03386 (56)
- Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (19962 voxels, overlap=0.960)
- Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (19962 voxels, peak = 60), gca=59.6
- gca peak = 0.13252 (56)
- mri peak = 0.03637 (57)
- Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (20018 voxels, overlap=0.923)
- Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (20018 voxels, peak = 59), gca=58.5
- gca peak = 0.18181 (84)
- mri peak = 0.05935 (86)
- Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (9208 voxels, overlap=0.789)
- Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (9208 voxels, peak = 87), gca=86.9
- gca peak = 0.20573 (83)
- mri peak = 0.07873 (85)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (7811 voxels, overlap=0.872)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (7811 voxels, peak = 86), gca=85.9
- gca peak = 0.21969 (57)
- mri peak = 0.10256 (70)
- Left_Amygdala (18): linear fit = 1.18 x + 0.0 (414 voxels, overlap=0.055)
- Left_Amygdala (18): linear fit = 1.18 x + 0.0 (414 voxels, peak = 68), gca=67.5
- gca peak = 0.39313 (56)
- mri peak = 0.06897 (68)
- Right_Amygdala (54): linear fit = 1.21 x + 0.0 (490 voxels, overlap=0.162)
- Right_Amygdala (54): linear fit = 1.21 x + 0.0 (490 voxels, peak = 67), gca=67.5
- gca peak = 0.14181 (85)
- mri peak = 0.04881 (92)
- Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5098 voxels, overlap=0.805)
- Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5098 voxels, peak = 91), gca=90.5
- gca peak = 0.11978 (83)
- mri peak = 0.05986 (88)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4346 voxels, overlap=0.929)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4346 voxels, peak = 85), gca=85.1
- gca peak = 0.13399 (79)
- mri peak = 0.04738 (81)
- Left_Putamen (12): linear fit = 1.01 x + 0.0 (2217 voxels, overlap=0.999)
- Left_Putamen (12): linear fit = 1.01 x + 0.0 (2217 voxels, peak = 80), gca=80.2
- gca peak = 0.14159 (79)
- mri peak = 0.05671 (75)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (2292 voxels, overlap=1.000)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (2292 voxels, peak = 78), gca=77.8
- gca peak = 0.10025 (80)
- mri peak = 0.08032 (87)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (11145 voxels, overlap=0.402)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (11145 voxels, peak = 88), gca=87.6
- gca peak = 0.13281 (86)
- mri peak = 0.06337 (91)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1274 voxels, overlap=0.724)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1274 voxels, peak = 89), gca=89.0
- gca peak = 0.12801 (89)
- mri peak = 0.06928 (93)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1549 voxels, overlap=0.850)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1549 voxels, peak = 92), gca=92.1
- gca peak = 0.20494 (23)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.15061 (21)
- mri peak = 0.11508 (16)
- Fourth_Ventricle (15): linear fit = 0.82 x + 0.0 (251 voxels, overlap=0.760)
- Fourth_Ventricle (15): linear fit = 0.82 x + 0.0 (251 voxels, peak = 17), gca=17.3
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.18056 (32)
- gca peak Left_Thalamus = 0.64095 (94)
- gca peak Third_Ventricle = 0.20494 (23)
- gca peak CSF = 0.20999 (34)
- gca peak Left_Accumbens_area = 0.39030 (62)
- gca peak Left_undetermined = 0.95280 (25)
- gca peak Left_vessel = 0.67734 (53)
- gca peak Left_choroid_plexus = 0.09433 (44)
- gca peak Right_Inf_Lat_Vent = 0.23544 (26)
- gca peak Right_Accumbens_area = 0.30312 (64)
- gca peak Right_vessel = 0.46315 (51)
- gca peak Right_choroid_plexus = 0.14086 (44)
- gca peak Fifth_Ventricle = 0.51669 (36)
- gca peak WM_hypointensities = 0.09722 (76)
- gca peak non_WM_hypointensities = 0.11899 (47)
- gca peak Optic_Chiasm = 0.39033 (72)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.14 x + 0.0
- estimating mean wm scale to be 1.04 x + 0.0
- estimating mean csf scale to be 0.94 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=0.690, neg=0, invalid=762
- 0105: dt=95.323944, rms=0.683 (0.904%), neg=0, invalid=762
- 0106: dt=221.952000, rms=0.681 (0.413%), neg=0, invalid=762
- 0107: dt=369.920000, rms=0.675 (0.833%), neg=0, invalid=762
- 0108: dt=73.984000, rms=0.673 (0.226%), neg=0, invalid=762
- 0109: dt=129.472000, rms=0.673 (0.089%), neg=0, invalid=762
- 0110: dt=1183.744000, rms=0.669 (0.629%), neg=0, invalid=762
- 0111: dt=92.480000, rms=0.667 (0.203%), neg=0, invalid=762
- 0112: dt=1183.744000, rms=0.665 (0.321%), neg=0, invalid=762
- 0113: dt=92.480000, rms=0.664 (0.150%), neg=0, invalid=762
- 0114: dt=369.920000, rms=0.663 (0.086%), neg=0, invalid=762
- 0115: dt=110.976000, rms=0.663 (0.044%), neg=0, invalid=762
- 0116: dt=110.976000, rms=0.663 (0.037%), neg=0, invalid=762
- 0117: dt=110.976000, rms=0.663 (0.050%), neg=0, invalid=762
- 0118: dt=110.976000, rms=0.662 (0.061%), neg=0, invalid=762
- 0119: dt=110.976000, rms=0.662 (0.069%), neg=0, invalid=762
- 0120: dt=110.976000, rms=0.661 (0.084%), neg=0, invalid=762
- 0121: dt=110.976000, rms=0.661 (0.092%), neg=0, invalid=762
- 0122: dt=110.976000, rms=0.660 (0.086%), neg=0, invalid=762
- 0123: dt=110.976000, rms=0.659 (0.086%), neg=0, invalid=762
- 0124: dt=110.976000, rms=0.659 (0.078%), neg=0, invalid=762
- 0125: dt=110.976000, rms=0.658 (0.079%), neg=0, invalid=762
- 0126: dt=110.976000, rms=0.658 (0.077%), neg=0, invalid=762
- 0127: dt=110.976000, rms=0.657 (0.068%), neg=0, invalid=762
- 0128: dt=110.976000, rms=0.657 (0.062%), neg=0, invalid=762
- 0129: dt=110.976000, rms=0.657 (0.056%), neg=0, invalid=762
- 0130: dt=110.976000, rms=0.656 (0.064%), neg=0, invalid=762
- 0131: dt=110.976000, rms=0.656 (0.062%), neg=0, invalid=762
- 0132: dt=110.976000, rms=0.656 (0.052%), neg=0, invalid=762
- 0133: dt=110.976000, rms=0.655 (0.054%), neg=0, invalid=762
- 0134: dt=110.976000, rms=0.655 (0.055%), neg=0, invalid=762
- 0135: dt=110.976000, rms=0.654 (0.061%), neg=0, invalid=762
- 0136: dt=110.976000, rms=0.654 (0.065%), neg=0, invalid=762
- 0137: dt=110.976000, rms=0.654 (0.062%), neg=0, invalid=762
- 0138: dt=110.976000, rms=0.653 (0.056%), neg=0, invalid=762
- 0139: dt=110.976000, rms=0.653 (0.058%), neg=0, invalid=762
- 0140: dt=110.976000, rms=0.652 (0.060%), neg=0, invalid=762
- 0141: dt=110.976000, rms=0.652 (0.056%), neg=0, invalid=762
- 0142: dt=110.976000, rms=0.652 (0.047%), neg=0, invalid=762
- 0143: dt=110.976000, rms=0.651 (0.043%), neg=0, invalid=762
- 0144: dt=110.976000, rms=0.651 (0.049%), neg=0, invalid=762
- 0145: dt=110.976000, rms=0.651 (0.050%), neg=0, invalid=762
- 0146: dt=110.976000, rms=0.651 (0.045%), neg=0, invalid=762
- 0147: dt=110.976000, rms=0.650 (0.040%), neg=0, invalid=762
- 0148: dt=110.976000, rms=0.650 (0.038%), neg=0, invalid=762
- 0149: dt=110.976000, rms=0.650 (0.035%), neg=0, invalid=762
- 0150: dt=110.976000, rms=0.650 (0.034%), neg=0, invalid=762
- 0151: dt=110.976000, rms=0.649 (0.034%), neg=0, invalid=762
- 0152: dt=110.976000, rms=0.649 (0.030%), neg=0, invalid=762
- 0153: dt=110.976000, rms=0.649 (0.031%), neg=0, invalid=762
- 0154: dt=110.976000, rms=0.649 (0.032%), neg=0, invalid=762
- 0155: dt=110.976000, rms=0.649 (0.035%), neg=0, invalid=762
- 0156: dt=110.976000, rms=0.648 (0.032%), neg=0, invalid=762
- 0157: dt=110.976000, rms=0.648 (0.026%), neg=0, invalid=762
- 0158: dt=110.976000, rms=0.648 (0.025%), neg=0, invalid=762
- 0159: dt=110.976000, rms=0.648 (0.024%), neg=0, invalid=762
- 0160: dt=110.976000, rms=0.648 (0.031%), neg=0, invalid=762
- 0161: dt=110.976000, rms=0.647 (0.028%), neg=0, invalid=762
- 0162: dt=110.976000, rms=0.647 (0.026%), neg=0, invalid=762
- 0163: dt=110.976000, rms=0.647 (0.024%), neg=0, invalid=762
- 0164: dt=110.976000, rms=0.647 (0.025%), neg=0, invalid=762
- 0165: dt=110.976000, rms=0.647 (0.022%), neg=0, invalid=762
- 0166: dt=1479.680000, rms=0.647 (0.007%), neg=0, invalid=762
- 0167: dt=1479.680000, rms=0.647 (-0.745%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.647, neg=0, invalid=762
- 0168: dt=129.472000, rms=0.646 (0.183%), neg=0, invalid=762
- 0169: dt=517.888000, rms=0.645 (0.132%), neg=0, invalid=762
- 0170: dt=295.936000, rms=0.645 (0.067%), neg=0, invalid=762
- 0171: dt=32.368000, rms=0.645 (-0.004%), neg=0, invalid=762
- 0172: dt=32.368000, rms=0.645 (0.002%), neg=0, invalid=762
- 0173: dt=32.368000, rms=0.645 (0.002%), neg=0, invalid=762
- 0174: dt=32.368000, rms=0.645 (-0.001%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.646, neg=0, invalid=762
- 0175: dt=122.721649, rms=0.643 (0.529%), neg=0, invalid=762
- 0176: dt=117.972350, rms=0.637 (0.855%), neg=0, invalid=762
- 0177: dt=52.571429, rms=0.635 (0.354%), neg=0, invalid=762
- 0178: dt=414.720000, rms=0.628 (1.125%), neg=0, invalid=762
- 0179: dt=47.030303, rms=0.624 (0.687%), neg=0, invalid=762
- 0180: dt=145.152000, rms=0.621 (0.375%), neg=0, invalid=762
- 0181: dt=145.152000, rms=0.619 (0.401%), neg=0, invalid=762
- 0182: dt=36.288000, rms=0.618 (0.050%), neg=0, invalid=762
- 0183: dt=36.288000, rms=0.618 (0.079%), neg=0, invalid=762
- 0184: dt=36.288000, rms=0.617 (0.142%), neg=0, invalid=762
- 0185: dt=18.144000, rms=0.617 (0.044%), neg=0, invalid=762
- 0186: dt=9.072000, rms=0.617 (0.018%), neg=0, invalid=762
- 0187: dt=4.536000, rms=0.617 (0.010%), neg=0, invalid=762
- 0188: dt=1.944000, rms=0.617 (0.004%), neg=0, invalid=762
- 0189: dt=0.243000, rms=0.617 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.617, neg=0, invalid=762
- 0190: dt=103.680000, rms=0.614 (0.486%), neg=0, invalid=762
- 0191: dt=36.288000, rms=0.613 (0.200%), neg=0, invalid=762
- 0192: dt=580.608000, rms=0.607 (0.911%), neg=0, invalid=762
- 0193: dt=36.288000, rms=0.606 (0.170%), neg=0, invalid=762
- 0194: dt=145.152000, rms=0.605 (0.141%), neg=0, invalid=762
- 0195: dt=124.416000, rms=0.604 (0.234%), neg=0, invalid=762
- 0196: dt=36.288000, rms=0.604 (0.047%), neg=0, invalid=762
- 0197: dt=36.288000, rms=0.603 (0.046%), neg=0, invalid=762
- 0198: dt=36.288000, rms=0.603 (0.059%), neg=0, invalid=762
- 0199: dt=36.288000, rms=0.602 (0.098%), neg=0, invalid=762
- 0200: dt=36.288000, rms=0.602 (0.138%), neg=0, invalid=762
- 0201: dt=36.288000, rms=0.601 (0.164%), neg=0, invalid=762
- 0202: dt=36.288000, rms=0.600 (0.175%), neg=0, invalid=762
- 0203: dt=36.288000, rms=0.598 (0.177%), neg=0, invalid=762
- 0204: dt=36.288000, rms=0.597 (0.184%), neg=0, invalid=762
- 0205: dt=36.288000, rms=0.596 (0.188%), neg=0, invalid=762
- 0206: dt=36.288000, rms=0.595 (0.191%), neg=0, invalid=762
- 0207: dt=36.288000, rms=0.594 (0.191%), neg=0, invalid=762
- 0208: dt=36.288000, rms=0.593 (0.186%), neg=0, invalid=762
- 0209: dt=36.288000, rms=0.592 (0.177%), neg=0, invalid=762
- 0210: dt=36.288000, rms=0.591 (0.167%), neg=0, invalid=762
- 0211: dt=36.288000, rms=0.590 (0.159%), neg=0, invalid=762
- 0212: dt=36.288000, rms=0.590 (0.019%), neg=0, invalid=762
- 0213: dt=36.288000, rms=0.590 (0.033%), neg=0, invalid=762
- 0214: dt=36.288000, rms=0.589 (0.044%), neg=0, invalid=762
- 0215: dt=36.288000, rms=0.589 (0.054%), neg=0, invalid=762
- 0216: dt=36.288000, rms=0.589 (0.063%), neg=0, invalid=762
- 0217: dt=36.288000, rms=0.588 (0.070%), neg=0, invalid=762
- 0218: dt=36.288000, rms=0.588 (0.079%), neg=0, invalid=762
- 0219: dt=36.288000, rms=0.587 (0.085%), neg=0, invalid=762
- 0220: dt=36.288000, rms=0.587 (0.085%), neg=0, invalid=762
- 0221: dt=36.288000, rms=0.586 (0.085%), neg=0, invalid=762
- 0222: dt=36.288000, rms=0.586 (0.088%), neg=0, invalid=762
- 0223: dt=36.288000, rms=0.585 (0.096%), neg=0, invalid=762
- 0224: dt=36.288000, rms=0.585 (0.017%), neg=0, invalid=762
- 0225: dt=36.288000, rms=0.585 (0.028%), neg=0, invalid=762
- 0226: dt=18.144000, rms=0.585 (0.004%), neg=0, invalid=762
- 0227: dt=9.072000, rms=0.585 (0.003%), neg=0, invalid=762
- 0228: dt=0.567000, rms=0.585 (0.001%), neg=0, invalid=762
- 0229: dt=0.141750, rms=0.585 (-0.000%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.591, neg=0, invalid=762
- 0230: dt=0.002734, rms=0.590 (0.094%), neg=0, invalid=762
- 0231: dt=0.001250, rms=0.590 (0.000%), neg=0, invalid=762
- 0232: dt=0.000078, rms=0.590 (0.000%), neg=0, invalid=762
- 0233: dt=0.000010, rms=0.590 (0.000%), neg=0, invalid=762
- 0234: dt=0.000001, rms=0.590 (0.000%), neg=0, invalid=762
- 0235: dt=0.000000, rms=0.590 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.591, neg=0, invalid=762
- 0236: dt=160.318937, rms=0.573 (2.974%), neg=0, invalid=762
- 0237: dt=44.800000, rms=0.565 (1.535%), neg=0, invalid=762
- 0238: dt=37.105058, rms=0.562 (0.429%), neg=0, invalid=762
- 0239: dt=38.400000, rms=0.560 (0.473%), neg=0, invalid=762
- 0240: dt=29.492537, rms=0.558 (0.287%), neg=0, invalid=762
- 0241: dt=44.800000, rms=0.556 (0.357%), neg=0, invalid=762
- 0242: dt=24.423676, rms=0.555 (0.250%), neg=0, invalid=762
- 0243: dt=80.313725, rms=0.553 (0.319%), neg=0, invalid=762
- 0244: dt=11.200000, rms=0.551 (0.323%), neg=0, invalid=762
- 0245: dt=25.600000, rms=0.550 (0.154%), neg=0, invalid=762
- 0246: dt=44.800000, rms=0.549 (0.255%), neg=0, invalid=762
- 0247: dt=25.600000, rms=0.548 (0.130%), neg=0, invalid=762
- 0248: dt=44.800000, rms=0.547 (0.210%), neg=0, invalid=762
- 0249: dt=25.600000, rms=0.546 (0.118%), neg=0, invalid=762
- 0250: dt=38.400000, rms=0.545 (0.163%), neg=0, invalid=762
- 0251: dt=11.200000, rms=0.545 (0.086%), neg=0, invalid=762
- 0252: dt=2.800000, rms=0.545 (0.017%), neg=0, invalid=762
- 0253: dt=2.800000, rms=0.545 (0.012%), neg=0, invalid=762
- 0254: dt=0.700000, rms=0.545 (0.002%), neg=0, invalid=762
- 0255: dt=0.043750, rms=0.545 (0.000%), neg=0, invalid=762
- 0256: dt=0.010937, rms=0.545 (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=0.562, neg=0, invalid=762
- 0257: dt=1.008000, rms=0.561 (0.106%), neg=0, invalid=762
- 0258: dt=0.864000, rms=0.561 (0.005%), neg=0, invalid=762
- 0259: dt=0.864000, rms=0.561 (0.000%), neg=0, invalid=762
- 0260: dt=0.864000, rms=0.561 (-0.018%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.562, neg=0, invalid=762
- 0261: dt=0.000000, rms=0.561 (0.092%), neg=0, invalid=762
- 0262: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=762
- 0263: dt=0.150000, rms=0.561 (-0.002%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.593, neg=0, invalid=762
- 0264: dt=1.536000, rms=0.591 (0.435%), neg=0, invalid=762
- 0265: dt=0.256000, rms=0.591 (0.007%), neg=0, invalid=762
- 0266: dt=0.256000, rms=0.591 (-0.003%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.591, neg=0, invalid=762
- 0267: dt=1.792000, rms=0.590 (0.302%), neg=0, invalid=762
- 0268: dt=0.256000, rms=0.590 (0.002%), neg=0, invalid=762
- 0269: dt=0.256000, rms=0.590 (-0.001%), 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=0.552, neg=0, invalid=762
- 0270: dt=0.448000, rms=0.537 (2.741%), neg=0, invalid=762
- 0271: dt=0.448000, rms=0.534 (0.683%), neg=0, invalid=762
- 0272: dt=0.448000, rms=0.531 (0.397%), neg=0, invalid=762
- 0273: dt=0.448000, rms=0.530 (0.253%), neg=0, invalid=762
- 0274: dt=0.448000, rms=0.529 (0.185%), neg=0, invalid=762
- 0275: dt=0.458333, rms=0.528 (0.143%), neg=0, invalid=762
- 0276: dt=0.448000, rms=0.528 (0.112%), neg=0, invalid=762
- 0277: dt=0.448000, rms=0.527 (0.086%), neg=0, invalid=762
- 0278: dt=0.448000, rms=0.527 (0.075%), neg=0, invalid=762
- 0279: dt=0.448000, rms=0.527 (0.057%), neg=0, invalid=762
- 0280: dt=0.448000, rms=0.526 (0.057%), neg=0, invalid=762
- 0281: dt=0.448000, rms=0.526 (0.041%), neg=0, invalid=762
- 0282: dt=0.448000, rms=0.526 (0.040%), neg=0, invalid=762
- 0283: dt=0.448000, rms=0.526 (0.064%), neg=0, invalid=762
- 0284: dt=0.448000, rms=0.525 (0.081%), neg=0, invalid=762
- 0285: dt=0.448000, rms=0.525 (0.088%), neg=0, invalid=762
- 0286: dt=0.448000, rms=0.524 (0.076%), neg=0, invalid=762
- 0287: dt=0.448000, rms=0.524 (0.061%), neg=0, invalid=762
- 0288: dt=0.448000, rms=0.524 (-0.009%), neg=0, invalid=762
- 0289: dt=0.000000, rms=0.524 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.525, neg=0, invalid=762
- 0290: dt=0.448000, rms=0.518 (1.179%), neg=0, invalid=762
- 0291: dt=0.448000, rms=0.518 (0.142%), neg=0, invalid=762
- 0292: dt=0.448000, rms=0.517 (0.035%), neg=0, invalid=762
- 0293: dt=0.448000, rms=0.517 (0.007%), neg=0, invalid=762
- 0294: dt=0.448000, rms=0.517 (-0.008%), 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=0.515, neg=0, invalid=762
- 0295: dt=0.000000, rms=0.515 (0.116%), neg=0, invalid=762
- 0296: dt=0.000000, rms=0.515 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.515, neg=0, invalid=762
- 0297: dt=129.472000, rms=0.514 (0.171%), neg=0, invalid=762
- 0298: dt=295.936000, rms=0.514 (0.039%), neg=0, invalid=762
- 0299: dt=295.936000, rms=0.514 (-0.044%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.515, neg=0, invalid=762
- 0300: dt=25.920000, rms=0.514 (0.162%), neg=0, invalid=762
- 0301: dt=15.552000, rms=0.514 (0.010%), neg=0, invalid=762
- 0302: dt=15.552000, rms=0.514 (0.007%), neg=0, invalid=762
- 0303: dt=15.552000, rms=0.514 (-0.005%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.514, neg=0, invalid=762
- 0304: dt=77.052632, rms=0.512 (0.454%), neg=0, invalid=762
- 0305: dt=36.288000, rms=0.511 (0.142%), neg=0, invalid=762
- 0306: dt=36.288000, rms=0.511 (0.060%), neg=0, invalid=762
- 0307: dt=36.288000, rms=0.510 (0.115%), neg=0, invalid=762
- 0308: dt=36.288000, rms=0.510 (0.146%), neg=0, invalid=762
- 0309: dt=36.288000, rms=0.509 (0.142%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0310: dt=36.288000, rms=0.508 (0.125%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0311: dt=36.288000, rms=0.508 (0.112%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0312: dt=36.288000, rms=0.507 (0.104%), neg=0, invalid=762
- 0313: dt=145.152000, rms=0.507 (0.063%), neg=0, invalid=762
- 0314: dt=145.152000, rms=0.507 (-0.092%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.508, neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 8 iterations, nbhd size=1, neg = 0
- 0315: dt=29.564014, rms=0.505 (0.489%), neg=0, invalid=762
- iter 0, gcam->neg = 16
- after 12 iterations, nbhd size=1, neg = 0
- 0316: dt=73.230769, rms=0.502 (0.701%), neg=0, invalid=762
- 0317: dt=11.200000, rms=0.501 (0.149%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 3 iterations, nbhd size=0, neg = 0
- 0318: dt=11.200000, rms=0.501 (0.092%), neg=0, invalid=762
- iter 0, gcam->neg = 6
- after 6 iterations, nbhd size=0, neg = 0
- 0319: dt=11.200000, rms=0.500 (0.099%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 4 iterations, nbhd size=0, neg = 0
- 0320: dt=11.200000, rms=0.499 (0.165%), neg=0, invalid=762
- iter 0, gcam->neg = 6
- after 2 iterations, nbhd size=0, neg = 0
- 0321: dt=11.200000, rms=0.498 (0.260%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 7 iterations, nbhd size=0, neg = 0
- 0322: dt=11.200000, rms=0.497 (0.267%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 10 iterations, nbhd size=1, neg = 0
- 0323: dt=11.200000, rms=0.496 (0.213%), neg=0, invalid=762
- iter 0, gcam->neg = 10
- after 14 iterations, nbhd size=1, neg = 0
- 0324: dt=11.200000, rms=0.495 (0.177%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 1 iterations, nbhd size=0, neg = 0
- 0325: dt=11.200000, rms=0.494 (0.142%), neg=0, invalid=762
- iter 0, gcam->neg = 11
- after 4 iterations, nbhd size=0, neg = 0
- 0326: dt=11.200000, rms=0.493 (0.098%), neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 5 iterations, nbhd size=0, neg = 0
- 0327: dt=11.200000, rms=0.493 (0.115%), neg=0, invalid=762
- iter 0, gcam->neg = 14
- after 11 iterations, nbhd size=1, neg = 0
- 0328: dt=11.200000, rms=0.492 (0.144%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 9 iterations, nbhd size=1, neg = 0
- 0329: dt=11.200000, rms=0.491 (0.146%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 4 iterations, nbhd size=0, neg = 0
- 0330: dt=11.200000, rms=0.491 (0.152%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0331: dt=11.200000, rms=0.490 (0.141%), neg=0, invalid=762
- iter 0, gcam->neg = 6
- after 8 iterations, nbhd size=1, neg = 0
- 0332: dt=11.200000, rms=0.489 (0.112%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 8 iterations, nbhd size=1, neg = 0
- 0333: dt=11.200000, rms=0.489 (0.101%), neg=0, invalid=762
- 0334: dt=38.400000, rms=0.489 (0.067%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0335: dt=38.400000, rms=0.489 (-0.021%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.489, neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 8 iterations, nbhd size=1, neg = 0
- 0336: dt=43.950207, rms=0.486 (0.758%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0337: dt=25.600000, rms=0.484 (0.364%), neg=0, invalid=762
- 0338: dt=32.000000, rms=0.483 (0.195%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0339: dt=32.000000, rms=0.482 (0.108%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0340: dt=32.000000, rms=0.481 (0.284%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0341: dt=32.000000, rms=0.480 (0.151%), neg=0, invalid=762
- 0342: dt=32.000000, rms=0.479 (0.205%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 3 iterations, nbhd size=0, neg = 0
- 0343: dt=32.000000, rms=0.479 (-0.046%), neg=0, invalid=762
- 0344: dt=32.000000, rms=0.479 (0.051%), neg=0, invalid=762
- 0345: dt=32.000000, rms=0.479 (0.070%), neg=0, invalid=762
- 0346: dt=11.200000, rms=0.478 (0.022%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.486, neg=0, invalid=762
- 0347: dt=1.500000, rms=0.485 (0.138%), neg=0, invalid=762
- 0348: dt=0.252000, rms=0.485 (-0.003%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.486, neg=0, invalid=762
- 0349: dt=4.941176, rms=0.485 (0.205%), neg=0, invalid=762
- 0350: dt=4.032000, rms=0.485 (0.041%), neg=0, invalid=762
- 0351: dt=4.032000, rms=0.485 (0.024%), neg=0, invalid=762
- 0352: dt=4.032000, rms=0.485 (0.002%), neg=0, invalid=762
- 0353: dt=4.032000, rms=0.485 (-0.089%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.492, neg=0, invalid=762
- 0354: dt=0.000000, rms=0.492 (0.122%), neg=0, invalid=762
- 0355: dt=0.000000, rms=0.492 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.492, neg=0, invalid=762
- 0356: dt=0.000000, rms=0.492 (0.122%), neg=0, invalid=762
- 0357: dt=0.000000, rms=0.492 (0.000%), neg=0, invalid=762
- resetting metric properties...
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.480, neg=0, invalid=762
- iter 0, gcam->neg = 967
- after 15 iterations, nbhd size=1, neg = 0
- 0358: dt=2.128411, rms=0.449 (6.540%), neg=0, invalid=762
- 0359: dt=0.028000, rms=0.449 (0.016%), neg=0, invalid=762
- 0360: dt=0.028000, rms=0.449 (0.003%), neg=0, invalid=762
- 0361: dt=0.028000, rms=0.449 (-0.028%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.450, neg=0, invalid=762
- 0362: dt=0.080000, rms=0.449 (0.206%), neg=0, invalid=762
- 0363: dt=0.001750, rms=0.449 (0.002%), neg=0, invalid=762
- 0364: dt=0.001750, rms=0.449 (-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=0.434, neg=0, invalid=762
- 0365: dt=0.000000, rms=0.434 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.434, neg=0, invalid=762
- 0366: dt=32.368000, rms=0.434 (0.003%), neg=0, invalid=762
- 0367: dt=23.120000, rms=0.434 (0.000%), neg=0, invalid=762
- 0368: dt=23.120000, rms=0.434 (-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=0.434, neg=0, invalid=762
- 0369: dt=0.000000, rms=0.434 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.434, neg=0, invalid=762
- 0370: dt=62.208000, rms=0.434 (0.043%), neg=0, invalid=762
- 0371: dt=124.416000, rms=0.433 (0.040%), neg=0, invalid=762
- 0372: dt=124.416000, rms=0.433 (-0.004%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.434, neg=0, invalid=762
- 0373: dt=9.600000, rms=0.434 (0.064%), neg=0, invalid=762
- 0374: dt=6.400000, rms=0.434 (0.012%), neg=0, invalid=762
- 0375: dt=6.400000, rms=0.434 (0.001%), neg=0, invalid=762
- 0376: dt=6.400000, rms=0.434 (-0.040%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.434, neg=0, invalid=762
- 0377: dt=38.400000, rms=0.432 (0.522%), neg=0, invalid=762
- 0378: dt=32.000000, rms=0.431 (0.206%), neg=0, invalid=762
- 0379: dt=32.000000, rms=0.430 (0.181%), neg=0, invalid=762
- 0380: dt=32.000000, rms=0.429 (0.239%), neg=0, invalid=762
- iter 0, gcam->neg = 8
- after 6 iterations, nbhd size=0, neg = 0
- 0381: dt=32.000000, rms=0.428 (0.241%), neg=0, invalid=762
- iter 0, gcam->neg = 11
- after 5 iterations, nbhd size=0, neg = 0
- 0382: dt=32.000000, rms=0.427 (0.216%), neg=0, invalid=762
- iter 0, gcam->neg = 22
- after 16 iterations, nbhd size=1, neg = 0
- 0383: dt=32.000000, rms=0.426 (0.150%), neg=0, invalid=762
- iter 0, gcam->neg = 11
- after 8 iterations, nbhd size=0, neg = 0
- 0384: dt=32.000000, rms=0.426 (0.166%), neg=0, invalid=762
- iter 0, gcam->neg = 14
- after 12 iterations, nbhd size=1, neg = 0
- 0385: dt=32.000000, rms=0.425 (0.141%), neg=0, invalid=762
- iter 0, gcam->neg = 11
- after 11 iterations, nbhd size=1, neg = 0
- 0386: dt=32.000000, rms=0.424 (0.143%), neg=0, invalid=762
- iter 0, gcam->neg = 11
- after 8 iterations, nbhd size=1, neg = 0
- 0387: dt=32.000000, rms=0.424 (0.130%), neg=0, invalid=762
- iter 0, gcam->neg = 10
- after 11 iterations, nbhd size=1, neg = 0
- 0388: dt=32.000000, rms=0.423 (0.117%), neg=0, invalid=762
- iter 0, gcam->neg = 23
- after 12 iterations, nbhd size=1, neg = 0
- 0389: dt=32.000000, rms=0.423 (0.078%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 8 iterations, nbhd size=1, neg = 0
- 0390: dt=32.000000, rms=0.423 (0.025%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0391: dt=32.000000, rms=0.423 (0.019%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 2 iterations, nbhd size=0, neg = 0
- 0392: dt=32.000000, rms=0.423 (0.032%), neg=0, invalid=762
- iter 0, gcam->neg = 10
- after 5 iterations, nbhd size=0, neg = 0
- 0393: dt=32.000000, rms=0.423 (0.029%), neg=0, invalid=762
- iter 0, gcam->neg = 8
- after 4 iterations, nbhd size=0, neg = 0
- 0394: dt=32.000000, rms=0.422 (0.012%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.427, neg=0, invalid=762
- 0395: dt=0.576000, rms=0.427 (0.002%), neg=0, invalid=762
- 0396: dt=0.063000, rms=0.427 (0.000%), neg=0, invalid=762
- 0397: dt=0.063000, rms=0.427 (0.000%), neg=0, invalid=762
- 0398: dt=0.063000, 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
- 0399: dt=4.032000, rms=0.427 (0.040%), neg=0, invalid=762
- 0400: dt=3.456000, rms=0.427 (0.013%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 4 iterations, nbhd size=0, neg = 0
- 0401: dt=3.456000, rms=0.427 (0.002%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0402: dt=3.456000, rms=0.427 (-0.024%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.435, neg=0, invalid=762
- 0403: dt=0.000050, rms=0.435 (0.000%), neg=0, invalid=762
- 0404: dt=0.000000, rms=0.435 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.435, neg=0, invalid=762
- 0405: dt=0.000000, rms=0.435 (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=0.422, neg=0, invalid=762
- iter 0, gcam->neg = 738
- after 14 iterations, nbhd size=1, neg = 0
- 0406: dt=1.280000, rms=0.411 (2.511%), neg=0, invalid=762
- 0407: dt=0.000023, rms=0.411 (0.000%), neg=0, invalid=762
- 0408: dt=0.000023, rms=0.411 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.411, neg=0, invalid=762
- 0409: dt=0.096000, rms=0.411 (0.053%), neg=0, invalid=762
- 0410: dt=0.064000, rms=0.411 (0.011%), neg=0, invalid=762
- 0411: dt=0.064000, rms=0.411 (0.003%), neg=0, invalid=762
- 0412: dt=0.064000, rms=0.411 (-0.029%), neg=0, invalid=762
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- mri_ca_register took 2 hours, 29 minutes and 26 seconds.
- mri_ca_register utimesec 9927.036861
- mri_ca_register stimesec 10.524400
- mri_ca_register ru_maxrss 1348824
- mri_ca_register ru_ixrss 0
- mri_ca_register ru_idrss 0
- mri_ca_register ru_isrss 0
- mri_ca_register ru_minflt 5313002
- mri_ca_register ru_majflt 0
- mri_ca_register ru_nswap 0
- mri_ca_register ru_inblock 0
- mri_ca_register ru_oublock 63232
- mri_ca_register ru_msgsnd 0
- mri_ca_register ru_msgrcv 0
- mri_ca_register ru_nsignals 0
- mri_ca_register ru_nvcsw 8852
- mri_ca_register ru_nivcsw 25874
- FSRUNTIME@ mri_ca_register 2.4906 hours 2 threads
- #--------------------------------------
- #@# SubCort Seg Sun Oct 8 03:18:49 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-598
- 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-6.0.0/0050379/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 6.25
- 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 = 0.08903 (17)
- Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (317 voxels, overlap=0.811)
- Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (317 voxels, peak = 15), gca=15.3
- gca peak = 0.17677 (13)
- mri peak = 0.10847 (16)
- Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (457 voxels, overlap=0.894)
- Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (457 voxels, peak = 15), gca=15.4
- gca peak = 0.28129 (95)
- mri peak = 0.09756 (95)
- Right_Pallidum (52): linear fit = 0.99 x + 0.0 (571 voxels, overlap=1.013)
- Right_Pallidum (52): linear fit = 0.99 x + 0.0 (571 voxels, peak = 94), gca=93.6
- gca peak = 0.16930 (96)
- mri peak = 0.09031 (98)
- Left_Pallidum (13): linear fit = 1.03 x + 0.0 (610 voxels, overlap=1.014)
- Left_Pallidum (13): linear fit = 1.03 x + 0.0 (610 voxels, peak = 99), gca=99.4
- gca peak = 0.24553 (55)
- mri peak = 0.07190 (62)
- Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1071 voxels, overlap=0.482)
- Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1071 voxels, peak = 60), gca=60.2
- gca peak = 0.30264 (59)
- mri peak = 0.07310 (66)
- Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1067 voxels, overlap=0.718)
- Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1067 voxels, peak = 65), gca=64.6
- gca peak = 0.07580 (103)
- mri peak = 0.09525 (103)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (31479 voxels, overlap=0.643)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (31479 voxels, peak = 107), gca=106.6
- gca peak = 0.07714 (104)
- mri peak = 0.10646 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (33861 voxels, overlap=0.567)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (33861 voxels, peak = 108), gca=107.6
- gca peak = 0.09712 (58)
- mri peak = 0.04196 (65)
- Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (37973 voxels, overlap=0.860)
- Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (37973 voxels, peak = 64), gca=63.5
- gca peak = 0.11620 (58)
- mri peak = 0.04384 (62)
- Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (31882 voxels, overlap=0.869)
- Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (31882 voxels, peak = 62), gca=62.4
- gca peak = 0.30970 (66)
- mri peak = 0.08874 (76)
- Right_Caudate (50): linear fit = 1.02 x + 0.0 (877 voxels, overlap=1.008)
- Right_Caudate (50): linear fit = 1.02 x + 0.0 (877 voxels, peak = 68), gca=67.7
- gca peak = 0.15280 (69)
- mri peak = 0.10394 (74)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (831 voxels, overlap=1.002)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (831 voxels, peak = 68), gca=68.0
- gca peak = 0.13902 (56)
- mri peak = 0.04693 (62)
- Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (17755 voxels, overlap=0.979)
- Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (17755 voxels, peak = 60), gca=59.6
- gca peak = 0.14777 (55)
- mri peak = 0.04602 (60)
- Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (16226 voxels, overlap=0.987)
- Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (16226 voxels, peak = 59), gca=58.6
- gca peak = 0.16765 (84)
- mri peak = 0.10528 (86)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5953 voxels, overlap=0.904)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5953 voxels, peak = 86), gca=86.1
- gca peak = 0.18739 (84)
- mri peak = 0.09205 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5712 voxels, overlap=0.862)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5712 voxels, peak = 87), gca=86.9
- gca peak = 0.29869 (57)
- mri peak = 0.09921 (70)
- Left_Amygdala (18): linear fit = 1.18 x + 0.0 (440 voxels, overlap=0.057)
- Left_Amygdala (18): linear fit = 1.18 x + 0.0 (440 voxels, peak = 68), gca=67.5
- gca peak = 0.33601 (57)
- mri peak = 0.07256 (67)
- Right_Amygdala (54): linear fit = 1.24 x + 0.0 (562 voxels, overlap=0.057)
- Right_Amygdala (54): linear fit = 1.24 x + 0.0 (562 voxels, peak = 70), gca=70.4
- gca peak = 0.11131 (90)
- mri peak = 0.06360 (89)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4366 voxels, overlap=0.974)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4366 voxels, peak = 91), gca=91.3
- gca peak = 0.11793 (83)
- mri peak = 0.07276 (86)
- Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3926 voxels, overlap=0.978)
- Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3926 voxels, peak = 87), gca=86.7
- gca peak = 0.08324 (81)
- mri peak = 0.06665 (83)
- Left_Putamen (12): linear fit = 1.02 x + 0.0 (1667 voxels, overlap=0.983)
- Left_Putamen (12): linear fit = 1.02 x + 0.0 (1667 voxels, peak = 83), gca=83.0
- gca peak = 0.10360 (77)
- mri peak = 0.07267 (75)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1557 voxels, overlap=0.996)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1557 voxels, peak = 77), gca=77.0
- gca peak = 0.08424 (78)
- mri peak = 0.08159 (88)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (10906 voxels, overlap=0.476)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (10906 voxels, peak = 85), gca=85.4
- gca peak = 0.12631 (89)
- mri peak = 0.08559 (91)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1851 voxels, overlap=0.823)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1851 voxels, peak = 92), gca=92.1
- gca peak = 0.14500 (87)
- mri peak = 0.06709 (88)
- Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1811 voxels, overlap=0.916)
- Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1811 voxels, peak = 89), gca=89.2
- gca peak = 0.14975 (24)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.19357 (14)
- mri peak = 0.15433 (16)
- Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (311 voxels, overlap=0.793)
- Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (311 voxels, peak = 14), gca=13.7
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.16825 (27)
- gca peak Left_Thalamus = 1.00000 (94)
- gca peak Third_Ventricle = 0.14975 (24)
- gca peak CSF = 0.23379 (36)
- gca peak Left_Accumbens_area = 0.70037 (62)
- gca peak Left_undetermined = 1.00000 (26)
- gca peak Left_vessel = 0.75997 (52)
- gca peak Left_choroid_plexus = 0.12089 (35)
- gca peak Right_Inf_Lat_Vent = 0.24655 (23)
- gca peak Right_Accumbens_area = 0.45042 (65)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14516 (37)
- gca peak Fifth_Ventricle = 0.65475 (32)
- gca peak WM_hypointensities = 0.07854 (76)
- gca peak non_WM_hypointensities = 0.08491 (43)
- gca peak Optic_Chiasm = 0.71127 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.13 x + 0.0
- estimating mean wm scale to be 1.03 x + 0.0
- estimating mean csf scale to be 0.97 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.18464 (14)
- mri peak = 0.08903 (17)
- Left_Lateral_Ventricle (4): linear fit = 1.17 x + 0.0 (317 voxels, overlap=0.975)
- Left_Lateral_Ventricle (4): linear fit = 1.17 x + 0.0 (317 voxels, peak = 16), gca=16.4
- gca peak = 0.18813 (15)
- mri peak = 0.10847 (16)
- Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (457 voxels, overlap=0.792)
- Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (457 voxels, peak = 13), gca=13.3
- gca peak = 0.24789 (93)
- mri peak = 0.09756 (95)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (571 voxels, overlap=1.011)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (571 voxels, peak = 93), gca=92.5
- gca peak = 0.17344 (100)
- mri peak = 0.09031 (98)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (610 voxels, overlap=1.015)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (610 voxels, peak = 100), gca=100.0
- gca peak = 0.26900 (61)
- mri peak = 0.07190 (62)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1071 voxels, overlap=1.003)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1071 voxels, peak = 61), gca=61.0
- gca peak = 0.22679 (65)
- mri peak = 0.07310 (66)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1067 voxels, overlap=1.012)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1067 voxels, peak = 65), gca=65.0
- gca peak = 0.07500 (106)
- mri peak = 0.09525 (103)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31479 voxels, overlap=0.787)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31479 voxels, peak = 105), gca=105.5
- gca peak = 0.07663 (108)
- mri peak = 0.10646 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33861 voxels, overlap=0.721)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33861 voxels, peak = 107), gca=107.5
- gca peak = 0.08747 (63)
- mri peak = 0.04196 (65)
- Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37973 voxels, overlap=0.977)
- Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37973 voxels, peak = 62), gca=62.1
- gca peak = 0.11106 (62)
- mri peak = 0.04384 (62)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (31882 voxels, overlap=0.968)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (31882 voxels, peak = 61), gca=61.1
- gca peak = 0.26577 (68)
- mri peak = 0.08874 (76)
- Right_Caudate (50): linear fit = 1.07 x + 0.0 (877 voxels, overlap=1.008)
- Right_Caudate (50): linear fit = 1.07 x + 0.0 (877 voxels, peak = 72), gca=72.4
- gca peak = 0.16051 (68)
- mri peak = 0.10394 (74)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (831 voxels, overlap=1.000)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (831 voxels, peak = 68), gca=68.0
- gca peak = 0.13229 (60)
- mri peak = 0.04693 (62)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (17755 voxels, overlap=1.000)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (17755 voxels, peak = 62), gca=61.5
- gca peak = 0.13815 (58)
- mri peak = 0.04602 (60)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (16226 voxels, overlap=0.998)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (16226 voxels, peak = 59), gca=59.4
- gca peak = 0.15744 (86)
- mri peak = 0.10528 (86)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5953 voxels, overlap=0.962)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5953 voxels, peak = 86), gca=85.6
- gca peak = 0.18296 (87)
- mri peak = 0.09205 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5712 voxels, overlap=0.963)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5712 voxels, peak = 87), gca=86.6
- gca peak = 0.24259 (69)
- mri peak = 0.09921 (70)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (440 voxels, overlap=1.016)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (440 voxels, peak = 69), gca=69.0
- gca peak = 0.32058 (70)
- mri peak = 0.07256 (67)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (562 voxels, overlap=1.004)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (562 voxels, peak = 70), gca=70.0
- gca peak = 0.12105 (90)
- mri peak = 0.06360 (89)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4366 voxels, overlap=1.000)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4366 voxels, peak = 90), gca=89.6
- gca peak = 0.09791 (90)
- mri peak = 0.07276 (86)
- Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3926 voxels, overlap=0.982)
- Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3926 voxels, peak = 88), gca=87.8
- gca peak = 0.09216 (77)
- mri peak = 0.06665 (83)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1667 voxels, overlap=0.989)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1667 voxels, peak = 77), gca=77.0
- gca peak = 0.09691 (77)
- mri peak = 0.07267 (75)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1557 voxels, overlap=0.996)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1557 voxels, peak = 77), gca=77.0
- gca peak = 0.07897 (86)
- mri peak = 0.08159 (88)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (10906 voxels, overlap=0.769)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (10906 voxels, peak = 86), gca=86.0
- gca peak = 0.12978 (87)
- mri peak = 0.08559 (91)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1851 voxels, overlap=0.869)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1851 voxels, peak = 87), gca=86.6
- gca peak = 0.13858 (89)
- mri peak = 0.06709 (88)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1811 voxels, overlap=0.945)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1811 voxels, peak = 89), gca=88.6
- gca peak = 0.20073 (25)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.19038 (14)
- mri peak = 0.15433 (16)
- Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (311 voxels, overlap=0.798)
- Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (311 voxels, peak = 14), gca=14.5
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.16376 (35)
- gca peak Left_Thalamus = 0.36646 (104)
- gca peak Third_Ventricle = 0.20073 (25)
- gca peak CSF = 0.22075 (35)
- gca peak Left_Accumbens_area = 0.51313 (62)
- gca peak Left_undetermined = 1.00000 (26)
- gca peak Left_vessel = 0.75962 (52)
- gca peak Left_choroid_plexus = 0.12089 (35)
- gca peak Right_Inf_Lat_Vent = 0.20538 (25)
- gca peak Right_Accumbens_area = 0.41186 (66)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14516 (37)
- gca peak Fifth_Ventricle = 0.65358 (31)
- gca peak WM_hypointensities = 0.07242 (78)
- gca peak non_WM_hypointensities = 0.08309 (45)
- gca peak Optic_Chiasm = 0.70942 (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 1.03 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
- 69396 voxels changed in iteration 0 of unlikely voxel relabeling
- 198 voxels changed in iteration 1 of unlikely voxel relabeling
- 6 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 39344 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels)
- 442 hippocampal voxels changed.
- 0 amygdala voxels changed.
- pass 1: 72635 changed. image ll: -2.116, PF=0.500
- pass 2: 20785 changed. image ll: -2.115, PF=0.500
- pass 3: 6098 changed.
- pass 4: 2094 changed.
- 45987 voxels changed in iteration 0 of unlikely voxel relabeling
- 333 voxels changed in iteration 1 of unlikely voxel relabeling
- 8 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 7317 voxels changed in iteration 0 of unlikely voxel relabeling
- 158 voxels changed in iteration 1 of unlikely voxel relabeling
- 4 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 6411 voxels changed in iteration 0 of unlikely voxel relabeling
- 43 voxels changed in iteration 1 of unlikely voxel relabeling
- 2 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 5027 voxels changed in iteration 0 of unlikely voxel relabeling
- 19 voxels changed in iteration 1 of unlikely voxel relabeling
- 4 voxels changed in iteration 2 of unlikely voxel relabeling
- 2 voxels changed in iteration 3 of unlikely voxel relabeling
- 0 voxels changed in iteration 4 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 3616.918144
- mri_ca_label stimesec 1.878714
- mri_ca_label ru_maxrss 2090708
- mri_ca_label ru_ixrss 0
- mri_ca_label ru_idrss 0
- mri_ca_label ru_isrss 0
- mri_ca_label ru_minflt 859303
- mri_ca_label ru_majflt 0
- mri_ca_label ru_nswap 0
- mri_ca_label ru_inblock 63224
- mri_ca_label ru_oublock 472
- mri_ca_label ru_msgsnd 0
- mri_ca_label ru_msgrcv 0
- mri_ca_label ru_nsignals 0
- mri_ca_label ru_nvcsw 354
- mri_ca_label ru_nivcsw 4791
- auto-labeling took 59 minutes and 31 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/transforms/cc_up.lta 0050379
- 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-6.0.0/0050379/mri/transforms/cc_up.lta
- reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/aseg.auto_noCCseg.mgz
- reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/norm.mgz
- 108103 voxels in left wm, 94578 in right wm, xrange [112, 134]
- searching rotation angles z=[-3 11], y=[ 1 15]
-
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.2
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.7
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.2
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.7
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.0
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.8
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.3
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.8
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.3
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.8
searching scale 1 Z rot 4.0
searching scale 1 Z rot 4.3
searching scale 1 Z rot 4.5
searching scale 1 Z rot 4.8
searching scale 1 Z rot 5.0
searching scale 1 Z rot 5.3
searching scale 1 Z rot 5.5
searching scale 1 Z rot 5.8
searching scale 1 Z rot 6.0
searching scale 1 Z rot 6.3
searching scale 1 Z rot 6.5
searching scale 1 Z rot 6.8
searching scale 1 Z rot 7.0
searching scale 1 Z rot 7.3
searching scale 1 Z rot 7.5
searching scale 1 Z rot 7.8
searching scale 1 Z rot 8.0
searching scale 1 Z rot 8.3
searching scale 1 Z rot 8.5
searching scale 1 Z rot 8.8
searching scale 1 Z rot 9.0
searching scale 1 Z rot 9.3
searching scale 1 Z rot 9.5
searching scale 1 Z rot 9.8
searching scale 1 Z rot 10.0
searching scale 1 Z rot 10.3
searching scale 1 Z rot 10.5
searching scale 1 Z rot 10.8
searching scale 1 Z rot 11.0 global minimum found at slice 122.7, rotations (7.57, 4.29)
- final transformation (x=122.7, yr=7.567, zr=4.286):
- 0.98852 -0.07473 0.13131 1.35671;
- 0.07408 0.99720 0.00984 -2.83045;
- -0.13168 0.00000 0.99129 35.10811;
- 0.00000 0.00000 0.00000 1.00000;
- updating x range to be [125, 130] in xformed coordinates
- best xformed slice 127
- cc center is found at 127 121 110
- eigenvectors:
- 0.00054 0.00407 0.99999;
- 0.14997 -0.98868 0.00394;
- 0.98869 0.14996 -0.00115;
- writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/aseg.auto.mgz...
- corpus callosum segmentation took 2.9 minutes
- #--------------------------------------
- #@# Merge ASeg Sun Oct 8 04:21:12 CEST 2017
- cp aseg.auto.mgz aseg.presurf.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Sun Oct 8 04:21:12 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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...
- 1220 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 69 (69), valley at 0 (-1)
- csf peak at 34, setting threshold to 57
- 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 67 (67), valley at 0 (-1)
- csf peak at 33, setting threshold to 55
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 3 minutes and 11 seconds.
- #--------------------------------------------
- #@# Mask BFS Sun Oct 8 04:24:25 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1519210 voxels in mask (pct= 9.06)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Sun Oct 8 04:24:26 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 (103.0): 103.9 +- 5.5 [79.0 --> 125.0]
- GM (72.0) : 69.6 +- 9.7 [30.0 --> 95.0]
- setting bottom of white matter range to 79.3
- setting top of gray matter range to 89.0
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- using local geometry to label remaining ambiguous voxels...
- reclassifying voxels using Gaussian border classifier...
- removing voxels with positive offset direction...
- smoothing T1 volume with sigma = 0.250
- removing 1-dimensional structures...
- 5577 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 3888 filled
- 1638 bright non-wm voxels segmented.
- 2430 diagonally connected voxels added...
- white matter segmentation took 1.5 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 0.57 minutes
- reading wm segmentation from wm.seg.mgz...
- 635 voxels added to wm to prevent paths from MTL structures to cortex
- 3029 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 33806 voxels turned on, 40010 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 0 new 0
- 115,126,128 old 0 new 0
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 34 found - 34 modified | TOTAL: 34
- pass 2 (xy+): 0 found - 34 modified | TOTAL: 34
- pass 1 (xy-): 18 found - 18 modified | TOTAL: 52
- pass 2 (xy-): 0 found - 18 modified | TOTAL: 52
- pass 1 (yz+): 18 found - 18 modified | TOTAL: 70
- pass 2 (yz+): 0 found - 18 modified | TOTAL: 70
- pass 1 (yz-): 19 found - 19 modified | TOTAL: 89
- pass 2 (yz-): 0 found - 19 modified | TOTAL: 89
- pass 1 (xz+): 18 found - 18 modified | TOTAL: 107
- pass 2 (xz+): 0 found - 18 modified | TOTAL: 107
- pass 1 (xz-): 21 found - 21 modified | TOTAL: 128
- pass 2 (xz-): 0 found - 21 modified | TOTAL: 128
- Iteration Number : 1
- pass 1 (+++): 25 found - 25 modified | TOTAL: 25
- pass 2 (+++): 0 found - 25 modified | TOTAL: 25
- pass 1 (+++): 21 found - 21 modified | TOTAL: 46
- pass 2 (+++): 0 found - 21 modified | TOTAL: 46
- pass 1 (+++): 27 found - 27 modified | TOTAL: 73
- pass 2 (+++): 0 found - 27 modified | TOTAL: 73
- pass 1 (+++): 27 found - 27 modified | TOTAL: 100
- pass 2 (+++): 0 found - 27 modified | TOTAL: 100
- Iteration Number : 1
- pass 1 (++): 66 found - 66 modified | TOTAL: 66
- pass 2 (++): 0 found - 66 modified | TOTAL: 66
- pass 1 (+-): 68 found - 68 modified | TOTAL: 134
- pass 2 (+-): 0 found - 68 modified | TOTAL: 134
- pass 1 (--): 48 found - 48 modified | TOTAL: 182
- pass 2 (--): 0 found - 48 modified | TOTAL: 182
- pass 1 (-+): 97 found - 97 modified | TOTAL: 279
- pass 2 (-+): 0 found - 97 modified | TOTAL: 279
- Iteration Number : 2
- pass 1 (xy+): 4 found - 4 modified | TOTAL: 4
- pass 2 (xy+): 0 found - 4 modified | TOTAL: 4
- pass 1 (xy-): 5 found - 5 modified | TOTAL: 9
- pass 2 (xy-): 0 found - 5 modified | TOTAL: 9
- pass 1 (yz+): 5 found - 5 modified | TOTAL: 14
- pass 2 (yz+): 0 found - 5 modified | TOTAL: 14
- pass 1 (yz-): 4 found - 4 modified | TOTAL: 18
- pass 2 (yz-): 0 found - 4 modified | TOTAL: 18
- pass 1 (xz+): 5 found - 5 modified | TOTAL: 23
- pass 2 (xz+): 0 found - 5 modified | TOTAL: 23
- pass 1 (xz-): 6 found - 6 modified | TOTAL: 29
- pass 2 (xz-): 0 found - 6 modified | TOTAL: 29
- Iteration Number : 2
- pass 1 (+++): 1 found - 1 modified | TOTAL: 1
- pass 2 (+++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+++): 4 found - 4 modified | TOTAL: 5
- pass 2 (+++): 0 found - 4 modified | TOTAL: 5
- pass 1 (+++): 0 found - 0 modified | TOTAL: 5
- pass 1 (+++): 2 found - 2 modified | TOTAL: 7
- pass 2 (+++): 0 found - 2 modified | TOTAL: 7
- 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 (--): 2 found - 2 modified | TOTAL: 5
- pass 2 (--): 0 found - 2 modified | TOTAL: 5
- pass 1 (-+): 2 found - 2 modified | TOTAL: 7
- pass 2 (-+): 0 found - 2 modified | TOTAL: 7
- Iteration Number : 3
- 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+): 0 found - 0 modified | TOTAL: 3
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 3
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 5
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 5
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 6
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 6
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 1 found - 1 modified | TOTAL: 1
- pass 2 (+-): 0 found - 1 modified | TOTAL: 1
- pass 1 (--): 0 found - 0 modified | TOTAL: 1
- pass 1 (-+): 0 found - 0 modified | TOTAL: 1
- 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 = 557 (out of 514660: 0.108227)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Sun Oct 8 04:26:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri
- mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
- logging cutting plane coordinates to ../scripts/ponscc.cut.log...
- INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
- using segmentation aseg.auto_noCCseg.mgz...
- reading input volume...done.
- searching for cutting planes...voxel to talairach voxel transform
- 1.02955 -0.07498 0.12682 -5.35045;
- 0.14683 1.20581 -0.04596 -57.05315;
- -0.11919 0.05994 1.00404 -0.79372;
- 0.00000 0.00000 0.00000 1.00000;
- voxel to talairach voxel transform
- 1.02955 -0.07498 0.12682 -5.35045;
- 0.14683 1.20581 -0.04596 -57.05315;
- -0.11919 0.05994 1.00404 -0.79372;
- 0.00000 0.00000 0.00000 1.00000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1188 (min = 350, max = 1400), aspect = 0.51 (min = 0.10, max = 0.75)
- no need to search
- using seed (125, 113, 93), TAL = (3.0, -35.0, 15.0)
- talairach voxel to voxel transform
- 0.94853 0.06479 -0.11684 8.67904;
- -0.11096 0.81986 0.05155 46.22254;
- 0.11922 -0.04125 0.97903 -0.93874;
- 0.00000 0.00000 0.00000 1.00000;
- segmentation indicates cc at (125, 113, 93) --> (3.0, -35.0, 15.0)
- done.
- writing output to filled.mgz...
- filling took 0.7 minutes
- talairach cc position changed to (3.00, -35.00, 15.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(21.00, -35.00, 15.00) SRC: (106.63, 131.79, 98.21)
- search lh wm seed point around talairach space (-15.00, -35.00, 15.00), SRC: (140.77, 127.79, 102.50)
- 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 04:27:20 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 2
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 3
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 3
- pass 1 (xz-): 2 found - 2 modified | TOTAL: 5
- pass 2 (xz-): 0 found - 2 modified | TOTAL: 5
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 1 found - 1 modified | TOTAL: 1
- pass 2 (-+): 0 found - 1 modified | TOTAL: 1
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 6 (out of 251845: 0.002382)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- slice 40: 825 vertices, 947 faces
- slice 50: 6305 vertices, 6537 faces
- slice 60: 13164 vertices, 13426 faces
- slice 70: 21025 vertices, 21334 faces
- slice 80: 30764 vertices, 31151 faces
- slice 90: 40455 vertices, 40860 faces
- slice 100: 51182 vertices, 51634 faces
- slice 110: 63393 vertices, 63857 faces
- slice 120: 76445 vertices, 76973 faces
- slice 130: 89967 vertices, 90514 faces
- slice 140: 102923 vertices, 103463 faces
- slice 150: 114102 vertices, 114581 faces
- slice 160: 122946 vertices, 123419 faces
- slice 170: 131052 vertices, 131462 faces
- slice 180: 137993 vertices, 138373 faces
- slice 190: 143103 vertices, 143421 faces
- slice 200: 145726 vertices, 145908 faces
- slice 210: 145818 vertices, 145986 faces
- slice 220: 145818 vertices, 145986 faces
- slice 230: 145818 vertices, 145986 faces
- slice 240: 145818 vertices, 145986 faces
- slice 250: 145818 vertices, 145986 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...
- 145818 voxel in cpt #1: X=-168 [v=145818,e=437958,f=291972] located at (-21.966560, -12.569696, -0.701649)
- For the whole surface: X=-168 [v=145818,e=437958,f=291972]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Tessellate rh Sun Oct 8 04:27:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz+): 4 found - 4 modified | TOTAL: 5
- pass 2 (yz+): 0 found - 4 modified | TOTAL: 5
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 5
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 5
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 5
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 5 (out of 243815: 0.002051)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
- $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- slice 40: 2961 vertices, 3133 faces
- slice 50: 9091 vertices, 9324 faces
- slice 60: 16620 vertices, 16918 faces
- slice 70: 25948 vertices, 26367 faces
- slice 80: 36681 vertices, 37089 faces
- slice 90: 47564 vertices, 47923 faces
- slice 100: 59388 vertices, 59834 faces
- slice 110: 71201 vertices, 71655 faces
- slice 120: 83583 vertices, 84069 faces
- slice 130: 95071 vertices, 95530 faces
- slice 140: 105392 vertices, 105809 faces
- slice 150: 114096 vertices, 114518 faces
- slice 160: 122422 vertices, 122824 faces
- slice 170: 129705 vertices, 130083 faces
- slice 180: 135206 vertices, 135540 faces
- slice 190: 139290 vertices, 139550 faces
- slice 200: 140776 vertices, 140940 faces
- slice 210: 140776 vertices, 140940 faces
- slice 220: 140776 vertices, 140940 faces
- slice 230: 140776 vertices, 140940 faces
- slice 240: 140776 vertices, 140940 faces
- slice 250: 140776 vertices, 140940 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...
- 140776 voxel in cpt #1: X=-164 [v=140776,e=422820,f=281880] located at (31.648527, -18.799767, -5.331072)
- For the whole surface: X=-164 [v=140776,e=422820,f=281880]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Sun Oct 8 04:27:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- #--------------------------------------------
- #@# Smooth1 rh Sun Oct 8 04:27:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- Waiting for PID 28063 of (28063 28066) to complete...
- Waiting for PID 28066 of (28063 28066) 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 (28063 28066) completed and logs appended.
- #--------------------------------------------
- #@# Inflation1 lh Sun Oct 8 04:27:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- #--------------------------------------------
- #@# Inflation1 rh Sun Oct 8 04:27:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Waiting for PID 28119 of (28119 28122) to complete...
- Waiting for PID 28122 of (28119 28122) 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 = 46.3 mm, total surface area = 76241 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.8 minutes
-
step 000: RMS=0.166 (target=0.015)
step 005: RMS=0.129 (target=0.015)
step 010: RMS=0.103 (target=0.015)
step 015: RMS=0.092 (target=0.015)
step 020: RMS=0.084 (target=0.015)
step 025: RMS=0.077 (target=0.015)
step 030: RMS=0.072 (target=0.015)
step 035: RMS=0.069 (target=0.015)
step 040: RMS=0.066 (target=0.015)
step 045: RMS=0.063 (target=0.015)
step 050: RMS=0.062 (target=0.015)
step 055: RMS=0.062 (target=0.015)
step 060: RMS=0.062 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 45.015156
- mris_inflate stimesec 0.126980
- mris_inflate ru_maxrss 213576
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 30846
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 10264
- mris_inflate ru_oublock 10280
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2300
- mris_inflate ru_nivcsw 3980
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Not saving sulc
- Reading ../surf/rh.smoothwm.nofix
- avg radius = 46.7 mm, total surface area = 73519 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 1.1 minutes
-
step 000: RMS=0.167 (target=0.015)
step 005: RMS=0.129 (target=0.015)
step 010: RMS=0.102 (target=0.015)
step 015: RMS=0.091 (target=0.015)
step 020: RMS=0.082 (target=0.015)
step 025: RMS=0.074 (target=0.015)
step 030: RMS=0.071 (target=0.015)
step 035: RMS=0.068 (target=0.015)
step 040: RMS=0.065 (target=0.015)
step 045: RMS=0.063 (target=0.015)
step 050: RMS=0.062 (target=0.015)
step 055: RMS=0.061 (target=0.015)
step 060: RMS=0.061 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 69.294465
- mris_inflate stimesec 0.102984
- mris_inflate ru_maxrss 206572
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 30116
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 9912
- mris_inflate ru_oublock 9928
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2882
- mris_inflate ru_nivcsw 4135
- PIDs (28119 28122) completed and logs appended.
- #--------------------------------------------
- #@# QSphere lh Sun Oct 8 04:28:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- #--------------------------------------------
- #@# QSphere rh Sun Oct 8 04:28:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- Waiting for PID 28189 of (28189 28193) to complete...
- Waiting for PID 28193 of (28189 28193) to complete...
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.95 +- 0.58 (0.00-->11.37) (max @ vno 43175 --> 44111)
- face area 0.02 +- 0.03 (-0.13-->1.50)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.301...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=177.079, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.821, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.266, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.535, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.703, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.812, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.890, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.950, avgs=0
- 040/300: dt: 0.9000, rms radial error=171.002, avgs=0
- 045/300: dt: 0.9000, rms radial error=170.052, avgs=0
- 050/300: dt: 0.9000, rms radial error=169.102, avgs=0
- 055/300: dt: 0.9000, rms radial error=168.154, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.211, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.271, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.335, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.405, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.481, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.562, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.648, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.739, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.835, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.936, avgs=0
- 110/300: dt: 0.9000, rms radial error=158.041, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.150, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.265, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.384, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.508, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.637, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.770, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.909, avgs=0
- 150/300: dt: 0.9000, rms radial error=151.052, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.201, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.354, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.512, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.675, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.843, avgs=0
- 180/300: dt: 0.9000, rms radial error=146.015, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.192, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.373, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.559, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.750, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.945, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.144, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.348, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.557, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.769, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.987, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.208, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.434, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.664, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.899, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.137, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.381, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.628, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.879, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.135, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.395, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.659, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.927, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.199, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.475, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 17280.13
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00005
- epoch 2 (K=40.0), pass 1, starting sse = 2986.24
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00002
- epoch 3 (K=160.0), pass 1, starting sse = 346.12
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.04/10 = 0.00387
- epoch 4 (K=640.0), pass 1, starting sse = 33.53
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.05/11 = 0.00410
- final distance error %27.53
- writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.07 hours
- mris_sphere utimesec 256.334031
- mris_sphere stimesec 0.208968
- mris_sphere ru_maxrss 213768
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 31403
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 10312
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 8464
- mris_sphere ru_nivcsw 19478
- FSRUNTIME@ mris_sphere 0.0721 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 0.97 +- 0.59 (0.00-->6.60) (max @ vno 51427 --> 51452)
- face area 0.02 +- 0.03 (-0.09-->0.57)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.296...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=177.474, avgs=0
- 005/300: dt: 0.9000, rms radial error=177.216, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.665, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.939, avgs=0
- 020/300: dt: 0.9000, rms radial error=175.110, avgs=0
- 025/300: dt: 0.9000, rms radial error=174.234, avgs=0
- 030/300: dt: 0.9000, rms radial error=173.324, avgs=0
- 035/300: dt: 0.9000, rms radial error=172.394, avgs=0
- 040/300: dt: 0.9000, rms radial error=171.445, avgs=0
- 045/300: dt: 0.9000, rms radial error=170.493, avgs=0
- 050/300: dt: 0.9000, rms radial error=169.543, avgs=0
- 055/300: dt: 0.9000, rms radial error=168.594, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.650, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.709, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.773, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.842, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.916, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.996, avgs=0
- 090/300: dt: 0.9000, rms radial error=162.080, avgs=0
- 095/300: dt: 0.9000, rms radial error=161.170, avgs=0
- 100/300: dt: 0.9000, rms radial error=160.264, avgs=0
- 105/300: dt: 0.9000, rms radial error=159.363, avgs=0
- 110/300: dt: 0.9000, rms radial error=158.467, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.576, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.689, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.808, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.930, avgs=0
- 135/300: dt: 0.9000, rms radial error=154.058, avgs=0
- 140/300: dt: 0.9000, rms radial error=153.191, avgs=0
- 145/300: dt: 0.9000, rms radial error=152.328, avgs=0
- 150/300: dt: 0.9000, rms radial error=151.470, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.616, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.767, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.923, avgs=0
- 170/300: dt: 0.9000, rms radial error=148.084, avgs=0
- 175/300: dt: 0.9000, rms radial error=147.249, avgs=0
- 180/300: dt: 0.9000, rms radial error=146.418, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.592, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.771, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.955, avgs=0
- 200/300: dt: 0.9000, rms radial error=143.143, avgs=0
- 205/300: dt: 0.9000, rms radial error=142.335, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.533, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.734, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.941, avgs=0
- 225/300: dt: 0.9000, rms radial error=139.151, avgs=0
- 230/300: dt: 0.9000, rms radial error=138.367, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.586, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.810, avgs=0
- 245/300: dt: 0.9000, rms radial error=136.038, avgs=0
- 250/300: dt: 0.9000, rms radial error=135.270, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.506, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.747, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.992, avgs=0
- 270/300: dt: 0.9000, rms radial error=132.241, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.495, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.752, avgs=0
- 285/300: dt: 0.9000, rms radial error=130.014, avgs=0
- 290/300: dt: 0.9000, rms radial error=129.279, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.549, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.823, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 16754.84
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00014
- epoch 2 (K=40.0), pass 1, starting sse = 2908.57
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00006
- epoch 3 (K=160.0), pass 1, starting sse = 352.07
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.07/11 = 0.00652
- epoch 4 (K=640.0), pass 1, starting sse = 35.69
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.08/10 = 0.00823
- final distance error %27.42
- writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.10 hours
- mris_sphere utimesec 381.341027
- mris_sphere stimesec 0.167974
- mris_sphere ru_maxrss 206796
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 30170
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 9952
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 7413
- mris_sphere ru_nivcsw 16654
- FSRUNTIME@ mris_sphere 0.0961 hours 1 threads
- PIDs (28189 28193) completed and logs appended.
- #--------------------------------------------
- #@# Fix Topology Copy lh Sun Oct 8 04:34:34 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- #--------------------------------------------
- #@# Fix Topology Copy rh Sun Oct 8 04:34:34 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- #@# Fix Topology lh Sun Oct 8 04:34:34 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050379 lh
- #@# Fix Topology rh Sun Oct 8 04:34:34 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050379 rh
- Waiting for PID 28465 of (28465 28468) to complete...
- Waiting for PID 28468 of (28465 28468) to complete...
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050379 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=-168 (nv=145818, nf=291972, ne=437958, g=85)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 11 iterations
- marking ambiguous vertices...
- 14865 ambiguous faces found in tessellation
- segmenting defects...
- 76 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 15 into 14
- -merging segment 31 into 30
- -merging segment 45 into 40
- -merging segment 43 into 40
- -merging segment 47 into 40
- -merging segment 54 into 40
- -merging segment 60 into 58
- 69 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.2169 (-4.6084)
- -vertex loglikelihood: -6.1963 (-3.0982)
- -normal dot loglikelihood: -3.5013 (-3.5013)
- -quad curv loglikelihood: -6.1096 (-3.0548)
- Total Loglikelihood : -25.0241
- CORRECTING DEFECT 0 (vertices=386, convex hull=260, v0=2)
- After retessellation of defect 0 (v0=2), euler #=-71 (136983,407751,270697) : difference with theory (-66) = 5
- CORRECTING DEFECT 1 (vertices=39, convex hull=75, v0=406)
- After retessellation of defect 1 (v0=406), euler #=-70 (137002,407837,270765) : difference with theory (-65) = 5
- CORRECTING DEFECT 2 (vertices=27, convex hull=49, v0=484)
- After retessellation of defect 2 (v0=484), euler #=-69 (137012,407882,270801) : difference with theory (-64) = 5
- CORRECTING DEFECT 3 (vertices=67, convex hull=98, v0=609)
- After retessellation of defect 3 (v0=609), euler #=-68 (137039,408009,270902) : difference with theory (-63) = 5
- CORRECTING DEFECT 4 (vertices=35, convex hull=69, v0=652)
- After retessellation of defect 4 (v0=652), euler #=-67 (137049,408070,270954) : difference with theory (-62) = 5
- CORRECTING DEFECT 5 (vertices=13, convex hull=24, v0=1698)
- After retessellation of defect 5 (v0=1698), euler #=-66 (137049,408075,270960) : difference with theory (-61) = 5
- CORRECTING DEFECT 6 (vertices=68, convex hull=63, v0=2382)
- After retessellation of defect 6 (v0=2382), euler #=-65 (137078,408191,271048) : difference with theory (-60) = 5
- CORRECTING DEFECT 7 (vertices=198, convex hull=114, v0=2661)
- After retessellation of defect 7 (v0=2661), euler #=-64 (137111,408337,271162) : difference with theory (-59) = 5
- CORRECTING DEFECT 8 (vertices=16, convex hull=40, v0=2750)
- After retessellation of defect 8 (v0=2750), euler #=-63 (137112,408354,271179) : difference with theory (-58) = 5
- CORRECTING DEFECT 9 (vertices=13, convex hull=35, v0=10221)
- After retessellation of defect 9 (v0=10221), euler #=-62 (137115,408377,271200) : difference with theory (-57) = 5
- CORRECTING DEFECT 10 (vertices=67, convex hull=45, v0=12100)
- After retessellation of defect 10 (v0=12100), euler #=-61 (137123,408415,271231) : difference with theory (-56) = 5
- CORRECTING DEFECT 11 (vertices=27, convex hull=61, v0=13588)
- After retessellation of defect 11 (v0=13588), euler #=-60 (137132,408467,271275) : difference with theory (-55) = 5
- CORRECTING DEFECT 12 (vertices=100, convex hull=135, v0=16970)
- After retessellation of defect 12 (v0=16970), euler #=-59 (137187,408689,271443) : difference with theory (-54) = 5
- CORRECTING DEFECT 13 (vertices=40, convex hull=61, v0=17556)
- After retessellation of defect 13 (v0=17556), euler #=-58 (137212,408789,271519) : difference with theory (-53) = 5
- CORRECTING DEFECT 14 (vertices=355, convex hull=331, v0=18256)
- After retessellation of defect 14 (v0=18256), euler #=-56 (137403,409512,272053) : difference with theory (-52) = 4
- CORRECTING DEFECT 15 (vertices=21, convex hull=44, v0=22492)
- After retessellation of defect 15 (v0=22492), euler #=-55 (137411,409551,272085) : difference with theory (-51) = 4
- CORRECTING DEFECT 16 (vertices=61, convex hull=76, v0=22665)
- After retessellation of defect 16 (v0=22665), euler #=-54 (137444,409684,272186) : difference with theory (-50) = 4
- CORRECTING DEFECT 17 (vertices=86, convex hull=98, v0=26682)
- After retessellation of defect 17 (v0=26682), euler #=-53 (137484,409851,272314) : difference with theory (-49) = 4
- CORRECTING DEFECT 18 (vertices=27, convex hull=51, v0=27939)
- After retessellation of defect 18 (v0=27939), euler #=-52 (137498,409914,272364) : difference with theory (-48) = 4
- CORRECTING DEFECT 19 (vertices=227, convex hull=255, v0=30532)
- normal vector of length zero at vertex 138714 with 3 faces
- normal vector of length zero at vertex 138722 with 3 faces
- normal vector of length zero at vertex 138705 with 3 faces
- normal vector of length zero at vertex 138705 with 3 faces
- normal vector of length zero at vertex 138705 with 3 faces
- normal vector of length zero at vertex 138714 with 3 faces
- normal vector of length zero at vertex 138714 with 3 faces
- normal vector of length zero at vertex 138714 with 3 faces
- normal vector of length zero at vertex 138714 with 3 faces
- normal vector of length zero at vertex 138714 with 3 faces
- normal vector of length zero at vertex 138714 with 3 faces
- After retessellation of defect 19 (v0=30532), euler #=-51 (137621,410414,272742) : difference with theory (-47) = 4
- CORRECTING DEFECT 20 (vertices=44, convex hull=58, v0=33708)
- After retessellation of defect 20 (v0=33708), euler #=-50 (137637,410486,272799) : difference with theory (-46) = 4
- CORRECTING DEFECT 21 (vertices=23, convex hull=63, v0=34617)
- After retessellation of defect 21 (v0=34617), euler #=-49 (137648,410543,272846) : difference with theory (-45) = 4
- CORRECTING DEFECT 22 (vertices=32, convex hull=64, v0=38161)
- After retessellation of defect 22 (v0=38161), euler #=-48 (137665,410617,272904) : difference with theory (-44) = 4
- CORRECTING DEFECT 23 (vertices=131, convex hull=156, v0=39497)
- After retessellation of defect 23 (v0=39497), euler #=-47 (137738,410913,273128) : difference with theory (-43) = 4
- CORRECTING DEFECT 24 (vertices=418, convex hull=92, v0=42498)
- After retessellation of defect 24 (v0=42498), euler #=-46 (137751,410992,273195) : difference with theory (-42) = 4
- CORRECTING DEFECT 25 (vertices=18, convex hull=57, v0=44429)
- After retessellation of defect 25 (v0=44429), euler #=-45 (137760,411041,273236) : difference with theory (-41) = 4
- CORRECTING DEFECT 26 (vertices=74, convex hull=79, v0=46980)
- After retessellation of defect 26 (v0=46980), euler #=-44 (137787,411153,273322) : difference with theory (-40) = 4
- CORRECTING DEFECT 27 (vertices=10, convex hull=31, v0=52021)
- After retessellation of defect 27 (v0=52021), euler #=-43 (137790,411171,273338) : difference with theory (-39) = 4
- CORRECTING DEFECT 28 (vertices=301, convex hull=166, v0=52249)
- After retessellation of defect 28 (v0=52249), euler #=-42 (137878,411519,273599) : difference with theory (-38) = 4
- CORRECTING DEFECT 29 (vertices=48, convex hull=76, v0=57147)
- After retessellation of defect 29 (v0=57147), euler #=-40 (137896,411609,273673) : difference with theory (-37) = 3
- CORRECTING DEFECT 30 (vertices=29, convex hull=56, v0=59263)
- After retessellation of defect 30 (v0=59263), euler #=-39 (137909,411668,273720) : difference with theory (-36) = 3
- CORRECTING DEFECT 31 (vertices=107, convex hull=40, v0=65942)
- After retessellation of defect 31 (v0=65942), euler #=-38 (137926,411734,273770) : difference with theory (-35) = 3
- CORRECTING DEFECT 32 (vertices=30, convex hull=37, v0=68885)
- After retessellation of defect 32 (v0=68885), euler #=-37 (137929,411759,273793) : difference with theory (-34) = 3
- CORRECTING DEFECT 33 (vertices=149, convex hull=58, v0=72421)
- After retessellation of defect 33 (v0=72421), euler #=-36 (137938,411809,273835) : difference with theory (-33) = 3
- CORRECTING DEFECT 34 (vertices=92, convex hull=118, v0=73526)
- After retessellation of defect 34 (v0=73526), euler #=-35 (137963,411934,273936) : difference with theory (-32) = 3
- CORRECTING DEFECT 35 (vertices=171, convex hull=146, v0=75100)
- After retessellation of defect 35 (v0=75100), euler #=-34 (138050,412282,274198) : difference with theory (-31) = 3
- CORRECTING DEFECT 36 (vertices=21, convex hull=13, v0=76266)
- After retessellation of defect 36 (v0=76266), euler #=-33 (138053,412292,274206) : difference with theory (-30) = 3
- CORRECTING DEFECT 37 (vertices=38, convex hull=83, v0=78774)
- After retessellation of defect 37 (v0=78774), euler #=-32 (138078,412402,274292) : difference with theory (-29) = 3
- CORRECTING DEFECT 38 (vertices=798, convex hull=727, v0=80042)
- XL defect detected...
- After retessellation of defect 38 (v0=80042), euler #=-27 (138478,413985,275480) : difference with theory (-28) = -1
- CORRECTING DEFECT 39 (vertices=613, convex hull=181, v0=81289)
- After retessellation of defect 39 (v0=81289), euler #=-26 (138593,414425,275806) : difference with theory (-27) = -1
- CORRECTING DEFECT 40 (vertices=41, convex hull=61, v0=81460)
- After retessellation of defect 40 (v0=81460), euler #=-25 (138610,414498,275863) : difference with theory (-26) = -1
- CORRECTING DEFECT 41 (vertices=32, convex hull=58, v0=84383)
- After retessellation of defect 41 (v0=84383), euler #=-24 (138619,414551,275908) : difference with theory (-25) = -1
- CORRECTING DEFECT 42 (vertices=282, convex hull=284, v0=88752)
- After retessellation of defect 42 (v0=88752), euler #=-23 (138760,415114,276331) : difference with theory (-24) = -1
- CORRECTING DEFECT 43 (vertices=51, convex hull=90, v0=90089)
- After retessellation of defect 43 (v0=90089), euler #=-22 (138786,415232,276424) : difference with theory (-23) = -1
- CORRECTING DEFECT 44 (vertices=12, convex hull=19, v0=91047)
- After retessellation of defect 44 (v0=91047), euler #=-21 (138787,415242,276434) : difference with theory (-22) = -1
- CORRECTING DEFECT 45 (vertices=369, convex hull=124, v0=92808)
- After retessellation of defect 45 (v0=92808), euler #=-20 (138828,415425,276577) : difference with theory (-21) = -1
- CORRECTING DEFECT 46 (vertices=51, convex hull=60, v0=93730)
- After retessellation of defect 46 (v0=93730), euler #=-19 (138837,415477,276621) : difference with theory (-20) = -1
- CORRECTING DEFECT 47 (vertices=19, convex hull=21, v0=94683)
- After retessellation of defect 47 (v0=94683), euler #=-18 (138840,415490,276632) : difference with theory (-19) = -1
- CORRECTING DEFECT 48 (vertices=75, convex hull=62, v0=97670)
- After retessellation of defect 48 (v0=97670), euler #=-17 (138843,415525,276665) : difference with theory (-18) = -1
- CORRECTING DEFECT 49 (vertices=27, convex hull=64, v0=97915)
- After retessellation of defect 49 (v0=97915), euler #=-16 (138860,415600,276724) : difference with theory (-17) = -1
- CORRECTING DEFECT 50 (vertices=221, convex hull=183, v0=99280)
- After retessellation of defect 50 (v0=99280), euler #=-16 (138939,415924,276969) : difference with theory (-16) = 0
- CORRECTING DEFECT 51 (vertices=36, convex hull=59, v0=99807)
- After retessellation of defect 51 (v0=99807), euler #=-15 (138959,416012,277038) : difference with theory (-15) = 0
- CORRECTING DEFECT 52 (vertices=586, convex hull=481, v0=100096)
- L defect detected...
- After retessellation of defect 52 (v0=100096), euler #=-13 (139153,416839,277673) : difference with theory (-14) = -1
- CORRECTING DEFECT 53 (vertices=153, convex hull=42, v0=101434)
- After retessellation of defect 53 (v0=101434), euler #=-12 (139162,416882,277708) : difference with theory (-13) = -1
- CORRECTING DEFECT 54 (vertices=169, convex hull=71, v0=106230)
- After retessellation of defect 54 (v0=106230), euler #=-11 (139188,416989,277790) : difference with theory (-12) = -1
- CORRECTING DEFECT 55 (vertices=394, convex hull=247, v0=106413)
- After retessellation of defect 55 (v0=106413), euler #=-10 (139296,417434,278128) : difference with theory (-11) = -1
- CORRECTING DEFECT 56 (vertices=190, convex hull=149, v0=108001)
- After retessellation of defect 56 (v0=108001), euler #=-9 (139344,417643,278290) : difference with theory (-10) = -1
- CORRECTING DEFECT 57 (vertices=12, convex hull=24, v0=108818)
- After retessellation of defect 57 (v0=108818), euler #=-8 (139344,417652,278300) : difference with theory (-9) = -1
- CORRECTING DEFECT 58 (vertices=137, convex hull=38, v0=115740)
- After retessellation of defect 58 (v0=115740), euler #=-7 (139353,417691,278331) : difference with theory (-8) = -1
- CORRECTING DEFECT 59 (vertices=51, convex hull=38, v0=116382)
- After retessellation of defect 59 (v0=116382), euler #=-6 (139366,417743,278371) : difference with theory (-7) = -1
- CORRECTING DEFECT 60 (vertices=187, convex hull=106, v0=116665)
- After retessellation of defect 60 (v0=116665), euler #=-5 (139411,417926,278510) : difference with theory (-6) = -1
- CORRECTING DEFECT 61 (vertices=54, convex hull=71, v0=122056)
- After retessellation of defect 61 (v0=122056), euler #=-4 (139437,418027,278586) : difference with theory (-5) = -1
- CORRECTING DEFECT 62 (vertices=392, convex hull=224, v0=122880)
- After retessellation of defect 62 (v0=122880), euler #=-3 (139496,418316,278817) : difference with theory (-4) = -1
- CORRECTING DEFECT 63 (vertices=64, convex hull=31, v0=124667)
- After retessellation of defect 63 (v0=124667), euler #=-3 (139499,418341,278839) : difference with theory (-3) = 0
- CORRECTING DEFECT 64 (vertices=22, convex hull=65, v0=125167)
- After retessellation of defect 64 (v0=125167), euler #=-2 (139508,418395,278885) : difference with theory (-2) = 0
- CORRECTING DEFECT 65 (vertices=192, convex hull=136, v0=131672)
- After retessellation of defect 65 (v0=131672), euler #=-1 (139530,418532,279001) : difference with theory (-1) = 0
- CORRECTING DEFECT 66 (vertices=24, convex hull=26, v0=133296)
- After retessellation of defect 66 (v0=133296), euler #=0 (139532,418543,279011) : difference with theory (0) = 0
- CORRECTING DEFECT 67 (vertices=58, convex hull=75, v0=142086)
- After retessellation of defect 67 (v0=142086), euler #=1 (139556,418649,279094) : difference with theory (1) = 0
- CORRECTING DEFECT 68 (vertices=15, convex hull=29, v0=145730)
- After retessellation of defect 68 (v0=145730), euler #=2 (139556,418662,279108) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.89 +- 0.25 (0.05-->8.23) (max @ vno 86926 --> 96862)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.89 +- 0.25 (0.05-->8.23) (max @ vno 86926 --> 96862)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 205 mutations (32.6%), 424 crossovers (67.4%), 314 vertices were eliminated
- building final representation...
- 6262 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=139556, nf=279108, ne=418662, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 58.6 minutes
- 0 defective edges
- removing intersecting faces
- 000: 676 intersecting
- 001: 36 intersecting
- mris_fix_topology utimesec 3515.807516
- mris_fix_topology stimesec 0.249962
- mris_fix_topology ru_maxrss 468912
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 62740
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 10272
- mris_fix_topology ru_oublock 13704
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 622
- mris_fix_topology ru_nivcsw 8067
- FSRUNTIME@ mris_fix_topology lh 0.9766 hours 1 threads
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050379 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=-164 (nv=140776, nf=281880, ne=422820, g=83)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 7 iterations
- marking ambiguous vertices...
- 14499 ambiguous faces found in tessellation
- segmenting defects...
- 78 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 1 into 0
- -merging segment 12 into 10
- -merging segment 48 into 44
- -merging segment 58 into 44
- 74 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.2865 (-4.6433)
- -vertex loglikelihood: -6.1900 (-3.0950)
- -normal dot loglikelihood: -3.5563 (-3.5563)
- -quad curv loglikelihood: -6.2094 (-3.1047)
- Total Loglikelihood : -25.2422
- CORRECTING DEFECT 0 (vertices=201, convex hull=185, v0=0)
- After retessellation of defect 0 (v0=0), euler #=-73 (132216,393825,261536) : difference with theory (-71) = 2
- CORRECTING DEFECT 1 (vertices=131, convex hull=77, v0=83)
- After retessellation of defect 1 (v0=83), euler #=-72 (132234,393915,261609) : difference with theory (-70) = 2
- CORRECTING DEFECT 2 (vertices=42, convex hull=38, v0=341)
- After retessellation of defect 2 (v0=341), euler #=-71 (132235,393932,261626) : difference with theory (-69) = 2
- CORRECTING DEFECT 3 (vertices=78, convex hull=112, v0=432)
- After retessellation of defect 3 (v0=432), euler #=-71 (132268,394088,261749) : difference with theory (-68) = 3
- CORRECTING DEFECT 4 (vertices=21, convex hull=57, v0=1028)
- After retessellation of defect 4 (v0=1028), euler #=-70 (132277,394133,261786) : difference with theory (-67) = 3
- CORRECTING DEFECT 5 (vertices=38, convex hull=66, v0=1131)
- After retessellation of defect 5 (v0=1131), euler #=-69 (132286,394187,261832) : difference with theory (-66) = 3
- CORRECTING DEFECT 6 (vertices=66, convex hull=112, v0=6478)
- After retessellation of defect 6 (v0=6478), euler #=-68 (132320,394336,261948) : difference with theory (-65) = 3
- CORRECTING DEFECT 7 (vertices=37, convex hull=53, v0=8794)
- After retessellation of defect 7 (v0=8794), euler #=-67 (132333,394397,261997) : difference with theory (-64) = 3
- CORRECTING DEFECT 8 (vertices=22, convex hull=21, v0=12548)
- After retessellation of defect 8 (v0=12548), euler #=-66 (132335,394409,262008) : difference with theory (-63) = 3
- CORRECTING DEFECT 9 (vertices=125, convex hull=147, v0=12970)
- After retessellation of defect 9 (v0=12970), euler #=-64 (132369,394584,262151) : difference with theory (-62) = 2
- CORRECTING DEFECT 10 (vertices=227, convex hull=76, v0=16467)
- After retessellation of defect 10 (v0=16467), euler #=-63 (132393,394692,262236) : difference with theory (-61) = 2
- CORRECTING DEFECT 11 (vertices=30, convex hull=74, v0=17259)
- After retessellation of defect 11 (v0=17259), euler #=-62 (132409,394770,262299) : difference with theory (-60) = 2
- CORRECTING DEFECT 12 (vertices=628, convex hull=345, v0=20497)
- After retessellation of defect 12 (v0=20497), euler #=-61 (132554,395377,262762) : difference with theory (-59) = 2
- CORRECTING DEFECT 13 (vertices=25, convex hull=57, v0=22941)
- After retessellation of defect 13 (v0=22941), euler #=-60 (132566,395434,262808) : difference with theory (-58) = 2
- CORRECTING DEFECT 14 (vertices=44, convex hull=49, v0=28323)
- After retessellation of defect 14 (v0=28323), euler #=-59 (132589,395523,262875) : difference with theory (-57) = 2
- CORRECTING DEFECT 15 (vertices=53, convex hull=87, v0=29702)
- After retessellation of defect 15 (v0=29702), euler #=-58 (132625,395670,262987) : difference with theory (-56) = 2
- CORRECTING DEFECT 16 (vertices=14, convex hull=20, v0=34362)
- After retessellation of defect 16 (v0=34362), euler #=-57 (132626,395682,262999) : difference with theory (-55) = 2
- CORRECTING DEFECT 17 (vertices=291, convex hull=82, v0=37676)
- After retessellation of defect 17 (v0=37676), euler #=-56 (132650,395791,263085) : difference with theory (-54) = 2
- CORRECTING DEFECT 18 (vertices=24, convex hull=24, v0=43001)
- After retessellation of defect 18 (v0=43001), euler #=-55 (132653,395808,263100) : difference with theory (-53) = 2
- CORRECTING DEFECT 19 (vertices=23, convex hull=43, v0=43051)
- After retessellation of defect 19 (v0=43051), euler #=-54 (132654,395826,263118) : difference with theory (-52) = 2
- CORRECTING DEFECT 20 (vertices=40, convex hull=58, v0=44969)
- After retessellation of defect 20 (v0=44969), euler #=-53 (132670,395896,263173) : difference with theory (-51) = 2
- CORRECTING DEFECT 21 (vertices=6, convex hull=9, v0=45083)
- After retessellation of defect 21 (v0=45083), euler #=-52 (132671,395901,263178) : difference with theory (-50) = 2
- CORRECTING DEFECT 22 (vertices=48, convex hull=78, v0=48820)
- After retessellation of defect 22 (v0=48820), euler #=-51 (132702,396023,263270) : difference with theory (-49) = 2
- CORRECTING DEFECT 23 (vertices=18, convex hull=24, v0=49470)
- After retessellation of defect 23 (v0=49470), euler #=-50 (132704,396037,263283) : difference with theory (-48) = 2
- CORRECTING DEFECT 24 (vertices=37, convex hull=76, v0=52536)
- After retessellation of defect 24 (v0=52536), euler #=-49 (132729,396140,263362) : difference with theory (-47) = 2
- CORRECTING DEFECT 25 (vertices=28, convex hull=59, v0=52912)
- After retessellation of defect 25 (v0=52912), euler #=-48 (132738,396188,263402) : difference with theory (-46) = 2
- CORRECTING DEFECT 26 (vertices=57, convex hull=66, v0=54375)
- After retessellation of defect 26 (v0=54375), euler #=-47 (132752,396258,263459) : difference with theory (-45) = 2
- CORRECTING DEFECT 27 (vertices=19, convex hull=24, v0=55615)
- After retessellation of defect 27 (v0=55615), euler #=-46 (132756,396278,263476) : difference with theory (-44) = 2
- CORRECTING DEFECT 28 (vertices=13, convex hull=26, v0=61455)
- After retessellation of defect 28 (v0=61455), euler #=-45 (132761,396302,263496) : difference with theory (-43) = 2
- CORRECTING DEFECT 29 (vertices=55, convex hull=97, v0=68822)
- After retessellation of defect 29 (v0=68822), euler #=-44 (132786,396416,263586) : difference with theory (-42) = 2
- CORRECTING DEFECT 30 (vertices=61, convex hull=85, v0=77274)
- After retessellation of defect 30 (v0=77274), euler #=-43 (132798,396485,263644) : difference with theory (-41) = 2
- CORRECTING DEFECT 31 (vertices=96, convex hull=91, v0=77364)
- After retessellation of defect 31 (v0=77364), euler #=-42 (132835,396640,263763) : difference with theory (-40) = 2
- CORRECTING DEFECT 32 (vertices=206, convex hull=88, v0=78417)
- After retessellation of defect 32 (v0=78417), euler #=-41 (132859,396749,263849) : difference with theory (-39) = 2
- CORRECTING DEFECT 33 (vertices=25, convex hull=26, v0=80997)
- After retessellation of defect 33 (v0=80997), euler #=-40 (132863,396767,263864) : difference with theory (-38) = 2
- CORRECTING DEFECT 34 (vertices=46, convex hull=62, v0=81019)
- After retessellation of defect 34 (v0=81019), euler #=-39 (132869,396814,263906) : difference with theory (-37) = 2
- CORRECTING DEFECT 35 (vertices=42, convex hull=35, v0=81778)
- After retessellation of defect 35 (v0=81778), euler #=-38 (132876,396849,263935) : difference with theory (-36) = 2
- CORRECTING DEFECT 36 (vertices=379, convex hull=101, v0=84554)
- After retessellation of defect 36 (v0=84554), euler #=-37 (132923,397039,264079) : difference with theory (-35) = 2
- CORRECTING DEFECT 37 (vertices=182, convex hull=134, v0=84827)
- After retessellation of defect 37 (v0=84827), euler #=-36 (132970,397237,264231) : difference with theory (-34) = 2
- CORRECTING DEFECT 38 (vertices=38, convex hull=67, v0=84963)
- After retessellation of defect 38 (v0=84963), euler #=-35 (132993,397331,264303) : difference with theory (-33) = 2
- CORRECTING DEFECT 39 (vertices=1785, convex hull=667, v0=85519)
- XL defect detected...
- After retessellation of defect 39 (v0=85519), euler #=-34 (133229,398400,265137) : difference with theory (-32) = 2
- CORRECTING DEFECT 40 (vertices=93, convex hull=105, v0=91308)
- After retessellation of defect 40 (v0=91308), euler #=-33 (133240,398490,265217) : difference with theory (-31) = 2
- CORRECTING DEFECT 41 (vertices=122, convex hull=44, v0=91687)
- After retessellation of defect 41 (v0=91687), euler #=-32 (133252,398544,265260) : difference with theory (-30) = 2
- CORRECTING DEFECT 42 (vertices=327, convex hull=311, v0=91766)
- After retessellation of defect 42 (v0=91766), euler #=-29 (133374,399100,265697) : difference with theory (-29) = 0
- CORRECTING DEFECT 43 (vertices=47, convex hull=67, v0=92705)
- After retessellation of defect 43 (v0=92705), euler #=-28 (133405,399218,265785) : difference with theory (-28) = 0
- CORRECTING DEFECT 44 (vertices=299, convex hull=159, v0=93851)
- After retessellation of defect 44 (v0=93851), euler #=-27 (133435,399375,265913) : difference with theory (-27) = 0
- CORRECTING DEFECT 45 (vertices=43, convex hull=82, v0=97022)
- After retessellation of defect 45 (v0=97022), euler #=-26 (133461,399490,266003) : difference with theory (-26) = 0
- CORRECTING DEFECT 46 (vertices=61, convex hull=86, v0=100381)
- After retessellation of defect 46 (v0=100381), euler #=-25 (133481,399584,266078) : difference with theory (-25) = 0
- CORRECTING DEFECT 47 (vertices=25, convex hull=60, v0=102503)
- After retessellation of defect 47 (v0=102503), euler #=-24 (133493,399640,266123) : difference with theory (-24) = 0
- CORRECTING DEFECT 48 (vertices=38, convex hull=72, v0=103600)
- After retessellation of defect 48 (v0=103600), euler #=-23 (133509,399717,266185) : difference with theory (-23) = 0
- CORRECTING DEFECT 49 (vertices=21, convex hull=27, v0=103926)
- After retessellation of defect 49 (v0=103926), euler #=-22 (133514,399741,266205) : difference with theory (-22) = 0
- CORRECTING DEFECT 50 (vertices=85, convex hull=52, v0=104282)
- After retessellation of defect 50 (v0=104282), euler #=-21 (133539,399834,266274) : difference with theory (-21) = 0
- CORRECTING DEFECT 51 (vertices=153, convex hull=137, v0=104517)
- After retessellation of defect 51 (v0=104517), euler #=-20 (133623,400152,266509) : difference with theory (-20) = 0
- CORRECTING DEFECT 52 (vertices=414, convex hull=264, v0=105207)
- After retessellation of defect 52 (v0=105207), euler #=-19 (133757,400692,266916) : difference with theory (-19) = 0
- CORRECTING DEFECT 53 (vertices=60, convex hull=38, v0=106094)
- After retessellation of defect 53 (v0=106094), euler #=-18 (133760,400718,266940) : difference with theory (-18) = 0
- CORRECTING DEFECT 54 (vertices=36, convex hull=73, v0=108803)
- After retessellation of defect 54 (v0=108803), euler #=-17 (133769,400775,266989) : difference with theory (-17) = 0
- CORRECTING DEFECT 55 (vertices=86, convex hull=93, v0=109518)
- After retessellation of defect 55 (v0=109518), euler #=-16 (133802,400912,267094) : difference with theory (-16) = 0
- CORRECTING DEFECT 56 (vertices=72, convex hull=56, v0=112509)
- After retessellation of defect 56 (v0=112509), euler #=-15 (133817,400981,267149) : difference with theory (-15) = 0
- CORRECTING DEFECT 57 (vertices=33, convex hull=56, v0=115476)
- After retessellation of defect 57 (v0=115476), euler #=-14 (133830,401040,267196) : difference with theory (-14) = 0
- CORRECTING DEFECT 58 (vertices=117, convex hull=141, v0=115710)
- After retessellation of defect 58 (v0=115710), euler #=-13 (133870,401232,267349) : difference with theory (-13) = 0
- CORRECTING DEFECT 59 (vertices=11, convex hull=33, v0=116634)
- After retessellation of defect 59 (v0=116634), euler #=-12 (133873,401251,267366) : difference with theory (-12) = 0
- CORRECTING DEFECT 60 (vertices=140, convex hull=61, v0=118178)
- After retessellation of defect 60 (v0=118178), euler #=-11 (133886,401317,267420) : difference with theory (-11) = 0
- CORRECTING DEFECT 61 (vertices=105, convex hull=65, v0=118847)
- After retessellation of defect 61 (v0=118847), euler #=-10 (133900,401395,267485) : difference with theory (-10) = 0
- CORRECTING DEFECT 62 (vertices=67, convex hull=44, v0=120750)
- After retessellation of defect 62 (v0=120750), euler #=-9 (133916,401462,267537) : difference with theory (-9) = 0
- CORRECTING DEFECT 63 (vertices=110, convex hull=101, v0=122342)
- After retessellation of defect 63 (v0=122342), euler #=-8 (133959,401638,267671) : difference with theory (-8) = 0
- CORRECTING DEFECT 64 (vertices=55, convex hull=87, v0=125347)
- After retessellation of defect 64 (v0=125347), euler #=-7 (133978,401732,267747) : difference with theory (-7) = 0
- CORRECTING DEFECT 65 (vertices=89, convex hull=71, v0=127241)
- After retessellation of defect 65 (v0=127241), euler #=-6 (134003,401838,267829) : difference with theory (-6) = 0
- CORRECTING DEFECT 66 (vertices=11, convex hull=24, v0=128286)
- After retessellation of defect 66 (v0=128286), euler #=-5 (134005,401850,267840) : difference with theory (-5) = 0
- CORRECTING DEFECT 67 (vertices=18, convex hull=40, v0=130796)
- After retessellation of defect 67 (v0=130796), euler #=-4 (134009,401875,267862) : difference with theory (-4) = 0
- CORRECTING DEFECT 68 (vertices=6, convex hull=17, v0=131356)
- After retessellation of defect 68 (v0=131356), euler #=-3 (134010,401883,267870) : difference with theory (-3) = 0
- CORRECTING DEFECT 69 (vertices=208, convex hull=105, v0=131362)
- After retessellation of defect 69 (v0=131362), euler #=-2 (134046,402053,268005) : difference with theory (-2) = 0
- CORRECTING DEFECT 70 (vertices=50, convex hull=71, v0=133820)
- After retessellation of defect 70 (v0=133820), euler #=-1 (134074,402167,268092) : difference with theory (-1) = 0
- CORRECTING DEFECT 71 (vertices=19, convex hull=55, v0=134652)
- After retessellation of defect 71 (v0=134652), euler #=0 (134085,402222,268137) : difference with theory (0) = 0
- CORRECTING DEFECT 72 (vertices=6, convex hull=15, v0=138719)
- After retessellation of defect 72 (v0=138719), euler #=1 (134086,402228,268143) : difference with theory (1) = 0
- CORRECTING DEFECT 73 (vertices=252, convex hull=50, v0=139281)
- After retessellation of defect 73 (v0=139281), euler #=2 (134102,402300,268200) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.89 +- 0.27 (0.06-->12.08) (max @ vno 19653 --> 27332)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.89 +- 0.27 (0.06-->12.08) (max @ vno 19653 --> 27332)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 212 mutations (32.2%), 446 crossovers (67.8%), 551 vertices were eliminated
- building final representation...
- 6674 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=134102, nf=268200, ne=402300, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 46.2 minutes
- 0 defective edges
- removing intersecting faces
- 000: 746 intersecting
- 001: 30 intersecting
- mris_fix_topology utimesec 2770.050888
- mris_fix_topology stimesec 0.207968
- mris_fix_topology ru_maxrss 455280
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 59489
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 9912
- mris_fix_topology ru_oublock 13128
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 648
- mris_fix_topology ru_nivcsw 5847
- FSRUNTIME@ mris_fix_topology rh 0.7696 hours 1 threads
- PIDs (28465 28468) completed and logs appended.
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 139556 - 418662 + 279108 = 2 --> 0 holes
- F =2V-4: 279108 = 279112-4 (0)
- 2E=3F: 837324 = 837324 (0)
- total defect index = 0
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 134102 - 402300 + 268200 = 2 --> 0 holes
- F =2V-4: 268200 = 268204-4 (0)
- 2E=3F: 804600 = 804600 (0)
- total defect index = 0
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 136 intersecting
- 001: 18 intersecting
- 002: 2 intersecting
- expanding nbhd size to 2
- 003: 2 intersecting
- expanding nbhd size to 3
- 004: 2 intersecting
- expanding nbhd size to 4
- 005: 2 intersecting
- expanding nbhd size to 5
- 006: 3 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 110 intersecting
- 001: 3 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Sun Oct 8 05:33:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050379 lh
- #--------------------------------------------
- #@# Make White Surf rh Sun Oct 8 05:33:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050379 rh
- Waiting for PID 31246 of (31246 31249) to complete...
- Waiting for PID 31249 of (31246 31249) to complete...
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050379 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-6.0.0/0050379/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- 13789 bright wm thresholded.
- 1867 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.orig...
- computing class statistics...
- border white: 257994 voxels (1.54%)
- border gray 306351 voxels (1.83%)
- WM (95.0): 96.1 +- 8.3 [70.0 --> 110.0]
- GM (72.0) : 70.8 +- 10.5 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 57.5 (was 70)
- setting MAX_BORDER_WHITE to 108.3 (was 105)
- setting MIN_BORDER_WHITE to 68.0 (was 85)
- setting MAX_CSF to 47.1 (was 40)
- setting MAX_GRAY to 91.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 57.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 36.6 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.23 (0.03-->4.49) (max @ vno 31803 --> 33492)
- face area 0.28 +- 0.13 (0.00-->3.43)
- mean absolute distance = 0.68 +- 0.85
- 4090 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=100+-6.1, GM=68+-7.8
- mean inside = 92.0, mean outside = 74.9
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=80.0, 165 (165) missing vertices, mean dist 0.3 [0.6 (%37.8)->0.8 (%62.2))]
- %68 local maxima, %27 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 +- 0.26 (0.10-->4.66) (max @ vno 31803 --> 33492)
- face area 0.28 +- 0.13 (0.00-->3.31)
- mean absolute distance = 0.37 +- 0.62
- 4894 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2797467.0, rms=9.043
- 001: dt: 0.5000, sse=1625876.2, rms=6.308 (30.252%)
- 002: dt: 0.5000, sse=1159268.8, rms=4.755 (24.613%)
- 003: dt: 0.5000, sse=969276.5, rms=3.953 (16.875%)
- 004: dt: 0.5000, sse=892632.6, rms=3.562 (9.883%)
- 005: dt: 0.5000, sse=855454.5, rms=3.365 (5.525%)
- 006: dt: 0.5000, sse=841872.2, rms=3.270 (2.826%)
- rms = 3.25, time step reduction 1 of 3 to 0.250...
- 007: dt: 0.5000, sse=839883.2, rms=3.249 (0.636%)
- 008: dt: 0.2500, sse=711288.7, rms=2.192 (32.532%)
- 009: dt: 0.2500, sse=670299.0, rms=1.957 (10.739%)
- 010: dt: 0.2500, sse=664917.7, rms=1.894 (3.221%)
- rms = 1.86, time step reduction 2 of 3 to 0.125...
- 011: dt: 0.2500, sse=660270.2, rms=1.856 (1.981%)
- 012: dt: 0.1250, sse=656413.5, rms=1.806 (2.705%)
- rms = 1.80, time step reduction 3 of 3 to 0.062...
- 013: dt: 0.1250, sse=657007.7, rms=1.802 (0.225%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=82.7, 153 (42) missing vertices, mean dist -0.2 [0.4 (%70.2)->0.3 (%29.8))]
- %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.26 (0.04-->4.60) (max @ vno 31803 --> 33492)
- face area 0.35 +- 0.17 (0.00-->4.12)
- mean absolute distance = 0.28 +- 0.44
- 3755 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1187485.1, rms=4.249
- 014: dt: 0.5000, sse=925800.6, rms=2.802 (34.062%)
- 015: dt: 0.5000, sse=902617.7, rms=2.687 (4.079%)
- rms = 2.74, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.2500, sse=813668.2, rms=2.041 (24.057%)
- 017: dt: 0.2500, sse=781603.1, rms=1.685 (17.433%)
- 018: dt: 0.2500, sse=774632.4, rms=1.595 (5.354%)
- 019: dt: 0.2500, sse=768399.8, rms=1.536 (3.694%)
- rms = 1.49, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=790342.0, rms=1.489 (3.047%)
- rms = 1.45, time step reduction 3 of 3 to 0.062...
- 021: dt: 0.1250, sse=761981.5, rms=1.445 (2.958%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- mean border=84.2, 197 (14) missing vertices, mean dist -0.1 [0.3 (%62.9)->0.2 (%37.1))]
- %82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.26 (0.05-->4.63) (max @ vno 31803 --> 33492)
- face area 0.34 +- 0.16 (0.00-->4.08)
- mean absolute distance = 0.26 +- 0.38
- 3815 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=865419.9, rms=2.559
- 022: dt: 0.5000, sse=824243.5, rms=2.146 (16.119%)
- rms = 2.34, time step reduction 1 of 3 to 0.250...
- 023: dt: 0.2500, sse=762521.4, rms=1.627 (24.205%)
- 024: dt: 0.2500, sse=749391.2, rms=1.398 (14.052%)
- 025: dt: 0.2500, sse=739104.5, rms=1.337 (4.366%)
- rms = 1.33, time step reduction 2 of 3 to 0.125...
- 026: dt: 0.2500, sse=740971.5, rms=1.331 (0.433%)
- rms = 1.29, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=735259.8, rms=1.289 (3.187%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=84.8, 223 (9) missing vertices, mean dist -0.0 [0.3 (%54.3)->0.2 (%45.7))]
- %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white.preaparc...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=755256.4, rms=1.627
- 028: dt: 0.5000, sse=751215.9, rms=1.503 (7.627%)
- rms = 1.97, time step reduction 1 of 3 to 0.250...
- 029: dt: 0.2500, sse=718824.5, rms=1.136 (24.373%)
- rms = 1.12, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=716119.5, rms=1.118 (1.651%)
- 031: dt: 0.1250, sse=708319.9, rms=1.041 (6.822%)
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=710313.1, rms=1.012 (2.799%)
- positioning took 0.6 minutes
- generating cortex label...
- 11 non-cortical segments detected
- only using segment with 7548 vertices
- erasing segment 1 (vno[0] = 71833)
- erasing segment 2 (vno[0] = 79115)
- erasing segment 3 (vno[0] = 92323)
- erasing segment 4 (vno[0] = 93399)
- erasing segment 5 (vno[0] = 94392)
- erasing segment 6 (vno[0] = 94499)
- erasing segment 7 (vno[0] = 96588)
- erasing segment 8 (vno[0] = 96636)
- erasing segment 9 (vno[0] = 99885)
- erasing segment 10 (vno[0] = 103199)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.area
- vertex spacing 0.89 +- 0.26 (0.03-->4.52) (max @ vno 31803 --> 33492)
- face area 0.34 +- 0.16 (0.00-->3.94)
- refinement took 5.2 minutes
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050379 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-6.0.0/0050379/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- 13789 bright wm thresholded.
- 1867 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.orig...
- computing class statistics...
- border white: 257994 voxels (1.54%)
- border gray 306351 voxels (1.83%)
- WM (95.0): 96.1 +- 8.3 [70.0 --> 110.0]
- GM (72.0) : 70.8 +- 10.5 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 56.5 (was 70)
- setting MAX_BORDER_WHITE to 108.3 (was 105)
- setting MIN_BORDER_WHITE to 67.0 (was 85)
- setting MAX_CSF to 46.1 (was 40)
- setting MAX_GRAY to 91.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 56.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 35.6 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.23 (0.02-->5.22) (max @ vno 0 --> 510)
- face area 0.28 +- 0.13 (0.00-->6.91)
- mean absolute distance = 0.71 +- 0.85
- 4308 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=100+-7.0, GM=67+-7.8
- mean inside = 91.8, mean outside = 75.0
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=79.3, 77 (77) missing vertices, mean dist 0.3 [0.6 (%35.2)->0.8 (%64.8))]
- %69 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.07-->5.10) (max @ vno 0 --> 510)
- face area 0.28 +- 0.14 (0.00-->5.41)
- mean absolute distance = 0.37 +- 0.61
- 4159 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2826044.0, rms=9.364
- 001: dt: 0.5000, sse=1661703.9, rms=6.623 (29.273%)
- 002: dt: 0.5000, sse=1170223.8, rms=4.992 (24.628%)
- 003: dt: 0.5000, sse=951955.6, rms=4.061 (18.649%)
- 004: dt: 0.5000, sse=860340.6, rms=3.518 (13.382%)
- 005: dt: 0.5000, sse=805617.2, rms=3.269 (7.079%)
- 006: dt: 0.5000, sse=784105.4, rms=3.129 (4.278%)
- rms = 3.09, time step reduction 1 of 3 to 0.250...
- 007: dt: 0.5000, sse=776871.8, rms=3.086 (1.359%)
- 008: dt: 0.2500, sse=645816.4, rms=1.997 (35.287%)
- 009: dt: 0.2500, sse=623367.2, rms=1.752 (12.266%)
- 010: dt: 0.2500, sse=618913.0, rms=1.684 (3.908%)
- rms = 1.65, time step reduction 2 of 3 to 0.125...
- 011: dt: 0.2500, sse=615541.1, rms=1.653 (1.837%)
- rms = 1.61, time step reduction 3 of 3 to 0.062...
- 012: dt: 0.1250, sse=611665.2, rms=1.610 (2.603%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- mean border=82.1, 104 (19) missing vertices, mean dist -0.2 [0.4 (%70.3)->0.3 (%29.7))]
- %77 local maxima, %18 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 +- 0.26 (0.13-->4.95) (max @ vno 0 --> 510)
- face area 0.35 +- 0.17 (0.00-->6.34)
- mean absolute distance = 0.29 +- 0.45
- 3662 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1148618.1, rms=4.280
- 013: dt: 0.5000, sse=874619.9, rms=2.765 (35.402%)
- 014: dt: 0.5000, sse=853652.6, rms=2.646 (4.288%)
- rms = 2.68, time step reduction 1 of 3 to 0.250...
- 015: dt: 0.2500, sse=778788.2, rms=1.985 (25.005%)
- 016: dt: 0.2500, sse=746365.0, rms=1.606 (19.086%)
- 017: dt: 0.2500, sse=738908.4, rms=1.520 (5.341%)
- 018: dt: 0.2500, sse=733676.8, rms=1.457 (4.157%)
- rms = 1.44, time step reduction 2 of 3 to 0.125...
- 019: dt: 0.2500, sse=731846.9, rms=1.438 (1.291%)
- 020: dt: 0.1250, sse=729055.6, rms=1.388 (3.487%)
- rms = 1.38, time step reduction 3 of 3 to 0.062...
- 021: dt: 0.1250, sse=728134.5, rms=1.377 (0.806%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- mean border=83.8, 108 (10) missing vertices, mean dist -0.1 [0.3 (%63.9)->0.2 (%36.1))]
- %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.26 (0.08-->4.83) (max @ vno 0 --> 510)
- face area 0.34 +- 0.17 (0.00-->6.26)
- mean absolute distance = 0.26 +- 0.38
- 3631 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=854824.8, rms=2.724
- 022: dt: 0.5000, sse=784485.6, rms=2.144 (21.268%)
- rms = 2.32, time step reduction 1 of 3 to 0.250...
- 023: dt: 0.2500, sse=733053.9, rms=1.608 (24.992%)
- 024: dt: 0.2500, sse=713901.1, rms=1.365 (15.105%)
- 025: dt: 0.2500, sse=711466.4, rms=1.314 (3.759%)
- rms = 1.30, time step reduction 2 of 3 to 0.125...
- 026: dt: 0.2500, sse=711871.8, rms=1.302 (0.901%)
- rms = 1.26, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=706395.9, rms=1.260 (3.283%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=84.4, 138 (7) missing vertices, mean dist -0.0 [0.3 (%54.6)->0.2 (%45.4))]
- %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.white.preaparc...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=723129.2, rms=1.590
- 028: dt: 0.5000, sse=714471.5, rms=1.500 (5.650%)
- rms = 1.97, time step reduction 1 of 3 to 0.250...
- 029: dt: 0.2500, sse=689874.6, rms=1.108 (26.108%)
- rms = 1.08, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=686788.8, rms=1.078 (2.782%)
- 031: dt: 0.1250, sse=687477.6, rms=0.988 (8.309%)
- rms = 0.97, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=679533.4, rms=0.968 (2.028%)
- positioning took 0.6 minutes
- generating cortex label...
- 11 non-cortical segments detected
- only using segment with 7350 vertices
- erasing segment 1 (vno[0] = 50541)
- erasing segment 2 (vno[0] = 51791)
- erasing segment 3 (vno[0] = 89884)
- erasing segment 4 (vno[0] = 93466)
- erasing segment 5 (vno[0] = 93488)
- erasing segment 6 (vno[0] = 93577)
- erasing segment 7 (vno[0] = 95333)
- erasing segment 8 (vno[0] = 99648)
- erasing segment 9 (vno[0] = 99677)
- erasing segment 10 (vno[0] = 100474)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.area
- vertex spacing 0.90 +- 0.26 (0.03-->4.76) (max @ vno 0 --> 510)
- face area 0.34 +- 0.16 (0.00-->6.18)
- refinement took 5.0 minutes
- PIDs (31246 31249) completed and logs appended.
- #--------------------------------------------
- #@# Smooth2 lh Sun Oct 8 05:38:37 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
- #--------------------------------------------
- #@# Smooth2 rh Sun Oct 8 05:38:37 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
- Waiting for PID 31591 of (31591 31594) to complete...
- Waiting for PID 31594 of (31591 31594) 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 (31591 31594) completed and logs appended.
- #--------------------------------------------
- #@# Inflation2 lh Sun Oct 8 05:38:50 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- #--------------------------------------------
- #@# Inflation2 rh Sun Oct 8 05:38:50 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Waiting for PID 31656 of (31656 31659) to complete...
- Waiting for PID 31659 of (31656 31659) to complete...
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- Reading ../surf/lh.smoothwm
- avg radius = 46.0 mm, total surface area = 84362 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.181 (target=0.015)
step 005: RMS=0.129 (target=0.015)
step 010: RMS=0.099 (target=0.015)
step 015: RMS=0.083 (target=0.015)
step 020: RMS=0.071 (target=0.015)
step 025: RMS=0.061 (target=0.015)
step 030: RMS=0.052 (target=0.015)
step 035: RMS=0.045 (target=0.015)
step 040: RMS=0.039 (target=0.015)
step 045: RMS=0.035 (target=0.015)
step 050: RMS=0.032 (target=0.015)
step 055: RMS=0.031 (target=0.015)
step 060: RMS=0.029 (target=0.015)
- inflation complete.
- inflation took 1.2 minutes
- mris_inflate utimesec 53.803820
- mris_inflate stimesec 0.098984
- mris_inflate ru_maxrss 204808
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 29804
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 10936
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 1932
- mris_inflate ru_nivcsw 5075
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Reading ../surf/rh.smoothwm
- avg radius = 46.5 mm, total surface area = 81533 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.182 (target=0.015)
step 005: RMS=0.128 (target=0.015)
step 010: RMS=0.098 (target=0.015)
step 015: RMS=0.081 (target=0.015)
step 020: RMS=0.068 (target=0.015)
step 025: RMS=0.056 (target=0.015)
step 030: RMS=0.048 (target=0.015)
step 035: RMS=0.042 (target=0.015)
step 040: RMS=0.036 (target=0.015)
step 045: RMS=0.032 (target=0.015)
step 050: RMS=0.029 (target=0.015)
step 055: RMS=0.027 (target=0.015)
step 060: RMS=0.025 (target=0.015)
- inflation complete.
- inflation took 1.2 minutes
- mris_inflate utimesec 52.609002
- mris_inflate stimesec 0.101984
- mris_inflate ru_maxrss 197148
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 28910
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 9440
- mris_inflate ru_oublock 10504
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 1952
- mris_inflate ru_nivcsw 5010
- PIDs (31656 31659) completed and logs appended.
- #--------------------------------------------
- #@# Curv .H and .K lh Sun Oct 8 05:40:01 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 05:40:01 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/surf
- reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 31874 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- Waiting for PID 31877 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- Waiting for PID 31880 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- Waiting for PID 31883 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- Waiting for PID 31886 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- Waiting for PID 31889 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- Waiting for PID 31892 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- Waiting for PID 31895 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- Waiting for PID 31898 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- Waiting for PID 31901 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- Waiting for PID 31905 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- Waiting for PID 31908 of (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) to complete...
- mris_curvature -w lh.white.preaparc
- total integrated curvature = 20.161*4pi (253.346) --> -19 handles
- ICI = 221.9, FI = 1909.3, variation=31227.280
- 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
- 175 vertices thresholded to be in k1 ~ [-0.28 1.22], k2 ~ [-0.17 0.12]
- total integrated curvature = 0.373*4pi (4.694) --> 1 handles
- ICI = 1.4, FI = 10.4, variation=173.147
- 141 vertices thresholded to be in [-0.05 0.02]
- writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.002
- 108 vertices thresholded to be in [-0.17 0.30]
- done.
- writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.024
- done.
- mris_curvature -w rh.white.preaparc
- total integrated curvature = 2.003*4pi (25.175) --> -1 handles
- ICI = 205.7, FI = 1754.7, variation=29058.418
- 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
- 137 vertices thresholded to be in k1 ~ [-0.31 0.49], k2 ~ [-0.11 0.09]
- total integrated curvature = 0.406*4pi (5.104) --> 1 handles
- ICI = 1.4, FI = 9.3, variation=159.640
- 111 vertices thresholded to be in [-0.01 0.02]
- 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 [-0.15 0.21]
- done.
- writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.022
- done.
- PIDs (31874 31877 31880 31883 31886 31889 31892 31895 31898 31901 31905 31908) completed and logs appended.
- #-----------------------------------------
- #@# Curvature Stats lh Sun Oct 8 05:41:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050379 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 [ 0050379/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 [ 284 ]
- Gb_filter = 0
- #-----------------------------------------
- #@# Curvature Stats rh Sun Oct 8 05:41:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050379 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 [ 0050379/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 [ 248 ]
- Gb_filter = 0
- #--------------------------------------------
- #@# Sphere lh Sun Oct 8 05:41:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- #--------------------------------------------
- #@# Sphere rh Sun Oct 8 05:41:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- Waiting for PID 32223 of (32223 32227) to complete...
- Waiting for PID 32227 of (32223 32227) to complete...
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.284...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.08
- pass 1: epoch 2 of 3 starting distance error %20.06
- unfolding complete - removing small folds...
- starting distance error %19.96
- removing remaining folds...
- final distance error %19.99
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 246 negative triangles
- 223: dt=0.9900, 246 negative triangles
- 224: dt=0.9900, 141 negative triangles
- 225: dt=0.9900, 127 negative triangles
- 226: dt=0.9900, 103 negative triangles
- 227: dt=0.9900, 106 negative triangles
- 228: dt=0.9900, 95 negative triangles
- 229: dt=0.9900, 99 negative triangles
- 230: dt=0.9900, 92 negative triangles
- 231: dt=0.9900, 90 negative triangles
- 232: dt=0.9900, 82 negative triangles
- 233: dt=0.9900, 82 negative triangles
- 234: dt=0.9900, 72 negative triangles
- 235: dt=0.9900, 66 negative triangles
- 236: dt=0.9900, 56 negative triangles
- 237: dt=0.9900, 54 negative triangles
- 238: dt=0.9900, 60 negative triangles
- 239: dt=0.9900, 52 negative triangles
- 240: dt=0.9900, 50 negative triangles
- 241: dt=0.9900, 48 negative triangles
- 242: dt=0.9900, 45 negative triangles
- 243: dt=0.9900, 50 negative triangles
- 244: dt=0.9900, 41 negative triangles
- 245: dt=0.9900, 46 negative triangles
- 246: dt=0.9900, 41 negative triangles
- 247: dt=0.9900, 43 negative triangles
- 248: dt=0.9900, 38 negative triangles
- 249: dt=0.9900, 36 negative triangles
- 250: dt=0.9900, 42 negative triangles
- 251: dt=0.9900, 35 negative triangles
- 252: dt=0.9900, 37 negative triangles
- 253: dt=0.9900, 37 negative triangles
- 254: dt=0.9900, 38 negative triangles
- 255: dt=0.9900, 38 negative triangles
- 256: dt=0.9900, 38 negative triangles
- 257: dt=0.9900, 31 negative triangles
- 258: dt=0.9900, 35 negative triangles
- 259: dt=0.9900, 30 negative triangles
- 260: dt=0.9900, 30 negative triangles
- 261: dt=0.9900, 33 negative triangles
- 262: dt=0.9900, 29 negative triangles
- 263: dt=0.9900, 31 negative triangles
- 264: dt=0.9900, 30 negative triangles
- 265: dt=0.9900, 30 negative triangles
- 266: dt=0.9900, 31 negative triangles
- 267: dt=0.9900, 30 negative triangles
- 268: dt=0.9900, 35 negative triangles
- 269: dt=0.9900, 34 negative triangles
- 270: dt=0.9900, 32 negative triangles
- 271: dt=0.9900, 30 negative triangles
- 272: dt=0.9900, 27 negative triangles
- 273: dt=0.9900, 23 negative triangles
- 274: dt=0.9900, 27 negative triangles
- 275: dt=0.9900, 25 negative triangles
- 276: dt=0.9900, 23 negative triangles
- 277: dt=0.9900, 19 negative triangles
- 278: dt=0.9900, 24 negative triangles
- 279: dt=0.9900, 21 negative triangles
- 280: dt=0.9900, 23 negative triangles
- 281: dt=0.9900, 26 negative triangles
- 282: dt=0.9900, 29 negative triangles
- 283: dt=0.9900, 24 negative triangles
- 284: dt=0.9900, 24 negative triangles
- 285: dt=0.9900, 26 negative triangles
- 286: dt=0.9900, 23 negative triangles
- 287: dt=0.9405, 19 negative triangles
- 288: dt=0.9405, 26 negative triangles
- 289: dt=0.9405, 22 negative triangles
- 290: dt=0.9405, 18 negative triangles
- 291: dt=0.9405, 23 negative triangles
- 292: dt=0.9405, 19 negative triangles
- 293: dt=0.9405, 22 negative triangles
- 294: dt=0.9405, 18 negative triangles
- 295: dt=0.9405, 19 negative triangles
- 296: dt=0.9405, 18 negative triangles
- 297: dt=0.9405, 16 negative triangles
- 298: dt=0.9405, 16 negative triangles
- 299: dt=0.9405, 22 negative triangles
- 300: dt=0.9405, 15 negative triangles
- 301: dt=0.9405, 17 negative triangles
- 302: dt=0.9405, 15 negative triangles
- 303: dt=0.9405, 16 negative triangles
- 304: dt=0.9405, 16 negative triangles
- 305: dt=0.9405, 15 negative triangles
- 306: dt=0.9405, 16 negative triangles
- 307: dt=0.9405, 13 negative triangles
- 308: dt=0.9405, 13 negative triangles
- 309: dt=0.9405, 12 negative triangles
- 310: dt=0.9405, 11 negative triangles
- 311: dt=0.9405, 12 negative triangles
- 312: dt=0.9405, 13 negative triangles
- 313: dt=0.9405, 11 negative triangles
- 314: dt=0.9405, 5 negative triangles
- 315: dt=0.9405, 3 negative triangles
- 316: dt=0.9405, 3 negative triangles
- 317: dt=0.9405, 2 negative triangles
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.85 hours
- mris_sphere utimesec 3607.801530
- mris_sphere stimesec 1.276805
- mris_sphere ru_maxrss 287232
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 51070
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 9888
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 126441
- mris_sphere ru_nivcsw 193101
- FSRUNTIME@ mris_sphere 0.8493 hours 1 threads
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0.281...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %42.17
- pass 1: epoch 2 of 3 starting distance error %19.93
- unfolding complete - removing small folds...
- starting distance error %19.82
- removing remaining folds...
- final distance error %19.84
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 167 negative triangles
- 181: dt=0.9900, 167 negative triangles
- 182: dt=0.9900, 72 negative triangles
- 183: dt=0.9900, 41 negative triangles
- 184: dt=0.9900, 36 negative triangles
- 185: dt=0.9900, 23 negative triangles
- 186: dt=0.9900, 20 negative triangles
- 187: dt=0.9900, 13 negative triangles
- 188: dt=0.9900, 13 negative triangles
- 189: dt=0.9900, 7 negative triangles
- 190: dt=0.9900, 10 negative triangles
- 191: dt=0.9900, 11 negative triangles
- 192: dt=0.9900, 14 negative triangles
- 193: dt=0.9900, 8 negative triangles
- 194: dt=0.9900, 11 negative triangles
- 195: dt=0.9900, 7 negative triangles
- 196: dt=0.9900, 8 negative triangles
- 197: dt=0.9900, 7 negative triangles
- 198: dt=0.9900, 7 negative triangles
- 199: dt=0.9405, 8 negative triangles
- 200: dt=0.9405, 3 negative triangles
- 201: dt=0.9405, 5 negative triangles
- 202: dt=0.9405, 2 negative triangles
- 203: dt=0.9405, 2 negative triangles
- 204: dt=0.9405, 3 negative triangles
- 205: dt=0.9405, 1 negative triangles
- 206: dt=0.9405, 1 negative triangles
- 207: dt=0.9405, 3 negative triangles
- 208: dt=0.9405, 1 negative triangles
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.62 hours
- mris_sphere utimesec 2239.453551
- mris_sphere stimesec 0.701893
- mris_sphere ru_maxrss 276332
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 48838
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 9480
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 95779
- mris_sphere ru_nivcsw 181875
- FSRUNTIME@ mris_sphere 0.6217 hours 1 threads
- PIDs (32223 32227) completed and logs appended.
- #--------------------------------------------
- #@# Surf Reg lh Sun Oct 8 06:32:34 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 06:32:34 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 4567 of (4567 4570) to complete...
- Waiting for PID 4570 of (4567 4570) to complete...
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 = 5.741
- curvature mean = 0.034, std = 0.813
- curvature mean = 0.016, std = 0.868
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, 0.00, 16.00) sse = 208350.2, tmin=1.3781
- d=4.00 min @ (0.00, -1.00, -1.00) sse = 204749.0, tmin=7.1043
- d=2.00 min @ (-0.50, 0.00, 0.50) sse = 204262.0, tmin=8.5574
- d=1.00 min @ (0.00, 0.00, -0.25) sse = 204133.1, tmin=10.0303
- d=0.50 min @ (0.12, 0.12, 0.00) sse = 204074.8, tmin=11.5429
- 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 11.54 min
- curvature mean = 0.011, std = 0.831
- curvature mean = 0.004, std = 0.952
- curvature mean = 0.009, std = 0.842
- curvature mean = 0.002, std = 0.981
- curvature mean = 0.009, std = 0.845
- curvature mean = 0.000, std = 0.992
- 2 Reading smoothwm
- curvature mean = -0.035, std = 0.323
- curvature mean = 0.040, std = 0.250
- curvature mean = 0.062, std = 0.322
- curvature mean = 0.032, std = 0.309
- curvature mean = 0.044, std = 0.477
- curvature mean = 0.031, std = 0.335
- curvature mean = 0.026, std = 0.605
- curvature mean = 0.031, std = 0.346
- curvature mean = 0.011, std = 0.713
- MRISregister() return, current seed 0
- -01: dt=0.0000, 175 negative triangles
- 110: dt=0.9900, 175 negative triangles
- expanding nbhd size to 1
- 111: dt=0.9900, 217 negative triangles
- 112: dt=0.9900, 164 negative triangles
- 113: dt=0.9900, 155 negative triangles
- 114: dt=0.9900, 157 negative triangles
- 115: dt=0.9900, 136 negative triangles
- 116: dt=0.9900, 132 negative triangles
- 117: dt=0.9900, 116 negative triangles
- 118: dt=0.9900, 108 negative triangles
- 119: dt=0.9900, 97 negative triangles
- 120: dt=0.9900, 96 negative triangles
- 121: dt=0.9900, 90 negative triangles
- 122: dt=0.9900, 78 negative triangles
- 123: dt=0.9900, 74 negative triangles
- 124: dt=0.9900, 68 negative triangles
- 125: dt=0.9900, 66 negative triangles
- 126: dt=0.9900, 56 negative triangles
- 127: dt=0.9900, 55 negative triangles
- 128: dt=0.9900, 48 negative triangles
- 129: dt=0.9900, 50 negative triangles
- 130: dt=0.9900, 48 negative triangles
- 131: dt=0.9900, 39 negative triangles
- 132: dt=0.9900, 32 negative triangles
- 133: dt=0.9900, 31 negative triangles
- 134: dt=0.9900, 25 negative triangles
- 135: dt=0.9900, 25 negative triangles
- 136: dt=0.9900, 24 negative triangles
- 137: dt=0.9900, 24 negative triangles
- 138: dt=0.9900, 23 negative triangles
- 139: dt=0.9900, 16 negative triangles
- 140: dt=0.9900, 16 negative triangles
- 141: dt=0.9900, 14 negative triangles
- 142: dt=0.9900, 14 negative triangles
- 143: dt=0.9900, 15 negative triangles
- 144: dt=0.9900, 14 negative triangles
- 145: dt=0.9900, 15 negative triangles
- 146: dt=0.9900, 15 negative triangles
- 147: dt=0.9900, 14 negative triangles
- 148: dt=0.9900, 13 negative triangles
- 149: dt=0.9900, 11 negative triangles
- 150: dt=0.9900, 12 negative triangles
- 151: dt=0.9900, 13 negative triangles
- 152: dt=0.9900, 12 negative triangles
- 153: dt=0.9900, 13 negative triangles
- 154: dt=0.9900, 11 negative triangles
- 155: dt=0.9900, 11 negative triangles
- 156: dt=0.9900, 13 negative triangles
- 157: dt=0.9900, 12 negative triangles
- 158: dt=0.9900, 15 negative triangles
- 159: dt=0.9405, 12 negative triangles
- 160: dt=0.9405, 13 negative triangles
- 161: dt=0.9405, 10 negative triangles
- 162: dt=0.9405, 9 negative triangles
- 163: dt=0.9405, 10 negative triangles
- 164: dt=0.9405, 11 negative triangles
- 165: dt=0.9405, 9 negative triangles
- 166: dt=0.9405, 10 negative triangles
- 167: dt=0.9405, 9 negative triangles
- 168: dt=0.9405, 9 negative triangles
- 169: dt=0.9405, 8 negative triangles
- 170: dt=0.9405, 9 negative triangles
- 171: dt=0.9405, 7 negative triangles
- 172: dt=0.9405, 5 negative triangles
- 173: dt=0.9405, 7 negative triangles
- 174: dt=0.9405, 6 negative triangles
- 175: dt=0.9405, 6 negative triangles
- 176: dt=0.9405, 5 negative triangles
- 177: dt=0.9405, 4 negative triangles
- 178: dt=0.9405, 5 negative triangles
- 179: dt=0.9405, 3 negative triangles
- 180: dt=0.9405, 2 negative triangles
- 181: dt=0.9405, 2 negative triangles
- 182: dt=0.9405, 4 negative triangles
- 183: dt=0.9405, 3 negative triangles
- 184: dt=0.9405, 5 negative triangles
- 185: dt=0.9405, 3 negative triangles
- 186: dt=0.9405, 3 negative triangles
- 187: dt=0.9405, 2 negative triangles
- 188: dt=0.9405, 3 negative triangles
- 189: dt=0.9405, 2 negative triangles
- 190: dt=0.9405, 1 negative triangles
- 191: dt=0.9405, 2 negative triangles
- 192: dt=0.9405, 2 negative triangles
- 193: dt=0.9405, 1 negative triangles
- 194: dt=0.9405, 1 negative triangles
- 195: dt=0.9405, 1 negative triangles
- writing registered surface to ../surf/lh.sphere.reg...
- registration took 1.75 hours
- mris_register utimesec 7486.228920
- mris_register stimesec 4.156368
- mris_register ru_maxrss 260340
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 40061
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 9824
- mris_register ru_oublock 9904
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 249505
- mris_register ru_nivcsw 238128
- FSRUNTIME@ mris_register 1.7512 hours 1 threads
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 = 5.662
- curvature mean = 0.048, std = 0.810
- curvature mean = 0.017, std = 0.870
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, 0.00, 16.00) sse = 209260.5, tmin=1.0125
- d=16.00 min @ (0.00, 0.00, 4.00) sse = 195721.8, tmin=3.0906
- d=8.00 min @ (2.00, 0.00, -2.00) sse = 189023.2, tmin=4.1501
- d=4.00 min @ (-1.00, -1.00, 0.00) sse = 185219.5, tmin=5.2264
- d=2.00 min @ (0.00, 0.00, 0.50) sse = 184881.8, tmin=6.3124
- d=1.00 min @ (-0.25, 0.00, 0.00) sse = 184753.8, tmin=7.3896
- d=0.50 min @ (0.12, 0.12, -0.12) sse = 184675.5, tmin=8.4616
- 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 8.46 min
- curvature mean = 0.008, std = 0.828
- curvature mean = 0.005, std = 0.952
- curvature mean = 0.002, std = 0.837
- curvature mean = 0.002, std = 0.981
- curvature mean = 0.001, std = 0.840
- curvature mean = 0.000, std = 0.992
- 2 Reading smoothwm
- curvature mean = -0.033, std = 0.303
- curvature mean = 0.034, std = 0.246
- curvature mean = 0.062, std = 0.340
- curvature mean = 0.027, std = 0.305
- curvature mean = 0.041, std = 0.515
- curvature mean = 0.026, std = 0.332
- curvature mean = 0.024, std = 0.650
- curvature mean = 0.026, std = 0.344
- curvature mean = 0.009, std = 0.757
- MRISregister() return, current seed 0
- -01: dt=0.0000, 68 negative triangles
- 111: dt=0.9900, 68 negative triangles
- expanding nbhd size to 1
- 112: dt=0.9900, 95 negative triangles
- 113: dt=0.9900, 61 negative triangles
- 114: dt=0.9900, 59 negative triangles
- 115: dt=0.9900, 54 negative triangles
- 116: dt=0.9900, 50 negative triangles
- 117: dt=0.9900, 44 negative triangles
- 118: dt=0.9900, 35 negative triangles
- 119: dt=0.9900, 35 negative triangles
- 120: dt=0.9900, 29 negative triangles
- 121: dt=0.9900, 26 negative triangles
- 122: dt=0.9900, 19 negative triangles
- 123: dt=0.9900, 15 negative triangles
- 124: dt=0.9900, 13 negative triangles
- 125: dt=0.9900, 11 negative triangles
- 126: dt=0.9900, 8 negative triangles
- 127: dt=0.9900, 7 negative triangles
- 128: dt=0.9900, 9 negative triangles
- 129: dt=0.9900, 8 negative triangles
- 130: dt=0.9900, 5 negative triangles
- 131: dt=0.9900, 4 negative triangles
- 132: dt=0.9900, 5 negative triangles
- 133: dt=0.9900, 2 negative triangles
- 134: dt=0.9900, 1 negative triangles
- 135: dt=0.9900, 2 negative triangles
- 136: dt=0.9900, 2 negative triangles
- 137: dt=0.9900, 2 negative triangles
- writing registered surface to ../surf/rh.sphere.reg...
- registration took 1.00 hours
- mris_register utimesec 3568.088568
- mris_register stimesec 1.454778
- mris_register ru_maxrss 250396
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 39545
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 9528
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 269310
- mris_register ru_nivcsw 179176
- FSRUNTIME@ mris_register 1.0021 hours 1 threads
- PIDs (4567 4570) completed and logs appended.
- #--------------------------------------------
- #@# Jacobian white lh Sun Oct 8 08:17:38 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# Jacobian white rh Sun Oct 8 08:17:38 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- Waiting for PID 8894 of (8894 8897) to complete...
- Waiting for PID 8897 of (8894 8897) 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 (8894 8897) completed and logs appended.
- #--------------------------------------------
- #@# AvgCurv lh Sun Oct 8 08:17:41 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 08:17:41 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 8939 of (8939 8942) to complete...
- Waiting for PID 8942 of (8939 8942) 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 (8939 8942) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc lh Sun Oct 8 08:17:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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 08:17:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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 8983 of (8983 8986) to complete...
- Waiting for PID 8986 of (8983 8986) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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...
- 1340 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3041 changed, 139556 examined...
- 001: 744 changed, 12946 examined...
- 002: 196 changed, 4179 examined...
- 003: 64 changed, 1190 examined...
- 004: 18 changed, 377 examined...
- 005: 11 changed, 110 examined...
- 006: 8 changed, 66 examined...
- 007: 3 changed, 43 examined...
- 008: 1 changed, 24 examined...
- 009: 0 changed, 5 examined...
- 210 labels changed using aseg
- 000: 119 total segments, 73 labels (243 vertices) changed
- 001: 44 total segments, 1 labels (2 vertices) changed
- 002: 43 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...
- 2091 vertices marked for relabeling...
- 2091 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 18 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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...
- 1218 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2678 changed, 134102 examined...
- 001: 610 changed, 11513 examined...
- 002: 110 changed, 3347 examined...
- 003: 28 changed, 637 examined...
- 004: 6 changed, 166 examined...
- 005: 1 changed, 33 examined...
- 006: 1 changed, 7 examined...
- 007: 1 changed, 7 examined...
- 008: 0 changed, 9 examined...
- 139 labels changed using aseg
- 000: 78 total segments, 41 labels (182 vertices) changed
- 001: 38 total segments, 1 labels (1 vertices) changed
- 002: 37 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 5 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1200 vertices marked for relabeling...
- 1200 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 16 seconds.
- PIDs (8983 8986) completed and logs appended.
- #--------------------------------------------
- #@# Make Pial Surf lh Sun Oct 8 08:18:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050379 lh
- #--------------------------------------------
- #@# Make Pial Surf rh Sun Oct 8 08:18:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050379 rh
- Waiting for PID 9038 of (9038 9041) to complete...
- Waiting for PID 9041 of (9038 9041) to complete...
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050379 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-6.0.0/0050379/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- 13789 bright wm thresholded.
- 1867 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.orig...
- computing class statistics...
- border white: 257994 voxels (1.54%)
- border gray 306351 voxels (1.83%)
- WM (95.0): 96.1 +- 8.3 [70.0 --> 110.0]
- GM (72.0) : 70.8 +- 10.5 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 57.5 (was 70)
- setting MAX_BORDER_WHITE to 108.3 (was 105)
- setting MIN_BORDER_WHITE to 68.0 (was 85)
- setting MAX_CSF to 47.1 (was 40)
- setting MAX_GRAY to 91.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 57.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 36.6 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=100+-6.1, GM=68+-7.8
- mean inside = 92.0, mean outside = 74.9
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.26 (0.03-->4.52) (max @ vno 31803 --> 33492)
- face area 0.33 +- 0.16 (0.00-->3.91)
- mean absolute distance = 0.59 +- 0.86
- 3681 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 2 with 253 points - only 0.00% unknown
- deleting segment 3 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- deleting segment 5 with 6 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 points - only 0.00% unknown
- mean border=79.7, 198 (198) missing vertices, mean dist 0.3 [0.7 (%18.5)->0.6 (%81.5))]
- %66 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.09-->4.48) (max @ vno 31803 --> 33492)
- face area 0.33 +- 0.17 (0.00-->3.72)
- mean absolute distance = 0.37 +- 0.61
- 4534 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1892116.6, rms=6.738
- 001: dt: 0.5000, sse=1159656.8, rms=4.242 (37.047%)
- 002: dt: 0.5000, sse=953775.7, rms=3.247 (23.439%)
- 003: dt: 0.5000, sse=928053.1, rms=3.078 (5.224%)
- 004: dt: 0.5000, sse=901396.6, rms=2.918 (5.201%)
- rms = 3.01, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.2500, sse=809162.5, rms=2.184 (25.158%)
- 006: dt: 0.2500, sse=767148.6, rms=1.822 (16.553%)
- 007: dt: 0.2500, sse=758090.8, rms=1.717 (5.796%)
- rms = 1.68, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=752905.6, rms=1.676 (2.348%)
- rms = 1.63, time step reduction 3 of 3 to 0.062...
- 009: dt: 0.1250, sse=748765.3, rms=1.629 (2.835%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 1 with 154 points - only 0.00% unknown
- deleting segment 2 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- mean border=82.6, 157 (61) missing vertices, mean dist -0.2 [0.4 (%71.1)->0.2 (%28.9))]
- %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.26 (0.08-->4.39) (max @ vno 31803 --> 33492)
- face area 0.35 +- 0.17 (0.00-->4.04)
- mean absolute distance = 0.28 +- 0.44
- 3694 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1177693.6, rms=4.165
- 010: dt: 0.5000, sse=915457.4, rms=2.711 (34.905%)
- 011: dt: 0.5000, sse=889674.9, rms=2.579 (4.876%)
- rms = 2.66, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.2500, sse=822022.6, rms=1.930 (25.180%)
- 013: dt: 0.2500, sse=792673.0, rms=1.560 (19.152%)
- 014: dt: 0.2500, sse=773930.6, rms=1.468 (5.925%)
- 015: dt: 0.2500, sse=771677.2, rms=1.417 (3.445%)
- rms = 1.39, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=772133.4, rms=1.393 (1.685%)
- rms = 1.36, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=766551.3, rms=1.365 (2.031%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 171 points - only 0.00% unknown
- deleting segment 1 with 9 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- mean border=84.1, 177 (37) missing vertices, mean dist -0.1 [0.3 (%63.2)->0.2 (%36.8))]
- %82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.26 (0.05-->4.35) (max @ vno 31803 --> 33492)
- face area 0.34 +- 0.17 (0.00-->3.94)
- mean absolute distance = 0.26 +- 0.38
- 3750 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=866799.8, rms=2.532
- 018: dt: 0.5000, sse=825800.8, rms=2.108 (16.739%)
- rms = 2.29, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=764385.6, rms=1.580 (25.049%)
- 020: dt: 0.2500, sse=747645.5, rms=1.355 (14.230%)
- 021: dt: 0.2500, sse=741047.4, rms=1.294 (4.498%)
- rms = 1.30, time step reduction 2 of 3 to 0.125...
- rms = 1.27, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=738159.1, rms=1.273 (1.661%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 194 points - only 0.00% unknown
- deleting segment 1 with 9 points - only 0.00% unknown
- deleting segment 2 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- mean border=84.7, 189 (27) missing vertices, mean dist -0.0 [0.3 (%54.3)->0.2 (%45.7))]
- %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=756122.4, rms=1.595
- 023: dt: 0.5000, sse=756980.3, rms=1.528 (4.218%)
- rms = 2.04, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=723397.0, rms=1.125 (26.374%)
- rms = 1.09, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.2500, sse=721350.4, rms=1.090 (3.127%)
- 026: dt: 0.1250, sse=713544.7, rms=1.000 (8.181%)
- rms = 0.98, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=711490.8, rms=0.978 (2.286%)
- positioning took 0.7 minutes
- generating cortex label...
- 13 non-cortical segments detected
- only using segment with 7536 vertices
- erasing segment 1 (vno[0] = 71833)
- erasing segment 2 (vno[0] = 79115)
- erasing segment 3 (vno[0] = 80055)
- erasing segment 4 (vno[0] = 90107)
- erasing segment 5 (vno[0] = 92323)
- erasing segment 6 (vno[0] = 93399)
- erasing segment 7 (vno[0] = 94392)
- erasing segment 8 (vno[0] = 94499)
- erasing segment 9 (vno[0] = 96588)
- erasing segment 10 (vno[0] = 96636)
- erasing segment 11 (vno[0] = 99885)
- erasing segment 12 (vno[0] = 103199)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.area
- vertex spacing 0.89 +- 0.27 (0.03-->4.35) (max @ vno 104927 --> 105742)
- face area 0.34 +- 0.17 (0.00-->3.94)
- 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...
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=55.9, 190 (190) missing vertices, mean dist 1.7 [0.0 (%0.0)->3.0 (%100.0))]
- %14 local maxima, %41 large gradients and %41 min vals, 618 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=24012870.0, rms=29.560
- 001: dt: 0.0500, sse=21387002.0, rms=27.848 (5.794%)
- 002: dt: 0.0500, sse=19496878.0, rms=26.547 (4.673%)
- 003: dt: 0.0500, sse=18041114.0, rms=25.499 (3.946%)
- 004: dt: 0.0500, sse=16854380.0, rms=24.612 (3.479%)
- 005: dt: 0.0500, sse=15846712.0, rms=23.833 (3.166%)
- 006: dt: 0.0500, sse=14968497.0, rms=23.132 (2.940%)
- 007: dt: 0.0500, sse=14186521.0, rms=22.490 (2.777%)
- 008: dt: 0.0500, sse=13480710.0, rms=21.894 (2.650%)
- 009: dt: 0.0500, sse=12836706.0, rms=21.335 (2.550%)
- 010: dt: 0.0500, sse=12243555.0, rms=20.808 (2.473%)
- positioning took 1.2 minutes
- mean border=55.7, 164 (106) missing vertices, mean dist 1.5 [0.3 (%0.0)->2.5 (%100.0))]
- %15 local maxima, %41 large gradients and %40 min vals, 553 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=13021916.0, rms=21.496
- 011: dt: 0.0500, sse=12468076.0, rms=21.007 (2.271%)
- 012: dt: 0.0500, sse=11953535.0, rms=20.543 (2.209%)
- 013: dt: 0.0500, sse=11473242.0, rms=20.100 (2.156%)
- 014: dt: 0.0500, sse=11025023.0, rms=19.678 (2.101%)
- 015: dt: 0.0500, sse=10606348.0, rms=19.275 (2.048%)
- 016: dt: 0.0500, sse=10215018.0, rms=18.891 (1.995%)
- 017: dt: 0.0500, sse=9849129.0, rms=18.524 (1.942%)
- 018: dt: 0.0500, sse=9507704.0, rms=18.175 (1.884%)
- 019: dt: 0.0500, sse=9188060.0, rms=17.842 (1.833%)
- 020: dt: 0.0500, sse=8889007.0, rms=17.524 (1.779%)
- positioning took 1.1 minutes
- mean border=55.5, 190 (89) missing vertices, mean dist 1.3 [0.1 (%1.4)->2.2 (%98.6))]
- %16 local maxima, %41 large gradients and %39 min vals, 556 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=9018310.0, rms=17.667
- 021: dt: 0.0500, sse=8729181.0, rms=17.357 (1.754%)
- 022: dt: 0.0500, sse=8459232.0, rms=17.063 (1.697%)
- 023: dt: 0.0500, sse=8204582.0, rms=16.780 (1.657%)
- 024: dt: 0.0500, sse=7966672.0, rms=16.512 (1.600%)
- 025: dt: 0.0500, sse=7744117.5, rms=16.256 (1.546%)
- 026: dt: 0.0500, sse=7535271.5, rms=16.013 (1.497%)
- 027: dt: 0.0500, sse=7338710.5, rms=15.780 (1.452%)
- 028: dt: 0.0500, sse=7151757.5, rms=15.556 (1.423%)
- 029: dt: 0.0500, sse=6973089.0, rms=15.338 (1.400%)
- 030: dt: 0.0500, sse=6802460.0, rms=15.127 (1.375%)
- positioning took 1.1 minutes
- mean border=55.5, 224 (77) missing vertices, mean dist 1.1 [0.1 (%10.1)->2.0 (%89.9))]
- %16 local maxima, %41 large gradients and %39 min vals, 507 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=6893520.5, rms=15.238
- 031: dt: 0.5000, sse=5693941.0, rms=13.678 (10.240%)
- 032: dt: 0.5000, sse=4861738.5, rms=12.473 (8.813%)
- 033: dt: 0.5000, sse=4218312.5, rms=11.455 (8.156%)
- 034: dt: 0.5000, sse=3726032.0, rms=10.604 (7.433%)
- 035: dt: 0.5000, sse=3319786.5, rms=9.847 (7.134%)
- 036: dt: 0.5000, sse=2993970.2, rms=9.192 (6.653%)
- 037: dt: 0.5000, sse=2703102.0, rms=8.569 (6.781%)
- 038: dt: 0.5000, sse=2452592.0, rms=7.992 (6.733%)
- 039: dt: 0.5000, sse=2226645.2, rms=7.437 (6.946%)
- 040: dt: 0.5000, sse=2053213.1, rms=6.978 (6.173%)
- 041: dt: 0.5000, sse=1910410.8, rms=6.579 (5.713%)
- 042: dt: 0.5000, sse=1812007.2, rms=6.287 (4.437%)
- 043: dt: 0.5000, sse=1735909.0, rms=6.054 (3.713%)
- 044: dt: 0.5000, sse=1686763.1, rms=5.896 (2.615%)
- 045: dt: 0.5000, sse=1642424.4, rms=5.753 (2.422%)
- 046: dt: 0.5000, sse=1618365.9, rms=5.671 (1.428%)
- 047: dt: 0.5000, sse=1589525.9, rms=5.575 (1.695%)
- rms = 5.53, time step reduction 1 of 3 to 0.250...
- 048: dt: 0.5000, sse=1578460.9, rms=5.535 (0.716%)
- 049: dt: 0.2500, sse=1468123.9, rms=5.104 (7.772%)
- 050: dt: 0.2500, sse=1438087.4, rms=4.991 (2.226%)
- rms = 4.97, time step reduction 2 of 3 to 0.125...
- 051: dt: 0.2500, sse=1433906.0, rms=4.973 (0.367%)
- 052: dt: 0.1250, sse=1407850.4, rms=4.867 (2.127%)
- rms = 4.85, time step reduction 3 of 3 to 0.062...
- 053: dt: 0.1250, sse=1403049.0, rms=4.848 (0.386%)
- positioning took 3.5 minutes
- mean border=54.3, 2438 (40) missing vertices, mean dist 0.2 [0.2 (%44.3)->0.6 (%55.7))]
- %27 local maxima, %33 large gradients and %34 min vals, 294 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=1712197.2, rms=5.196
- 054: dt: 0.5000, sse=1626663.9, rms=4.886 (5.976%)
- 055: dt: 0.5000, sse=1556541.5, rms=4.639 (5.047%)
- rms = 4.76, time step reduction 1 of 3 to 0.250...
- 056: dt: 0.2500, sse=1449597.8, rms=4.141 (10.751%)
- 057: dt: 0.2500, sse=1424578.4, rms=4.009 (3.186%)
- rms = 4.00, time step reduction 2 of 3 to 0.125...
- 058: dt: 0.2500, sse=1422994.4, rms=4.002 (0.173%)
- 059: dt: 0.1250, sse=1389236.1, rms=3.829 (4.304%)
- rms = 3.80, time step reduction 3 of 3 to 0.062...
- 060: dt: 0.1250, sse=1382715.1, rms=3.797 (0.834%)
- positioning took 1.4 minutes
- mean border=53.6, 2794 (31) missing vertices, mean dist 0.1 [0.2 (%47.1)->0.5 (%52.9))]
- %34 local maxima, %26 large gradients and %33 min vals, 361 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=1432098.2, rms=4.009
- rms = 4.40, time step reduction 1 of 3 to 0.250...
- 061: dt: 0.2500, sse=1404259.1, rms=3.870 (3.453%)
- rms = 3.84, time step reduction 2 of 3 to 0.125...
- 062: dt: 0.2500, sse=1396138.8, rms=3.837 (0.860%)
- 063: dt: 0.1250, sse=1384091.8, rms=3.774 (1.651%)
- rms = 3.74, time step reduction 3 of 3 to 0.062...
- 064: dt: 0.1250, sse=1376836.8, rms=3.741 (0.862%)
- positioning took 0.9 minutes
- mean border=53.1, 5702 (30) missing vertices, mean dist 0.1 [0.2 (%47.5)->0.4 (%52.5))]
- %38 local maxima, %22 large gradients and %32 min vals, 363 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-6.0.0/0050379/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1398571.8, rms=3.836
- rms = 4.07, time step reduction 1 of 3 to 0.250...
- 065: dt: 0.2500, sse=1378906.2, rms=3.739 (2.541%)
- 066: dt: 0.2500, sse=1362413.0, rms=3.674 (1.729%)
- rms = 3.67, time step reduction 2 of 3 to 0.125...
- 067: dt: 0.2500, sse=1359568.0, rms=3.671 (0.080%)
- 068: dt: 0.1250, sse=1336332.9, rms=3.547 (3.389%)
- rms = 3.51, time step reduction 3 of 3 to 0.062...
- 069: dt: 0.1250, sse=1328802.1, rms=3.512 (0.971%)
- positioning took 1.1 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.area.pial
- vertex spacing 1.04 +- 0.48 (0.04-->8.64) (max @ vno 94413 --> 93292)
- face area 0.42 +- 0.36 (0.00-->7.81)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 139556 vertices processed
- 25000 of 139556 vertices processed
- 50000 of 139556 vertices processed
- 75000 of 139556 vertices processed
- 100000 of 139556 vertices processed
- 125000 of 139556 vertices processed
- 0 of 139556 vertices processed
- 25000 of 139556 vertices processed
- 50000 of 139556 vertices processed
- 75000 of 139556 vertices processed
- 100000 of 139556 vertices processed
- 125000 of 139556 vertices processed
- thickness calculation complete, 572:2381 truncations.
- 27898 vertices at 0 distance
- 87857 vertices at 1 distance
- 85199 vertices at 2 distance
- 41958 vertices at 3 distance
- 15524 vertices at 4 distance
- 5334 vertices at 5 distance
- 1936 vertices at 6 distance
- 823 vertices at 7 distance
- 312 vertices at 8 distance
- 181 vertices at 9 distance
- 115 vertices at 10 distance
- 83 vertices at 11 distance
- 58 vertices at 12 distance
- 41 vertices at 13 distance
- 24 vertices at 14 distance
- 19 vertices at 15 distance
- 17 vertices at 16 distance
- 26 vertices at 17 distance
- 20 vertices at 18 distance
- 19 vertices at 19 distance
- 6 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.thickness
- positioning took 18.5 minutes
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050379 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-6.0.0/0050379/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- 13789 bright wm thresholded.
- 1867 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.orig...
- computing class statistics...
- border white: 257994 voxels (1.54%)
- border gray 306351 voxels (1.83%)
- WM (95.0): 96.1 +- 8.3 [70.0 --> 110.0]
- GM (72.0) : 70.8 +- 10.5 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 56.5 (was 70)
- setting MAX_BORDER_WHITE to 108.3 (was 105)
- setting MIN_BORDER_WHITE to 67.0 (was 85)
- setting MAX_CSF to 46.1 (was 40)
- setting MAX_GRAY to 91.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 56.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 35.6 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=100+-7.0, GM=67+-7.8
- mean inside = 91.8, mean outside = 75.0
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.26 (0.03-->4.76) (max @ vno 0 --> 510)
- face area 0.34 +- 0.16 (0.00-->6.14)
- mean absolute distance = 0.60 +- 0.85
- 3457 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- deleting segment 2 with 289 points - only 0.00% unknown
- deleting segment 3 with 27 points - only 0.00% unknown
- mean border=79.1, 118 (118) missing vertices, mean dist 0.4 [0.6 (%18.1)->0.6 (%81.9))]
- %67 local maxima, %29 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 +- 0.27 (0.07-->4.77) (max @ vno 0 --> 510)
- face area 0.34 +- 0.17 (0.00-->5.80)
- mean absolute distance = 0.38 +- 0.61
- 4002 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1942208.1, rms=7.092
- 001: dt: 0.5000, sse=1159290.1, rms=4.452 (37.225%)
- 002: dt: 0.5000, sse=931604.8, rms=3.330 (25.210%)
- 003: dt: 0.5000, sse=888057.0, rms=3.078 (7.543%)
- 004: dt: 0.5000, sse=857265.6, rms=2.898 (5.849%)
- rms = 2.96, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.2500, sse=771473.7, rms=2.183 (24.668%)
- 006: dt: 0.2500, sse=737912.8, rms=1.822 (16.561%)
- 007: dt: 0.2500, sse=730448.9, rms=1.731 (5.009%)
- rms = 1.69, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=726967.1, rms=1.686 (2.559%)
- rms = 1.64, time step reduction 3 of 3 to 0.062...
- 009: dt: 0.1250, sse=723615.2, rms=1.642 (2.645%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 2 with 162 points - only 0.00% unknown
- deleting segment 3 with 23 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- mean border=82.0, 117 (43) missing vertices, mean dist -0.2 [0.4 (%71.1)->0.3 (%28.9))]
- %77 local maxima, %19 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 +- 0.26 (0.07-->4.70) (max @ vno 0 --> 510)
- face area 0.36 +- 0.18 (0.00-->6.29)
- mean absolute distance = 0.29 +- 0.45
- 3808 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1148645.6, rms=4.217
- 010: dt: 0.5000, sse=881778.1, rms=2.708 (35.779%)
- 011: dt: 0.5000, sse=855777.2, rms=2.563 (5.372%)
- rms = 2.62, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.2500, sse=784733.0, rms=1.915 (25.271%)
- 013: dt: 0.2500, sse=753383.3, rms=1.523 (20.448%)
- 014: dt: 0.2500, sse=745216.4, rms=1.440 (5.485%)
- 015: dt: 0.2500, sse=741767.6, rms=1.387 (3.667%)
- rms = 1.38, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=743102.4, rms=1.382 (0.373%)
- rms = 1.34, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=738581.8, rms=1.340 (3.009%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 2 with 131 points - only 0.00% unknown
- deleting segment 3 with 25 points - only 0.00% unknown
- deleting segment 4 with 23 points - only 0.00% unknown
- deleting segment 5 with 15 points - only 0.00% unknown
- mean border=83.7, 136 (33) missing vertices, mean dist -0.1 [0.3 (%64.3)->0.2 (%35.7))]
- %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.26 (0.02-->4.67) (max @ vno 0 --> 510)
- face area 0.34 +- 0.17 (0.00-->6.28)
- mean absolute distance = 0.26 +- 0.39
- 3738 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=861868.2, rms=2.731
- 018: dt: 0.5000, sse=799612.2, rms=2.143 (21.546%)
- rms = 2.30, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=739445.4, rms=1.597 (25.481%)
- 020: dt: 0.2500, sse=721087.8, rms=1.346 (15.721%)
- 021: dt: 0.2500, sse=715228.3, rms=1.275 (5.291%)
- rms = 1.28, time step reduction 2 of 3 to 0.125...
- rms = 1.25, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=712309.1, rms=1.254 (1.630%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 2 with 133 points - only 0.00% unknown
- deleting segment 3 with 25 points - only 0.00% unknown
- deleting segment 4 with 7 points - only 0.00% unknown
- deleting segment 5 with 40 points - only 0.00% unknown
- mean border=84.3, 146 (25) missing vertices, mean dist -0.0 [0.3 (%54.5)->0.2 (%45.5))]
- %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=729317.2, rms=1.592
- 023: dt: 0.5000, sse=732669.9, rms=1.538 (3.392%)
- rms = 2.06, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=696382.9, rms=1.115 (27.490%)
- rms = 1.08, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.2500, sse=693476.6, rms=1.076 (3.513%)
- 026: dt: 0.1250, sse=686686.9, rms=0.981 (8.863%)
- rms = 0.96, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=685124.5, rms=0.958 (2.335%)
- positioning took 0.6 minutes
- generating cortex label...
- 11 non-cortical segments detected
- only using segment with 7324 vertices
- erasing segment 1 (vno[0] = 50541)
- erasing segment 2 (vno[0] = 61732)
- erasing segment 3 (vno[0] = 81617)
- erasing segment 4 (vno[0] = 89699)
- erasing segment 5 (vno[0] = 93466)
- erasing segment 6 (vno[0] = 93577)
- erasing segment 7 (vno[0] = 95333)
- erasing segment 8 (vno[0] = 99648)
- erasing segment 9 (vno[0] = 99677)
- erasing segment 10 (vno[0] = 100474)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.area
- vertex spacing 0.90 +- 0.26 (0.03-->4.57) (max @ vno 0 --> 510)
- face area 0.34 +- 0.17 (0.00-->6.20)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=55.1, 101 (101) missing vertices, mean dist 1.7 [3.4 (%0.0)->3.0 (%100.0))]
- %14 local maxima, %40 large gradients and %42 min vals, 396 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=23504874.0, rms=29.862
- 001: dt: 0.0500, sse=20975884.0, rms=28.162 (5.695%)
- 002: dt: 0.0500, sse=19151706.0, rms=26.868 (4.594%)
- 003: dt: 0.0500, sse=17742918.0, rms=25.824 (3.884%)
- 004: dt: 0.0500, sse=16595687.0, rms=24.942 (3.416%)
- 005: dt: 0.0500, sse=15621949.0, rms=24.168 (3.104%)
- 006: dt: 0.0500, sse=14772484.0, rms=23.472 (2.881%)
- 007: dt: 0.0500, sse=14016647.0, rms=22.835 (2.716%)
- 008: dt: 0.0500, sse=13333511.0, rms=22.243 (2.592%)
- 009: dt: 0.0500, sse=12709535.0, rms=21.688 (2.494%)
- 010: dt: 0.0500, sse=12135057.0, rms=21.164 (2.415%)
- positioning took 0.9 minutes
- mean border=55.0, 107 (60) missing vertices, mean dist 1.4 [0.7 (%0.0)->2.5 (%100.0))]
- %15 local maxima, %40 large gradients and %41 min vals, 377 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=12943855.0, rms=21.899
- 011: dt: 0.0500, sse=12406274.0, rms=21.414 (2.214%)
- 012: dt: 0.0500, sse=11906169.0, rms=20.953 (2.153%)
- 013: dt: 0.0500, sse=11439157.0, rms=20.513 (2.100%)
- 014: dt: 0.0500, sse=11002482.0, rms=20.093 (2.048%)
- 015: dt: 0.0500, sse=10594199.0, rms=19.692 (1.996%)
- 016: dt: 0.0500, sse=10212069.0, rms=19.309 (1.945%)
- 017: dt: 0.0500, sse=9853800.0, rms=18.943 (1.897%)
- 018: dt: 0.0500, sse=9518206.0, rms=18.593 (1.846%)
- 019: dt: 0.0500, sse=9203571.0, rms=18.259 (1.796%)
- 020: dt: 0.0500, sse=8908396.0, rms=17.940 (1.747%)
- positioning took 0.9 minutes
- mean border=54.8, 106 (40) missing vertices, mean dist 1.3 [0.1 (%1.1)->2.2 (%98.9))]
- %15 local maxima, %40 large gradients and %40 min vals, 392 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=9026750.0, rms=18.073
- 021: dt: 0.0500, sse=8741746.0, rms=17.762 (1.722%)
- 022: dt: 0.0500, sse=8475056.0, rms=17.466 (1.668%)
- 023: dt: 0.0500, sse=8223042.5, rms=17.181 (1.631%)
- 024: dt: 0.0500, sse=7987286.5, rms=16.910 (1.577%)
- 025: dt: 0.0500, sse=7766129.0, rms=16.652 (1.527%)
- 026: dt: 0.0500, sse=7558715.5, rms=16.406 (1.477%)
- 027: dt: 0.0500, sse=7362999.5, rms=16.170 (1.436%)
- 028: dt: 0.0500, sse=7176622.0, rms=15.943 (1.408%)
- 029: dt: 0.0500, sse=6998883.0, rms=15.722 (1.382%)
- 030: dt: 0.0500, sse=6829490.0, rms=15.509 (1.354%)
- positioning took 0.9 minutes
- mean border=54.7, 138 (37) missing vertices, mean dist 1.1 [0.1 (%8.4)->2.0 (%91.6))]
- %16 local maxima, %40 large gradients and %40 min vals, 371 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=6923725.0, rms=15.628
- 031: dt: 0.5000, sse=5725537.5, rms=14.044 (10.133%)
- 032: dt: 0.5000, sse=4894683.5, rms=12.824 (8.688%)
- 033: dt: 0.5000, sse=4248522.0, rms=11.790 (8.066%)
- 034: dt: 0.5000, sse=3752392.5, rms=10.922 (7.364%)
- 035: dt: 0.5000, sse=3341736.2, rms=10.150 (7.065%)
- 036: dt: 0.5000, sse=3008242.5, rms=9.473 (6.672%)
- 037: dt: 0.5000, sse=2701536.0, rms=8.810 (6.998%)
- 038: dt: 0.5000, sse=2448640.0, rms=8.219 (6.703%)
- 039: dt: 0.5000, sse=2224128.5, rms=7.662 (6.778%)
- 040: dt: 0.5000, sse=2052942.8, rms=7.204 (5.980%)
- 041: dt: 0.5000, sse=1912189.9, rms=6.808 (5.501%)
- 042: dt: 0.5000, sse=1814786.9, rms=6.516 (4.285%)
- 043: dt: 0.5000, sse=1735299.8, rms=6.272 (3.747%)
- 044: dt: 0.5000, sse=1681198.4, rms=6.096 (2.807%)
- 045: dt: 0.5000, sse=1635814.2, rms=5.948 (2.429%)
- 046: dt: 0.5000, sse=1607021.2, rms=5.848 (1.671%)
- 047: dt: 0.5000, sse=1582368.2, rms=5.766 (1.409%)
- rms = 5.72, time step reduction 1 of 3 to 0.250...
- 048: dt: 0.5000, sse=1568538.5, rms=5.716 (0.858%)
- 049: dt: 0.2500, sse=1458247.4, rms=5.283 (7.581%)
- 050: dt: 0.2500, sse=1425238.8, rms=5.158 (2.358%)
- rms = 5.16, time step reduction 2 of 3 to 0.125...
- 051: dt: 0.2500, sse=1426123.0, rms=5.158 (0.001%)
- 052: dt: 0.1250, sse=1399833.6, rms=5.052 (2.064%)
- rms = 5.03, time step reduction 3 of 3 to 0.062...
- 053: dt: 0.1250, sse=1394678.6, rms=5.032 (0.400%)
- positioning took 2.9 minutes
- mean border=53.4, 2463 (23) missing vertices, mean dist 0.2 [0.2 (%42.4)->0.7 (%57.6))]
- %27 local maxima, %31 large gradients and %35 min vals, 187 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=1706583.2, rms=5.414
- 054: dt: 0.5000, sse=1621995.9, rms=5.111 (5.589%)
- 055: dt: 0.5000, sse=1542488.2, rms=4.828 (5.553%)
- rms = 4.98, time step reduction 1 of 3 to 0.250...
- 056: dt: 0.2500, sse=1429752.6, rms=4.303 (10.858%)
- 057: dt: 0.2500, sse=1404731.4, rms=4.171 (3.067%)
- rms = 4.17, time step reduction 2 of 3 to 0.125...
- 058: dt: 0.2500, sse=1403851.8, rms=4.168 (0.094%)
- 059: dt: 0.1250, sse=1367062.6, rms=3.980 (4.503%)
- rms = 3.94, time step reduction 3 of 3 to 0.062...
- 060: dt: 0.1250, sse=1359464.4, rms=3.943 (0.925%)
- positioning took 1.2 minutes
- mean border=52.7, 2797 (23) missing vertices, mean dist 0.1 [0.2 (%44.0)->0.5 (%56.0))]
- %34 local maxima, %24 large gradients and %35 min vals, 233 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=1415930.2, rms=4.183
- rms = 4.63, time step reduction 1 of 3 to 0.250...
- 061: dt: 0.2500, sse=1382239.0, rms=4.016 (3.974%)
- rms = 3.98, time step reduction 2 of 3 to 0.125...
- 062: dt: 0.2500, sse=1373862.2, rms=3.983 (0.836%)
- 063: dt: 0.1250, sse=1360059.0, rms=3.910 (1.816%)
- rms = 3.88, time step reduction 3 of 3 to 0.062...
- 064: dt: 0.1250, sse=1353873.2, rms=3.883 (0.696%)
- positioning took 0.8 minutes
- mean border=52.1, 5885 (23) missing vertices, mean dist 0.1 [0.2 (%45.9)->0.4 (%54.1))]
- %37 local maxima, %21 large gradients and %33 min vals, 256 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-6.0.0/0050379/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=1370921.6, rms=3.956
- rms = 4.27, time step reduction 1 of 3 to 0.250...
- 065: dt: 0.2500, sse=1350947.8, rms=3.856 (2.518%)
- 066: dt: 0.2500, sse=1335024.1, rms=3.796 (1.574%)
- rms = 3.79, time step reduction 2 of 3 to 0.125...
- 067: dt: 0.2500, sse=1332079.9, rms=3.794 (0.045%)
- 068: dt: 0.1250, sse=1307466.1, rms=3.660 (3.520%)
- rms = 3.62, time step reduction 3 of 3 to 0.062...
- 069: dt: 0.1250, sse=1299899.8, rms=3.625 (0.980%)
- positioning took 1.0 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.area.pial
- vertex spacing 1.04 +- 0.48 (0.08-->7.86) (max @ vno 87809 --> 86815)
- face area 0.43 +- 0.37 (0.00-->9.40)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 134102 vertices processed
- 25000 of 134102 vertices processed
- 50000 of 134102 vertices processed
- 75000 of 134102 vertices processed
- 100000 of 134102 vertices processed
- 125000 of 134102 vertices processed
- 0 of 134102 vertices processed
- 25000 of 134102 vertices processed
- 50000 of 134102 vertices processed
- 75000 of 134102 vertices processed
- 100000 of 134102 vertices processed
- 125000 of 134102 vertices processed
- thickness calculation complete, 718:2206 truncations.
- 27042 vertices at 0 distance
- 83683 vertices at 1 distance
- 81607 vertices at 2 distance
- 40368 vertices at 3 distance
- 14876 vertices at 4 distance
- 5199 vertices at 5 distance
- 1941 vertices at 6 distance
- 753 vertices at 7 distance
- 361 vertices at 8 distance
- 185 vertices at 9 distance
- 107 vertices at 10 distance
- 89 vertices at 11 distance
- 64 vertices at 12 distance
- 45 vertices at 13 distance
- 48 vertices at 14 distance
- 37 vertices at 15 distance
- 16 vertices at 16 distance
- 10 vertices at 17 distance
- 9 vertices at 18 distance
- 16 vertices at 19 distance
- 16 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.thickness
- positioning took 15.4 minutes
- PIDs (9038 9041) completed and logs appended.
- #--------------------------------------------
- #@# Surf Volume lh Sun Oct 8 08:36:29 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0050379 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/lh.cortex.label
- Total face volume 275874
- Total vertex volume 272443 (mask=0)
- #@# 0050379 lh 272443
-
- vertexvol Done
- #--------------------------------------------
- #@# Surf Volume rh Sun Oct 8 08:36:34 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0050379 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/rh.cortex.label
- Total face volume 266947
- Total vertex volume 263106 (mask=0)
- #@# 0050379 rh 263106
-
- vertexvol Done
- #--------------------------------------------
- #@# Cortical ribbon mask Sun Oct 8 08:36:38 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0050379
- 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 = 439
- writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/ribbon.mgz
- mris_volmask took 20.81 minutes
- writing ribbon files
- #-----------------------------------------
- #@# Parcellation Stats lh Sun Oct 8 08:57:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0050379 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 0050379 lh pial
- #-----------------------------------------
- #@# Parcellation Stats rh Sun Oct 8 08:57:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0050379 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 0050379 rh pial
- Waiting for PID 10374 of (10374 10377 10380 10383) to complete...
- Waiting for PID 10377 of (10374 10377 10380 10383) to complete...
- Waiting for PID 10380 of (10374 10377 10380 10383) to complete...
- Waiting for PID 10383 of (10374 10377 10380 10383) 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 0050379 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 275874
- Total vertex volume 272443 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 1038 734 1866 2.536 0.479 0.097 0.019 7 0.8 bankssts
- 930 555 1889 3.249 0.684 0.112 0.024 10 0.9 caudalanteriorcingulate
- 3149 2178 7074 2.998 0.592 0.118 0.030 28 4.0 caudalmiddlefrontal
- 2612 1737 3716 1.902 0.474 0.153 0.050 47 5.3 cuneus
- 955 592 1725 2.276 0.754 0.166 0.073 20 3.2 entorhinal
- 5682 3794 11995 2.770 0.705 0.136 0.039 84 9.7 fusiform
- 4950 3423 11147 2.709 0.714 0.137 0.038 68 7.7 inferiorparietal
- 5388 3690 12938 2.829 0.861 0.129 0.040 78 8.8 inferiortemporal
- 1748 1169 3353 2.635 0.968 0.137 0.036 22 2.8 isthmuscingulate
- 7167 4631 11439 2.133 0.717 0.147 0.045 119 13.6 lateraloccipital
- 4731 3172 9878 2.819 0.720 0.139 0.050 63 10.2 lateralorbitofrontal
- 4901 3293 7308 2.056 0.656 0.140 0.043 75 8.1 lingual
- 2681 1827 5204 2.306 0.817 0.129 0.042 48 4.4 medialorbitofrontal
- 4182 2932 10319 2.791 0.738 0.133 0.034 57 6.4 middletemporal
- 1283 797 2655 2.813 1.043 0.124 0.047 21 2.4 parahippocampal
- 2174 1472 4407 2.684 0.710 0.118 0.028 19 2.8 paracentral
- 2654 1753 6134 2.834 0.636 0.116 0.029 26 3.0 parsopercularis
- 1279 861 3855 3.011 0.839 0.153 0.053 25 2.7 parsorbitalis
- 1902 1286 4403 2.756 0.664 0.124 0.029 20 2.2 parstriangularis
- 2358 1684 2624 1.687 0.485 0.134 0.033 26 3.2 pericalcarine
- 6870 4423 10430 2.150 0.714 0.112 0.027 67 7.5 postcentral
- 1632 1113 3281 2.817 0.662 0.136 0.037 23 2.4 posteriorcingulate
- 8625 5551 16667 2.773 0.668 0.114 0.030 70 11.0 precentral
- 5105 3528 10264 2.577 0.806 0.134 0.034 62 6.9 precuneus
- 1254 834 3008 2.936 0.959 0.125 0.030 15 1.5 rostralanteriorcingulate
- 8736 5920 19210 2.701 0.704 0.131 0.035 112 12.3 rostralmiddlefrontal
- 10960 7439 28312 3.080 0.825 0.139 0.046 163 22.9 superiorfrontal
- 7644 5237 13349 2.296 0.633 0.131 0.035 99 10.1 superiorparietal
- 6007 4012 13685 2.816 0.747 0.112 0.028 54 7.4 superiortemporal
- 7631 5289 18063 2.929 0.698 0.140 0.037 102 11.4 supramarginal
- 342 228 1220 3.102 0.815 0.181 0.074 10 1.0 frontalpole
- 697 573 3042 3.459 0.743 0.151 0.042 11 1.3 temporalpole
- 895 531 1147 2.070 0.452 0.121 0.033 9 1.2 transversetemporal
- 3400 2293 6779 2.990 1.015 0.133 0.049 47 7.1 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 0050379 lh pial
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 275874
- Total vertex volume 272443 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 1038 775 1866 2.536 0.479 0.123 0.031 13 1.4 bankssts
- 930 672 1889 3.249 0.684 0.118 0.030 19 1.1 caudalanteriorcingulate
- 3149 2474 7074 2.998 0.592 0.124 0.030 36 3.9 caudalmiddlefrontal
- 2612 2245 3716 1.902 0.474 0.157 0.039 39 4.5 cuneus
- 955 856 1725 2.276 0.754 0.183 0.062 19 2.6 entorhinal
- 5682 4955 11995 2.770 0.705 0.166 0.045 95 12.2 fusiform
- 4950 4612 11147 2.709 0.714 0.162 0.045 86 9.1 inferiorparietal
- 5388 5189 12938 2.829 0.861 0.175 0.042 83 10.7 inferiortemporal
- 1748 1380 3353 2.635 0.968 0.152 0.044 41 3.3 isthmuscingulate
- 7167 6045 11439 2.133 0.717 0.146 0.038 106 12.3 lateraloccipital
- 4731 3585 9878 2.819 0.720 0.152 0.044 83 10.1 lateralorbitofrontal
- 4901 4034 7308 2.056 0.656 0.156 0.042 77 9.6 lingual
- 2681 2617 5204 2.306 0.817 0.182 0.049 43 5.8 medialorbitofrontal
- 4182 4245 10319 2.791 0.738 0.174 0.040 54 8.1 middletemporal
- 1283 1052 2655 2.813 1.043 0.151 0.040 21 2.0 parahippocampal
- 2174 1784 4407 2.684 0.710 0.135 0.032 22 3.6 paracentral
- 2654 2395 6134 2.834 0.636 0.150 0.035 29 4.1 parsopercularis
- 1279 1505 3855 3.011 0.839 0.187 0.036 14 2.2 parsorbitalis
- 1902 1786 4403 2.756 0.664 0.164 0.041 23 3.3 parstriangularis
- 2358 1556 2624 1.687 0.485 0.123 0.029 32 3.0 pericalcarine
- 6870 5425 10430 2.150 0.714 0.126 0.028 62 8.6 postcentral
- 1632 1266 3281 2.817 0.662 0.147 0.045 47 3.3 posteriorcingulate
- 8625 6271 16667 2.773 0.668 0.116 0.028 100 10.6 precentral
- 5105 4251 10264 2.577 0.806 0.155 0.038 71 8.9 precuneus
- 1254 1165 3008 2.936 0.959 0.188 0.052 30 3.3 rostralanteriorcingulate
- 8736 7762 19210 2.701 0.704 0.158 0.038 110 15.2 rostralmiddlefrontal
- 10960 10212 28312 3.080 0.825 0.166 0.046 197 22.9 superiorfrontal
- 7644 6118 13349 2.296 0.633 0.139 0.031 105 10.3 superiorparietal
- 6007 5395 13685 2.816 0.747 0.152 0.036 70 10.1 superiortemporal
- 7631 6772 18063 2.929 0.698 0.157 0.039 137 13.9 supramarginal
- 342 521 1220 3.102 0.815 0.282 0.064 6 1.1 frontalpole
- 697 1174 3042 3.459 0.743 0.241 0.047 11 1.6 temporalpole
- 895 645 1147 2.070 0.452 0.127 0.033 13 1.4 transversetemporal
- 3400 2211 6779 2.990 1.015 0.159 0.062 116 6.7 insula
- mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050379 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 266947
- Total vertex volume 263106 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 1252 861 2500 2.994 0.497 0.098 0.020 7 1.0 bankssts
- 1083 719 2358 2.752 0.739 0.129 0.039 16 1.6 caudalanteriorcingulate
- 3414 2337 8292 3.044 0.663 0.131 0.035 42 4.9 caudalmiddlefrontal
- 2469 1614 3402 1.881 0.484 0.143 0.037 37 3.8 cuneus
- 706 431 1757 2.929 0.897 0.132 0.068 12 1.7 entorhinal
- 5010 3378 10276 2.682 0.642 0.147 0.049 79 9.6 fusiform
- 7119 4925 16866 2.818 0.679 0.134 0.042 100 14.2 inferiorparietal
- 4610 3108 9970 2.575 0.819 0.143 0.049 86 9.8 inferiortemporal
- 1605 1051 3409 2.592 0.995 0.136 0.039 22 2.2 isthmuscingulate
- 7060 4611 11652 2.203 0.768 0.141 0.044 103 12.4 lateraloccipital
- 4316 2904 7943 2.659 0.756 0.137 0.046 56 8.3 lateralorbitofrontal
- 4805 3384 7588 1.983 0.610 0.147 0.040 71 7.7 lingual
- 2313 1655 5584 2.970 0.955 0.126 0.030 36 2.6 medialorbitofrontal
- 4216 2889 10528 2.980 0.738 0.129 0.039 59 6.7 middletemporal
- 1077 697 2085 2.562 0.857 0.102 0.019 9 0.7 parahippocampal
- 2871 1810 5361 2.706 0.566 0.110 0.028 25 3.4 paracentral
- 2039 1360 4430 2.708 0.607 0.118 0.032 23 2.6 parsopercularis
- 1545 1030 4162 2.979 0.882 0.144 0.050 27 3.0 parsorbitalis
- 2101 1499 4997 2.643 0.660 0.140 0.038 28 3.2 parstriangularis
- 2485 1755 2857 1.676 0.400 0.137 0.034 32 3.1 pericalcarine
- 6110 3973 8960 2.048 0.614 0.107 0.029 54 6.8 postcentral
- 1988 1355 4466 2.814 0.839 0.142 0.034 31 2.6 posteriorcingulate
- 8403 5359 16567 2.779 0.590 0.106 0.030 78 10.0 precentral
- 5259 3662 10501 2.536 0.691 0.132 0.033 68 6.7 precuneus
- 751 532 2241 3.080 0.891 0.126 0.030 9 1.0 rostralanteriorcingulate
- 8042 5530 18398 2.777 0.673 0.139 0.040 117 12.9 rostralmiddlefrontal
- 10616 7297 27419 3.180 0.739 0.136 0.040 135 17.8 superiorfrontal
- 7359 4935 13512 2.346 0.605 0.119 0.029 81 8.4 superiorparietal
- 5077 3574 11475 2.767 0.755 0.124 0.041 68 10.4 superiortemporal
- 5668 3923 12464 2.766 0.672 0.142 0.044 80 10.2 supramarginal
- 377 253 1362 3.369 0.672 0.167 0.056 8 0.8 frontalpole
- 628 451 2267 3.150 0.892 0.162 0.052 13 1.6 temporalpole
- 585 352 831 2.331 0.493 0.148 0.053 11 1.2 transversetemporal
- 3217 2242 6587 2.983 0.930 0.140 0.053 41 7.5 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 0050379 rh pial
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 266947
- Total vertex volume 263106 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 1252 802 2500 2.994 0.497 0.129 0.038 15 2.2 bankssts
- 1083 949 2358 2.752 0.739 0.167 0.045 38 1.7 caudalanteriorcingulate
- 3414 2922 8292 3.044 0.663 0.143 0.035 50 5.3 caudalmiddlefrontal
- 2469 2081 3402 1.881 0.484 0.155 0.038 37 4.4 cuneus
- 706 724 1757 2.929 0.897 0.195 0.058 12 1.9 entorhinal
- 5010 4386 10276 2.682 0.642 0.169 0.048 105 11.9 fusiform
- 7119 6658 16866 2.818 0.679 0.163 0.041 101 13.3 inferiorparietal
- 4610 4431 9970 2.575 0.819 0.176 0.048 69 10.3 inferiortemporal
- 1605 1400 3409 2.592 0.995 0.158 0.042 25 2.9 isthmuscingulate
- 7060 5629 11652 2.203 0.768 0.140 0.034 106 11.3 lateraloccipital
- 4316 3183 7943 2.659 0.756 0.153 0.044 64 9.2 lateralorbitofrontal
- 4805 4343 7588 1.983 0.610 0.163 0.041 69 8.5 lingual
- 2313 2211 5584 2.970 0.955 0.169 0.045 35 4.5 medialorbitofrontal
- 4216 4063 10528 2.980 0.738 0.164 0.039 72 7.7 middletemporal
- 1077 932 2085 2.562 0.857 0.157 0.037 14 1.9 parahippocampal
- 2871 2083 5361 2.706 0.566 0.124 0.029 30 3.6 paracentral
- 2039 1828 4430 2.708 0.607 0.160 0.039 23 3.7 parsopercularis
- 1545 1595 4162 2.979 0.882 0.170 0.036 29 2.7 parsorbitalis
- 2101 2146 4997 2.643 0.660 0.192 0.047 35 4.4 parstriangularis
- 2485 1742 2857 1.676 0.400 0.133 0.033 44 3.4 pericalcarine
- 6110 4849 8960 2.048 0.614 0.123 0.028 48 7.5 postcentral
- 1988 1735 4466 2.814 0.839 0.160 0.042 48 3.6 posteriorcingulate
- 8403 6328 16567 2.779 0.590 0.114 0.026 86 9.4 precentral
- 5259 4509 10501 2.536 0.691 0.146 0.033 72 7.7 precuneus
- 751 891 2241 3.080 0.891 0.202 0.046 16 1.9 rostralanteriorcingulate
- 8042 7390 18398 2.777 0.673 0.169 0.042 132 15.7 rostralmiddlefrontal
- 10616 9472 27419 3.180 0.739 0.154 0.040 176 19.6 superiorfrontal
- 7359 6189 13512 2.346 0.605 0.140 0.029 91 9.9 superiorparietal
- 5077 4775 11475 2.767 0.755 0.166 0.041 68 9.9 superiortemporal
- 5668 4895 12464 2.766 0.672 0.158 0.043 95 11.3 supramarginal
- 377 539 1362 3.369 0.672 0.241 0.052 5 0.9 frontalpole
- 628 976 2267 3.150 0.892 0.251 0.053 7 1.8 temporalpole
- 585 391 831 2.331 0.493 0.136 0.036 6 1.0 transversetemporal
- 3217 2203 6587 2.983 0.930 0.158 0.105 160 19.9 insula
- PIDs (10374 10377 10380 10383) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 2 lh Sun Oct 8 08:59:05 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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 08:59:05 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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 10484 of (10484 10487) to complete...
- Waiting for PID 10487 of (10484 10487) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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...
- 12 labels changed using aseg
- relabeling using gibbs priors...
- 000: 8931 changed, 139556 examined...
- 001: 1976 changed, 34498 examined...
- 002: 550 changed, 10394 examined...
- 003: 230 changed, 3201 examined...
- 004: 129 changed, 1335 examined...
- 005: 61 changed, 706 examined...
- 006: 34 changed, 341 examined...
- 007: 20 changed, 205 examined...
- 008: 6 changed, 99 examined...
- 009: 3 changed, 43 examined...
- 010: 2 changed, 21 examined...
- 011: 1 changed, 13 examined...
- 012: 0 changed, 6 examined...
- 3 labels changed using aseg
- 000: 272 total segments, 184 labels (1660 vertices) changed
- 001: 93 total segments, 6 labels (45 vertices) changed
- 002: 89 total segments, 2 labels (5 vertices) changed
- 003: 87 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 39 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1420 vertices marked for relabeling...
- 1420 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 0 minutes and 23 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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...
- 23 labels changed using aseg
- relabeling using gibbs priors...
- 000: 8324 changed, 134102 examined...
- 001: 1917 changed, 32821 examined...
- 002: 536 changed, 10078 examined...
- 003: 197 changed, 3013 examined...
- 004: 85 changed, 1115 examined...
- 005: 36 changed, 498 examined...
- 006: 13 changed, 200 examined...
- 007: 4 changed, 62 examined...
- 008: 3 changed, 23 examined...
- 009: 0 changed, 15 examined...
- 16 labels changed using aseg
- 000: 216 total segments, 135 labels (2386 vertices) changed
- 001: 89 total segments, 8 labels (78 vertices) changed
- 002: 81 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 37 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 973 vertices marked for relabeling...
- 973 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 0 minutes and 22 seconds.
- PIDs (10484 10487) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Sun Oct 8 08:59:29 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0050379 lh white
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Sun Oct 8 08:59:29 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0050379 rh white
- Waiting for PID 10533 of (10533 10536) to complete...
- Waiting for PID 10536 of (10533 10536) 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 0050379 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 275874
- Total vertex volume 272443 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 1303 871 2661 2.375 0.754 0.153 0.056 24 2.9 G&S_frontomargin
- 1548 1003 2877 2.423 0.746 0.159 0.054 32 3.4 G&S_occipital_inf
- 1648 1009 2869 2.341 0.682 0.116 0.034 16 2.2 G&S_paracentral
- 1802 1164 4040 2.897 0.648 0.137 0.035 24 2.5 G&S_subcentral
- 637 438 2162 2.891 0.881 0.160 0.050 14 1.4 G&S_transv_frontopol
- 2087 1459 5192 3.108 0.835 0.123 0.031 22 2.6 G&S_cingul-Ant
- 1308 865 2787 3.212 0.700 0.104 0.021 9 1.0 G&S_cingul-Mid-Ant
- 1236 872 2423 2.681 0.536 0.118 0.031 12 1.7 G&S_cingul-Mid-Post
- 727 480 2056 3.359 0.748 0.163 0.039 12 1.2 G_cingul-Post-dorsal
- 482 310 863 2.293 1.062 0.147 0.059 8 1.2 G_cingul-Post-ventral
- 2453 1616 3538 1.867 0.500 0.157 0.054 47 5.6 G_cuneus
- 1366 889 3673 2.962 0.552 0.127 0.038 17 2.0 G_front_inf-Opercular
- 457 300 1525 3.254 0.698 0.155 0.051 8 0.9 G_front_inf-Orbital
- 1073 716 3190 3.006 0.684 0.130 0.035 14 1.4 G_front_inf-Triangul
- 4550 3075 13813 3.136 0.681 0.151 0.044 79 8.0 G_front_middle
- 7837 5192 21604 3.114 0.850 0.152 0.056 145 20.3 G_front_sup
- 492 346 1310 3.389 0.934 0.137 0.050 5 1.1 G_Ins_lg&S_cent_ins
- 702 480 2196 3.312 0.802 0.131 0.046 11 1.4 G_insular_short
- 1960 1245 4946 2.810 0.709 0.146 0.043 32 3.3 G_occipital_middle
- 1256 841 2040 2.001 0.568 0.143 0.040 21 1.8 G_occipital_sup
- 2299 1455 5671 2.944 0.772 0.151 0.049 48 4.5 G_oc-temp_lat-fusifor
- 3432 2250 5349 1.993 0.672 0.154 0.054 69 6.9 G_oc-temp_med-Lingual
- 2170 1318 4142 2.457 0.912 0.164 0.075 47 7.8 G_oc-temp_med-Parahip
- 3114 2043 8291 2.824 0.863 0.160 0.073 64 9.8 G_orbital
- 2096 1508 6508 2.942 0.760 0.162 0.056 42 4.9 G_pariet_inf-Angular
- 3958 2722 11358 3.170 0.728 0.152 0.044 67 7.1 G_pariet_inf-Supramar
- 2963 2028 6440 2.424 0.756 0.148 0.049 52 5.5 G_parietal_sup
- 2531 1524 4024 2.145 0.665 0.123 0.036 30 3.8 G_postcentral
- 3330 2060 7676 2.934 0.762 0.127 0.039 35 5.9 G_precentral
- 2300 1616 6311 2.897 0.767 0.161 0.049 43 4.5 G_precuneus
- 960 663 2447 2.505 0.811 0.139 0.050 21 1.6 G_rectus
- 753 461 735 1.618 1.022 0.139 0.079 25 2.2 G_subcallosal
- 657 362 944 2.121 0.612 0.118 0.036 6 1.0 G_temp_sup-G_T_transv
- 2038 1381 6824 3.180 0.783 0.153 0.050 35 4.4 G_temp_sup-Lateral
- 763 551 2079 3.013 0.878 0.084 0.019 3 0.5 G_temp_sup-Plan_polar
- 999 681 1864 2.639 0.743 0.089 0.015 4 0.7 G_temp_sup-Plan_tempo
- 3019 2070 9208 3.147 0.901 0.149 0.051 60 6.3 G_temporal_inf
- 2208 1534 6893 3.048 0.741 0.153 0.043 41 4.4 G_temporal_middle
- 277 186 460 2.607 0.478 0.100 0.019 2 0.2 Lat_Fis-ant-Horizont
- 365 256 681 2.749 0.552 0.128 0.021 3 0.4 Lat_Fis-ant-Vertical
- 1280 848 1776 2.764 0.550 0.120 0.026 10 1.3 Lat_Fis-post
- 2170 1368 2998 1.832 0.631 0.155 0.056 44 5.5 Pole_occipital
- 1446 1116 4893 2.807 0.805 0.160 0.055 32 3.6 Pole_temporal
- 2845 2063 3276 1.815 0.593 0.120 0.026 23 3.0 S_calcarine
- 3465 2309 4405 2.088 0.706 0.092 0.018 16 2.5 S_central
- 1045 733 1592 2.340 0.532 0.095 0.016 5 0.7 S_cingul-Marginalis
- 665 456 1044 2.864 0.668 0.104 0.024 3 0.7 S_circular_insula_ant
- 1391 965 2347 2.957 0.783 0.100 0.032 9 2.2 S_circular_insula_inf
- 1622 1127 2442 2.764 0.510 0.108 0.020 8 1.4 S_circular_insula_sup
- 1361 900 2162 2.709 0.646 0.098 0.019 7 1.1 S_collat_transv_ant
- 518 358 572 2.005 0.383 0.141 0.036 5 0.8 S_collat_transv_post
- 2520 1698 4685 2.711 0.596 0.103 0.019 15 1.9 S_front_inf
- 1659 1115 2427 2.432 0.602 0.119 0.026 15 1.9 S_front_middle
- 2807 1989 5322 2.722 0.610 0.107 0.023 19 2.9 S_front_sup
- 241 181 457 2.656 0.452 0.137 0.030 2 0.3 S_interm_prim-Jensen
- 2669 1862 4050 2.436 0.471 0.108 0.021 18 2.2 S_intrapariet&P_trans
- 996 661 1113 1.872 0.361 0.117 0.027 7 1.0 S_oc_middle&Lunatus
- 1061 709 1366 2.185 0.494 0.119 0.022 10 1.0 S_oc_sup&transversal
- 547 394 842 1.844 0.621 0.140 0.033 7 0.8 S_occipital_ant
- 1041 706 1557 2.541 0.431 0.095 0.016 4 0.8 S_oc-temp_lat
- 2398 1628 3933 2.614 0.741 0.110 0.021 17 2.0 S_oc-temp_med&Lingual
- 407 288 625 2.217 0.447 0.111 0.019 2 0.3 S_orbital_lateral
- 751 499 956 2.182 0.545 0.122 0.027 7 0.8 S_orbital_med-olfact
- 1745 1189 3250 2.965 0.503 0.120 0.029 15 1.8 S_orbital-H_Shaped
- 2322 1598 3153 2.127 0.662 0.132 0.029 24 2.6 S_parieto_occipital
- 1297 785 1668 2.717 0.943 0.116 0.023 17 1.2 S_pericallosal
- 3931 2722 6104 2.364 0.520 0.119 0.023 36 3.5 S_postcentral
- 1715 1186 2818 2.796 0.529 0.099 0.017 9 1.2 S_precentral-inf-part
- 1728 1201 2872 2.745 0.466 0.097 0.018 8 1.3 S_precentral-sup-part
- 818 566 1418 2.321 0.903 0.136 0.021 10 0.8 S_suborbital
- 892 615 1513 2.761 0.629 0.117 0.023 7 0.9 S_subparietal
- 1518 1111 2339 2.420 0.603 0.113 0.022 9 1.5 S_temporal_inf
- 5010 3415 8104 2.544 0.590 0.102 0.020 34 4.3 S_temporal_sup
- 554 364 693 2.227 0.505 0.116 0.019 5 0.4 S_temporal_transverse
- mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050379 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 266947
- Total vertex volume 263106 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 914 651 2216 2.876 0.591 0.165 0.053 16 2.0 G&S_frontomargin
- 1152 775 2519 2.719 0.834 0.141 0.042 17 1.7 G&S_occipital_inf
- 1613 972 3098 2.559 0.591 0.113 0.030 15 1.9 G&S_paracentral
- 1323 865 2605 2.483 0.600 0.125 0.047 18 2.0 G&S_subcentral
- 985 683 3018 3.358 0.684 0.170 0.059 20 2.4 G&S_transv_frontopol
- 2575 1793 6287 3.243 0.698 0.117 0.027 30 2.8 G&S_cingul-Ant
- 1419 999 3331 3.131 0.650 0.118 0.036 15 2.0 G&S_cingul-Mid-Ant
- 1656 1158 3611 2.961 0.615 0.128 0.030 17 1.8 G&S_cingul-Mid-Post
- 595 402 2132 3.576 0.805 0.163 0.047 11 1.0 G_cingul-Post-dorsal
- 456 267 1017 2.495 1.117 0.143 0.062 8 1.0 G_cingul-Post-ventral
- 2390 1571 3407 1.845 0.521 0.152 0.042 41 4.0 G_cuneus
- 1259 786 3329 2.877 0.597 0.134 0.049 23 2.2 G_front_inf-Opercular
- 363 238 1039 2.929 0.660 0.146 0.052 7 0.7 G_front_inf-Orbital
- 867 639 2825 2.925 0.613 0.170 0.049 17 1.8 G_front_inf-Triangul
- 3628 2460 11242 3.139 0.677 0.154 0.051 69 7.5 G_front_middle
- 7377 4978 21625 3.258 0.775 0.154 0.050 123 15.7 G_front_sup
- 460 337 1264 3.472 1.064 0.156 0.067 6 1.6 G_Ins_lg&S_cent_ins
- 1023 686 2110 2.560 0.939 0.167 0.079 21 3.6 G_insular_short
- 2066 1403 5952 2.977 0.824 0.160 0.074 44 7.5 G_occipital_middle
- 1311 838 2238 2.150 0.631 0.137 0.042 20 1.9 G_occipital_sup
- 2546 1672 5808 2.711 0.654 0.157 0.058 48 5.9 G_oc-temp_lat-fusifor
- 3027 2106 5365 2.077 0.670 0.163 0.048 56 5.7 G_oc-temp_med-Lingual
- 1456 899 3372 2.816 0.935 0.137 0.060 25 3.1 G_oc-temp_med-Parahip
- 3414 2244 8521 2.788 0.885 0.157 0.058 69 8.4 G_orbital
- 2898 2003 8941 3.123 0.675 0.158 0.056 58 6.7 G_pariet_inf-Angular
- 2762 1888 7540 2.871 0.739 0.152 0.053 48 6.0 G_pariet_inf-Supramar
- 2559 1698 5689 2.500 0.640 0.126 0.036 38 3.8 G_parietal_sup
- 2283 1402 3794 2.128 0.651 0.117 0.037 26 3.2 G_postcentral
- 3276 1971 8054 3.042 0.539 0.117 0.038 44 5.3 G_precentral
- 2169 1490 5972 2.855 0.682 0.160 0.049 44 4.0 G_precuneus
- 788 556 2157 2.662 0.927 0.139 0.040 14 1.2 G_rectus
- 99 79 221 2.904 1.019 0.104 0.044 1 0.1 G_subcallosal
- 442 246 710 2.276 0.503 0.150 0.155 20 4.1 G_temp_sup-G_T_transv
- 1743 1250 5517 3.068 0.707 0.160 0.059 37 4.6 G_temp_sup-Lateral
- 590 471 1434 2.745 0.997 0.147 0.049 7 1.0 G_temp_sup-Plan_polar
- 1042 731 2187 2.657 0.697 0.134 0.033 14 1.6 G_temp_sup-Plan_tempo
- 2413 1608 6372 2.662 0.886 0.173 0.073 68 7.7 G_temporal_inf
- 2496 1702 7686 3.197 0.724 0.147 0.050 48 5.2 G_temporal_middle
- 274 190 372 2.089 0.701 0.103 0.019 2 0.2 Lat_Fis-ant-Horizont
- 250 179 355 2.268 0.434 0.111 0.021 1 0.2 Lat_Fis-ant-Vertical
- 1352 913 1910 2.742 0.593 0.110 0.024 8 1.2 Lat_Fis-post
- 3594 2298 4535 1.770 0.522 0.143 0.046 59 6.8 Pole_occipital
- 1446 1050 4009 2.505 0.846 0.168 0.058 35 3.6 Pole_temporal
- 2401 1831 3035 1.764 0.457 0.132 0.028 22 2.7 S_calcarine
- 2910 1988 3534 2.057 0.669 0.092 0.018 13 2.1 S_central
- 1445 982 2278 2.441 0.564 0.088 0.016 6 0.9 S_cingul-Marginalis
- 666 459 1001 2.666 0.600 0.107 0.022 4 0.6 S_circular_insula_ant
- 1175 814 2079 2.974 0.987 0.094 0.024 6 1.1 S_circular_insula_inf
- 1273 868 1920 2.638 0.568 0.103 0.020 6 1.1 S_circular_insula_sup
- 1176 818 1820 2.533 0.624 0.102 0.017 7 0.8 S_collat_transv_ant
- 518 346 565 1.907 0.474 0.126 0.030 4 0.7 S_collat_transv_post
- 1835 1263 2785 2.412 0.556 0.110 0.024 13 1.9 S_front_inf
- 2585 1791 4560 2.605 0.566 0.120 0.028 23 3.0 S_front_middle
- 2686 1885 5311 2.832 0.519 0.108 0.023 19 2.4 S_front_sup
- 596 414 887 2.487 0.596 0.109 0.019 3 0.6 S_interm_prim-Jensen
- 3367 2298 5182 2.296 0.506 0.109 0.020 26 2.7 S_intrapariet&P_trans
- 918 631 1062 1.954 0.405 0.111 0.020 5 0.8 S_oc_middle&Lunatus
- 1257 872 1675 2.214 0.446 0.116 0.023 10 1.3 S_oc_sup&transversal
- 633 441 988 2.380 0.504 0.102 0.016 3 0.5 S_occipital_ant
- 1118 762 1943 2.526 0.678 0.121 0.028 10 1.1 S_oc-temp_lat
- 2080 1405 2968 2.405 0.622 0.106 0.020 14 1.8 S_oc-temp_med&Lingual
- 679 469 1156 2.448 0.701 0.111 0.023 4 0.6 S_orbital_lateral
- 568 406 848 2.339 0.638 0.117 0.033 5 0.4 S_orbital_med-olfact
- 1786 1199 3033 2.838 0.722 0.121 0.037 16 2.7 S_orbital-H_Shaped
- 2205 1493 3086 2.159 0.568 0.122 0.025 20 2.1 S_parieto_occipital
- 1495 953 1567 2.105 0.644 0.127 0.023 20 1.1 S_pericallosal
- 2608 1798 3612 2.313 0.539 0.112 0.025 19 2.7 S_postcentral
- 1658 1169 3013 2.604 0.530 0.106 0.021 12 1.4 S_precentral-inf-part
- 2077 1393 3473 2.805 0.514 0.100 0.023 14 1.9 S_precentral-sup-part
- 284 208 723 3.542 0.853 0.121 0.016 2 0.2 S_suborbital
- 1100 757 2042 2.713 0.589 0.114 0.021 9 0.9 S_subparietal
- 1163 804 1899 2.747 0.721 0.120 0.021 8 1.0 S_temporal_inf
- 5256 3581 9202 2.767 0.558 0.097 0.018 28 4.0 S_temporal_sup
- 319 225 477 2.556 0.591 0.134 0.020 3 0.3 S_temporal_transverse
- PIDs (10533 10536) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 3 lh Sun Oct 8 09:00:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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 09:00:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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 10621 of (10621 10624) to complete...
- Waiting for PID 10624 of (10621 10624) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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...
- 1432 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2053 changed, 139556 examined...
- 001: 465 changed, 9705 examined...
- 002: 131 changed, 2682 examined...
- 003: 67 changed, 818 examined...
- 004: 43 changed, 375 examined...
- 005: 20 changed, 230 examined...
- 006: 17 changed, 118 examined...
- 007: 7 changed, 95 examined...
- 008: 1 changed, 37 examined...
- 009: 1 changed, 7 examined...
- 010: 1 changed, 7 examined...
- 011: 1 changed, 10 examined...
- 012: 2 changed, 4 examined...
- 013: 3 changed, 10 examined...
- 014: 2 changed, 13 examined...
- 015: 2 changed, 12 examined...
- 016: 1 changed, 7 examined...
- 017: 1 changed, 9 examined...
- 018: 1 changed, 8 examined...
- 019: 1 changed, 8 examined...
- 020: 2 changed, 8 examined...
- 021: 0 changed, 10 examined...
- 178 labels changed using aseg
- 000: 52 total segments, 19 labels (175 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 3 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 863 vertices marked for relabeling...
- 863 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas.annot...
- classification took 0 minutes and 17 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050379 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...
- 1362 labels changed using aseg
- relabeling using gibbs priors...
- 000: 1985 changed, 134102 examined...
- 001: 463 changed, 9317 examined...
- 002: 112 changed, 2657 examined...
- 003: 51 changed, 670 examined...
- 004: 26 changed, 287 examined...
- 005: 15 changed, 142 examined...
- 006: 11 changed, 81 examined...
- 007: 13 changed, 64 examined...
- 008: 9 changed, 51 examined...
- 009: 5 changed, 40 examined...
- 010: 2 changed, 24 examined...
- 011: 1 changed, 10 examined...
- 012: 1 changed, 7 examined...
- 013: 0 changed, 8 examined...
- 184 labels changed using aseg
- 000: 59 total segments, 26 labels (223 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 2 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 818 vertices marked for relabeling...
- 818 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas.annot...
- classification took 0 minutes and 16 seconds.
- PIDs (10621 10624) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Sun Oct 8 09:00:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0050379 lh white
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Sun Oct 8 09:00:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0050379 rh white
- Waiting for PID 10665 of (10665 10668) to complete...
- Waiting for PID 10668 of (10665 10668) 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 0050379 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 275874
- Total vertex volume 272443 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 1473 930 3098 3.341 0.688 0.110 0.024 14 1.4 caudalanteriorcingulate
- 3395 2337 7732 3.012 0.590 0.117 0.030 30 4.2 caudalmiddlefrontal
- 3499 2337 4833 1.899 0.462 0.145 0.044 56 6.1 cuneus
- 931 563 1619 2.246 0.772 0.172 0.082 21 3.6 entorhinal
- 5240 3462 10819 2.777 0.717 0.133 0.037 73 7.9 fusiform
- 5137 3559 11655 2.701 0.709 0.139 0.038 73 8.1 inferiorparietal
- 5495 3785 13225 2.827 0.846 0.130 0.041 82 9.3 inferiortemporal
- 1769 1175 3356 2.649 0.953 0.135 0.035 22 2.9 isthmuscingulate
- 7226 4666 11581 2.137 0.718 0.147 0.045 120 13.8 lateraloccipital
- 5234 3447 10877 2.713 0.808 0.148 0.058 87 13.1 lateralorbitofrontal
- 4937 3321 7328 2.046 0.653 0.141 0.043 75 8.2 lingual
- 2438 1616 4613 2.251 0.954 0.134 0.049 53 4.5 medialorbitofrontal
- 5336 3751 12687 2.753 0.712 0.130 0.033 69 8.0 middletemporal
- 1349 833 2729 2.767 1.027 0.125 0.046 22 2.6 parahippocampal
- 2595 1730 5243 2.754 0.698 0.119 0.029 23 3.5 paracentral
- 2520 1657 5862 2.871 0.633 0.119 0.030 26 3.0 parsopercularis
- 1145 766 3030 2.946 0.780 0.119 0.031 13 1.3 parsorbitalis
- 2384 1626 4937 2.663 0.640 0.121 0.027 22 2.6 parstriangularis
- 2384 1700 2648 1.681 0.485 0.135 0.034 27 3.4 pericalcarine
- 7766 5032 11606 2.153 0.709 0.114 0.027 77 8.7 postcentral
- 1752 1204 3453 2.778 0.701 0.132 0.036 23 2.5 posteriorcingulate
- 8423 5423 16273 2.774 0.665 0.115 0.030 70 10.9 precentral
- 4857 3376 10210 2.618 0.811 0.138 0.036 63 6.8 precuneus
- 1674 1139 3884 2.886 0.971 0.131 0.034 23 2.2 rostralanteriorcingulate
- 6414 4378 15182 2.809 0.664 0.132 0.034 81 8.9 rostralmiddlefrontal
- 12128 8239 30857 2.963 0.843 0.139 0.046 187 24.6 superiorfrontal
- 6168 4206 11092 2.373 0.610 0.129 0.036 78 8.3 superiorparietal
- 7480 5137 18099 2.851 0.769 0.116 0.030 73 9.7 superiortemporal
- 7012 4867 16849 2.955 0.702 0.140 0.037 95 10.4 supramarginal
- 868 514 1115 2.065 0.451 0.121 0.033 9 1.1 transversetemporal
- 2562 1789 5952 3.282 0.764 0.125 0.041 26 4.9 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 0050379 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 266947
- Total vertex volume 263106 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 1199 795 2493 2.695 0.760 0.131 0.038 18 1.8 caudalanteriorcingulate
- 3519 2415 8482 3.053 0.648 0.131 0.035 44 5.1 caudalmiddlefrontal
- 3006 1978 4289 1.913 0.512 0.145 0.038 45 4.6 cuneus
- 607 377 1531 2.925 0.924 0.135 0.071 11 1.6 entorhinal
- 4733 3172 9494 2.676 0.646 0.144 0.048 71 8.8 fusiform
- 7342 5076 17494 2.816 0.682 0.135 0.043 104 14.8 inferiorparietal
- 4964 3352 10853 2.576 0.799 0.145 0.049 94 10.6 inferiortemporal
- 1621 1062 3409 2.592 0.978 0.137 0.039 23 2.3 isthmuscingulate
- 7099 4627 11751 2.197 0.768 0.141 0.044 105 12.3 lateraloccipital
- 4999 3342 9577 2.688 0.788 0.144 0.052 73 10.3 lateralorbitofrontal
- 4689 3308 7464 1.989 0.603 0.149 0.040 70 7.6 lingual
- 1776 1260 4646 2.918 0.953 0.132 0.034 33 2.4 medialorbitofrontal
- 5067 3484 12151 2.976 0.724 0.129 0.037 68 7.7 middletemporal
- 1165 751 2248 2.589 0.852 0.103 0.019 9 0.8 parahippocampal
- 3052 1913 5648 2.701 0.566 0.113 0.031 29 4.0 paracentral
- 2253 1528 4803 2.683 0.588 0.118 0.031 25 2.7 parsopercularis
- 1288 847 2830 2.824 0.643 0.120 0.032 16 1.7 parsorbitalis
- 2168 1536 5200 2.658 0.714 0.147 0.041 30 3.7 parstriangularis
- 2391 1693 2709 1.672 0.387 0.134 0.032 29 2.9 pericalcarine
- 6707 4365 9953 2.061 0.632 0.110 0.031 62 7.9 postcentral
- 2022 1385 4609 2.856 0.816 0.141 0.034 30 2.5 posteriorcingulate
- 8096 5123 15873 2.771 0.587 0.108 0.030 78 9.6 precentral
- 5265 3674 10748 2.538 0.695 0.132 0.033 68 6.6 precuneus
- 905 623 2560 3.289 0.955 0.119 0.027 10 1.1 rostralanteriorcingulate
- 5920 4070 13971 2.749 0.701 0.137 0.040 87 9.5 rostralmiddlefrontal
- 13093 9091 33608 3.152 0.727 0.135 0.040 165 21.3 superiorfrontal
- 6178 4163 11363 2.354 0.595 0.115 0.028 66 6.8 superiorparietal
- 6672 4668 15579 2.812 0.756 0.126 0.042 91 13.5 superiortemporal
- 5138 3572 11201 2.788 0.663 0.139 0.041 68 8.6 supramarginal
- 589 349 843 2.343 0.488 0.144 0.052 11 1.2 transversetemporal
- 2665 1868 5725 3.035 0.953 0.134 0.048 29 6.0 insula
- PIDs (10665 10668) completed and logs appended.
- #-----------------------------------------
- #@# WM/GM Contrast lh Sun Oct 8 09:01:13 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- pctsurfcon --s 0050379 --lh-only
- #-----------------------------------------
- #@# WM/GM Contrast rh Sun Oct 8 09:01:13 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts
- pctsurfcon --s 0050379 --rh-only
- Waiting for PID 10749 of (10749 10752) to complete...
- Waiting for PID 10752 of (10749 10752) to complete...
- pctsurfcon --s 0050379 --lh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts/pctsurfcon.log
- Sun Oct 8 09:01:13 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-6.0.0/0050379/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-598 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-6.0.0/0050379/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10749/lh.wm.mgh --regheader 0050379 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00003;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 = 70051
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10749/lh.wm.mgh
- Dim: 139556 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10749/lh.gm.mgh --projfrac 0.3 --regheader 0050379 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00003;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 = 83058
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10749/lh.gm.mgh
- Dim: 139556 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10749/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10749/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/surf/lh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.w-g.pct.mgh --annot 0050379 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/surf/lh.w-g.pct.mgh --annot 0050379 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-598
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/surf/lh.w-g.pct.mgh
- Vertex Area is 0.671157 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 0050379 --rh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/scripts/pctsurfcon.log
- Sun Oct 8 09:01:13 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-6.0.0/0050379/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-598 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-6.0.0/0050379/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10752/rh.wm.mgh --regheader 0050379 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00003;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 = 67579
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10752/rh.wm.mgh
- Dim: 134102 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10752/rh.gm.mgh --projfrac 0.3 --regheader 0050379 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00003;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 = 80095
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10752/rh.gm.mgh
- Dim: 134102 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10752/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/tmp.pctsurfcon.10752/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/surf/rh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.w-g.pct.mgh --annot 0050379 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/surf/rh.w-g.pct.mgh --annot 0050379 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-598
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/surf/rh.w-g.pct.mgh
- Vertex Area is 0.675192 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 (10749 10752) completed and logs appended.
- #-----------------------------------------
- #@# Relabel Hypointensities Sun Oct 8 09:01:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri
- mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
- reading input surface ../surf/lh.white...
- relabeling lh hypointensities...
- 1986 voxels changed to hypointensity...
- reading input surface ../surf/rh.white...
- relabeling rh hypointensities...
- 1965 voxels changed to hypointensity...
- 3922 hypointense voxels neighboring cortex changed
- #-----------------------------------------
- #@# AParc-to-ASeg aparc Sun Oct 8 09:01:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379
- mri_aparc2aseg --s 0050379 --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 09:01:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379
- mri_aparc2aseg --s 0050379 --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 09:01:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379
- mri_aparc2aseg --s 0050379 --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 10930 of (10930 10933 10936) to complete...
- Waiting for PID 10933 of (10930 10933 10936) to complete...
- Waiting for PID 10936 of (10930 10933 10936) to complete...
- mri_aparc2aseg --s 0050379 --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 0050379
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/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-6.0.0/0050379/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 6.25
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 107
- rescaling Left_Cerebral_Cortex from 61 --> 62
- rescaling Left_Lateral_Ventricle from 13 --> 16
- rescaling Left_Inf_Lat_Vent from 34 --> 35
- rescaling Left_Cerebellum_White_Matter from 86 --> 86
- rescaling Left_Cerebellum_Cortex from 60 --> 62
- rescaling Left_Thalamus from 94 --> 103
- rescaling Left_Thalamus_Proper from 84 --> 90
- rescaling Left_Caudate from 75 --> 68
- rescaling Left_Putamen from 80 --> 77
- rescaling Left_Pallidum from 98 --> 100
- rescaling Third_Ventricle from 25 --> 26
- rescaling Fourth_Ventricle from 22 --> 14
- rescaling Brain_Stem from 81 --> 86
- rescaling Left_Hippocampus from 57 --> 65
- rescaling Left_Amygdala from 56 --> 69
- rescaling CSF from 32 --> 36
- rescaling Left_Accumbens_area from 62 --> 62
- rescaling Left_VentralDC from 87 --> 89
- rescaling Right_Cerebral_White_Matter from 105 --> 105
- rescaling Right_Cerebral_Cortex from 58 --> 61
- rescaling Right_Lateral_Ventricle from 13 --> 13
- rescaling Right_Inf_Lat_Vent from 25 --> 25
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 59
- rescaling Right_Thalamus_Proper from 85 --> 88
- rescaling Right_Caudate from 62 --> 72
- rescaling Right_Putamen from 80 --> 77
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 61
- rescaling Right_Amygdala from 55 --> 70
- rescaling Right_Accumbens_area from 65 --> 70
- rescaling Right_VentralDC from 86 --> 87
- rescaling Fifth_Ventricle from 40 --> 32
- rescaling WM_hypointensities from 78 --> 78
- 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 = 531122
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 124 changed.
- pass 2: 7 changed.
- pass 3: 3 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/aparc+aseg.mgz
- mri_aparc2aseg --s 0050379 --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 0050379
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/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-6.0.0/0050379/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 6.25
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 107
- rescaling Left_Cerebral_Cortex from 61 --> 62
- rescaling Left_Lateral_Ventricle from 13 --> 16
- rescaling Left_Inf_Lat_Vent from 34 --> 35
- rescaling Left_Cerebellum_White_Matter from 86 --> 86
- rescaling Left_Cerebellum_Cortex from 60 --> 62
- rescaling Left_Thalamus from 94 --> 103
- rescaling Left_Thalamus_Proper from 84 --> 90
- rescaling Left_Caudate from 75 --> 68
- rescaling Left_Putamen from 80 --> 77
- rescaling Left_Pallidum from 98 --> 100
- rescaling Third_Ventricle from 25 --> 26
- rescaling Fourth_Ventricle from 22 --> 14
- rescaling Brain_Stem from 81 --> 86
- rescaling Left_Hippocampus from 57 --> 65
- rescaling Left_Amygdala from 56 --> 69
- rescaling CSF from 32 --> 36
- rescaling Left_Accumbens_area from 62 --> 62
- rescaling Left_VentralDC from 87 --> 89
- rescaling Right_Cerebral_White_Matter from 105 --> 105
- rescaling Right_Cerebral_Cortex from 58 --> 61
- rescaling Right_Lateral_Ventricle from 13 --> 13
- rescaling Right_Inf_Lat_Vent from 25 --> 25
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 59
- rescaling Right_Thalamus_Proper from 85 --> 88
- rescaling Right_Caudate from 62 --> 72
- rescaling Right_Putamen from 80 --> 77
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 61
- rescaling Right_Amygdala from 55 --> 70
- rescaling Right_Accumbens_area from 65 --> 70
- rescaling Right_VentralDC from 86 --> 87
- rescaling Fifth_Ventricle from 40 --> 32
- rescaling WM_hypointensities from 78 --> 78
- 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 = 531156
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 124 changed.
- pass 2: 7 changed.
- pass 3: 3 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/aparc.a2009s+aseg.mgz
- mri_aparc2aseg --s 0050379 --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 0050379
- outvol mri/aparc.DKTatlas+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/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-6.0.0/0050379/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 6.25
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 107
- rescaling Left_Cerebral_Cortex from 61 --> 62
- rescaling Left_Lateral_Ventricle from 13 --> 16
- rescaling Left_Inf_Lat_Vent from 34 --> 35
- rescaling Left_Cerebellum_White_Matter from 86 --> 86
- rescaling Left_Cerebellum_Cortex from 60 --> 62
- rescaling Left_Thalamus from 94 --> 103
- rescaling Left_Thalamus_Proper from 84 --> 90
- rescaling Left_Caudate from 75 --> 68
- rescaling Left_Putamen from 80 --> 77
- rescaling Left_Pallidum from 98 --> 100
- rescaling Third_Ventricle from 25 --> 26
- rescaling Fourth_Ventricle from 22 --> 14
- rescaling Brain_Stem from 81 --> 86
- rescaling Left_Hippocampus from 57 --> 65
- rescaling Left_Amygdala from 56 --> 69
- rescaling CSF from 32 --> 36
- rescaling Left_Accumbens_area from 62 --> 62
- rescaling Left_VentralDC from 87 --> 89
- rescaling Right_Cerebral_White_Matter from 105 --> 105
- rescaling Right_Cerebral_Cortex from 58 --> 61
- rescaling Right_Lateral_Ventricle from 13 --> 13
- rescaling Right_Inf_Lat_Vent from 25 --> 25
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 59
- rescaling Right_Thalamus_Proper from 85 --> 88
- rescaling Right_Caudate from 62 --> 72
- rescaling Right_Putamen from 80 --> 77
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 61
- rescaling Right_Amygdala from 55 --> 70
- rescaling Right_Accumbens_area from 65 --> 70
- rescaling Right_VentralDC from 86 --> 87
- rescaling Fifth_Ventricle from 40 --> 32
- rescaling WM_hypointensities from 78 --> 78
- 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 = 531156
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 124 changed.
- pass 2: 7 changed.
- pass 3: 3 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
- PIDs (10930 10933 10936) completed and logs appended.
- #-----------------------------------------
- #@# APas-to-ASeg Sun Oct 8 09:10:00 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri
- apas2aseg --i aparc+aseg.mgz --o aseg.mgz
- Sun Oct 8 09:10:00 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-6.0.0/0050379/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-598 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-6.0.0/0050379/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-598
- 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 09:10:00 CEST 2017
- Ended at Sun Oct 8 09:10:06 CEST 2017
- Apas2aseg-Run-Time-Sec 6
-
- apas2aseg Done
- #--------------------------------------------
- #@# ASeg Stats Sun Oct 8 09:10:06 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379
- 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 0050379
- $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 0050379
- sysname Linux
- hostname tars-598
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1459333 mm^3 (det: 1.334928 )
- Computing euler number
- orig.nofix lheno = -168, rheno = -164
- orig.nofix lhholes = 85, rhholes = 83
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 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 09:11:46 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379
- mri_aparc2aseg --s 0050379 --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 0050379
- 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-6.0.0/0050379/mri/aparc+aseg.mgz
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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-6.0.0/0050379/mri/ribbon.mgz
- Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/ribbon.mgz
- Ripping vertices labeled as unkown
- Ripped 7994 vertices from left hemi
- Ripped 7926 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-6.0.0/0050379/mri/aseg.mgz
- Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 = 959522
- Used brute-force search on 25 voxels
- Fixing Parahip LH WM
- Found 14 clusters
- 0 k 2.000000
- 1 k 19.000000
- 2 k 1.000000
- 3 k 1.000000
- 4 k 2.000000
- 5 k 1.000000
- 6 k 2.000000
- 7 k 1.000000
- 8 k 1.000000
- 9 k 9.000000
- 10 k 1.000000
- 11 k 1.000000
- 12 k 1566.000000
- 13 k 1.000000
- Fixing Parahip RH WM
- Found 6 clusters
- 0 k 1458.000000
- 1 k 1.000000
- 2 k 2.000000
- 3 k 6.000000
- 4 k 1.000000
- 5 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 0050379 --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 0050379 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname tars-598
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1459333 mm^3 (det: 1.334928 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 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-6.0.0/0050379/label
- #--------------------------------------------
- #@# BA_exvivo Labels lh Sun Oct 8 09:20:42 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 0050379 --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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 11989 of (11989 11992 12001 12007 12013) to complete...
- Waiting for PID 11992 of (11989 11992 12001 12007 12013) to complete...
- Waiting for PID 12001 of (11989 11992 12001 12007 12013) to complete...
- Waiting for PID 12007 of (11989 11992 12001 12007 12013) to complete...
- Waiting for PID 12013 of (11989 11992 12001 12007 12013) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 445
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.label 4574
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 920
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.label 8829
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 163
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.label 4240
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 470
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.label 6453
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 726
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.label 6510
- mri_label2label: Done
- PIDs (11989 11992 12001 12007 12013) 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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 12067 of (12067 12073 12079 12084) to complete...
- Waiting for PID 12073 of (12067 12073 12079 12084) to complete...
- Waiting for PID 12079 of (12067 12073 12079 12084) to complete...
- Waiting for PID 12084 of (12067 12073 12079 12084) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 338
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.label 4408
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 2072
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.label 15661
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 401
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.label 4582
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 802
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.label 4224
- mri_label2label: Done
- PIDs (12067 12073 12079 12084) 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 0050379 --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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 12127 of (12127 12133 12139 12143 12150) to complete...
- Waiting for PID 12133 of (12127 12133 12139 12143 12150) to complete...
- Waiting for PID 12139 of (12127 12133 12139 12143 12150) to complete...
- Waiting for PID 12143 of (12127 12133 12139 12143 12150) to complete...
- Waiting for PID 12150 of (12127 12133 12139 12143 12150) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 1802
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.label 6443
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 3121
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.label 11235
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 268
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.label 2286
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 552
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.label 1842
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 523
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.label 1722
- mri_label2label: Done
- PIDs (12127 12133 12139 12143 12150) 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 0050379 --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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 12293 of (12293 12299 12305 12311 12316) to complete...
- Waiting for PID 12299 of (12293 12299 12305 12311 12316) to complete...
- Waiting for PID 12305 of (12293 12299 12305 12311 12316) to complete...
- Waiting for PID 12311 of (12293 12299 12305 12311 12316) to complete...
- Waiting for PID 12316 of (12293 12299 12305 12311 12316) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 115
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.thresh.label 1129
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 205
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.thresh.label 2297
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 60
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.thresh.label 1564
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 108
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.thresh.label 2104
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 237
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.thresh.label 2556
- mri_label2label: Done
- PIDs (12293 12299 12305 12311 12316) 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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 12361 of (12361 12367 12373 12379) to complete...
- Waiting for PID 12367 of (12361 12367 12373 12379) to complete...
- Waiting for PID 12373 of (12361 12367 12373 12379) to complete...
- Waiting for PID 12379 of (12361 12367 12373 12379) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 95
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.thresh.label 1644
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 1322
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.thresh.label 8357
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 171
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.thresh.label 2083
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 319
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.thresh.label 1470
- mri_label2label: Done
- PIDs (12361 12367 12373 12379) 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 0050379 --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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 12427 of (12427 12433 12439 12445 12450) to complete...
- Waiting for PID 12433 of (12427 12433 12439 12445 12450) to complete...
- Waiting for PID 12439 of (12427 12433 12439 12445 12450) to complete...
- Waiting for PID 12445 of (12427 12433 12439 12445 12450) to complete...
- Waiting for PID 12450 of (12427 12433 12439 12445 12450) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 1318
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.thresh.label 4723
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 1497
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.thresh.label 4831
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 57
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.thresh.label 570
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 291
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.thresh.label 761
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 139556
- Number of reverse mapping hits = 205
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.thresh.label 655
- mri_label2label: Done
- PIDs (12427 12433 12439 12445 12450) completed and logs appended.
- mris_label2annot --s 0050379 --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-6.0.0/0050379/label
- cmdline mris_label2annot --s 0050379 --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-598
- machine x86_64
- user ntraut
- subject 0050379
- 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-6.0.0/0050379/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 93514 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/lh.BA_exvivo.annot
- mris_label2annot --s 0050379 --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-6.0.0/0050379/label
- cmdline mris_label2annot --s 0050379 --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-598
- machine x86_64
- user ntraut
- subject 0050379
- 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-6.0.0/0050379/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 111687 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0050379 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 275874
- Total vertex volume 272443 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 1298 742 2126 2.214 0.727 0.133 0.044 18 2.6 BA1_exvivo
- 4894 3275 8103 2.446 0.639 0.117 0.025 46 4.7 BA2_exvivo
- 1141 747 1201 1.978 0.493 0.120 0.028 9 1.1 BA3a_exvivo
- 2512 1664 3740 1.909 0.768 0.105 0.023 25 2.1 BA3b_exvivo
- 1793 1178 3731 2.710 0.770 0.122 0.036 16 3.1 BA4a_exvivo
- 1510 970 2675 2.805 0.596 0.097 0.024 9 1.7 BA4p_exvivo
- 10812 7091 24874 2.927 0.787 0.134 0.046 147 23.3 BA6_exvivo
- 2367 1582 5122 2.819 0.552 0.112 0.026 22 2.2 BA44_exvivo
- 3198 2148 6992 2.725 0.642 0.123 0.029 31 3.8 BA45_exvivo
- 4067 2885 4944 1.673 0.516 0.140 0.036 54 6.1 V1_exvivo
- 8593 5582 12444 1.975 0.609 0.147 0.049 150 17.4 V2_exvivo
- 1744 1204 3596 2.342 0.680 0.138 0.034 25 2.4 MT_exvivo
- 1033 603 1687 2.289 0.807 0.142 0.064 19 2.9 perirhinal_exvivo
- 1080 741 2825 2.913 0.934 0.177 0.075 25 4.0 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 0050379 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 275874
- Total vertex volume 272443 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 798 443 1292 2.175 0.596 0.143 0.047 13 1.6 BA1_exvivo
- 1750 1153 2716 2.278 0.531 0.102 0.024 14 1.5 BA2_exvivo
- 988 646 964 1.948 0.447 0.126 0.028 8 1.1 BA3a_exvivo
- 1479 1008 1570 1.491 0.365 0.082 0.014 7 0.9 BA3b_exvivo
- 1814 1171 3511 2.729 0.758 0.111 0.032 14 3.0 BA4a_exvivo
- 1168 779 2036 2.684 0.576 0.093 0.023 7 1.1 BA4p_exvivo
- 6658 4157 13414 2.810 0.773 0.137 0.052 97 16.6 BA6_exvivo
- 1531 1045 3252 2.761 0.599 0.118 0.028 14 1.7 BA44_exvivo
- 1325 882 3782 2.983 0.667 0.136 0.036 18 1.9 BA45_exvivo
- 4283 3033 5382 1.698 0.551 0.144 0.038 61 7.0 V1_exvivo
- 4455 2953 6577 1.950 0.592 0.155 0.054 84 10.2 V2_exvivo
- 426 304 630 1.996 0.593 0.130 0.034 5 0.6 MT_exvivo
- 600 329 840 2.237 0.774 0.132 0.061 10 1.5 perirhinal_exvivo
- 594 417 1465 2.694 0.845 0.190 0.091 14 2.7 entorhinal_exvivo
- #--------------------------------------------
- #@# BA_exvivo Labels rh Sun Oct 8 09:23:59 CEST 2017
- mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0050379 --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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 12572 of (12572 12578 12584 12589 12596) to complete...
- Waiting for PID 12578 of (12572 12578 12584 12589 12596) to complete...
- Waiting for PID 12584 of (12572 12578 12584 12589 12596) to complete...
- Waiting for PID 12589 of (12572 12578 12584 12589 12596) to complete...
- Waiting for PID 12596 of (12572 12578 12584 12589 12596) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 308
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.label 4270
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 348
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.label 7035
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 109
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.label 4089
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 246
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.label 4768
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 856
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.label 6603
- mri_label2label: Done
- PIDs (12572 12578 12584 12589 12596) 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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 12638 of (12638 12644 12650 12655) to complete...
- Waiting for PID 12644 of (12638 12644 12650 12655) to complete...
- Waiting for PID 12650 of (12638 12644 12650 12655) to complete...
- Waiting for PID 12655 of (12638 12644 12650 12655) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 236
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.label 4709
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 2174
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.label 14430
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 710
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.label 7622
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 949
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.label 6304
- mri_label2label: Done
- PIDs (12638 12644 12650 12655) 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 0050379 --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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 12703 of (12703 12709 12715 12721 12726) to complete...
- Waiting for PID 12709 of (12703 12709 12715 12721 12726) to complete...
- Waiting for PID 12715 of (12703 12709 12715 12721 12726) to complete...
- Waiting for PID 12721 of (12703 12709 12715 12721 12726) to complete...
- Waiting for PID 12726 of (12703 12709 12715 12721 12726) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 1786
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.label 6513
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 2742
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.label 10758
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 269
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.label 2201
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 205
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.label 1243
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 179
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.label 931
- mri_label2label: Done
- PIDs (12703 12709 12715 12721 12726) 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 0050379 --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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 12779 of (12779 12785 12791 12797 12803) to complete...
- Waiting for PID 12785 of (12779 12785 12791 12797 12803) to complete...
- Waiting for PID 12791 of (12779 12785 12791 12797 12803) to complete...
- Waiting for PID 12797 of (12779 12785 12791 12797 12803) to complete...
- Waiting for PID 12803 of (12779 12785 12791 12797 12803) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 117
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.thresh.label 993
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 95
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.thresh.label 2783
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 52
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.thresh.label 1750
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 84
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.thresh.label 2267
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 157
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.thresh.label 1545
- mri_label2label: Done
- PIDs (12779 12785 12791 12797 12803) 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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 12841 of (12841 12847 12853 12857) to complete...
- Waiting for PID 12847 of (12841 12847 12853 12857) to complete...
- Waiting for PID 12853 of (12841 12847 12853 12857) to complete...
- Waiting for PID 12857 of (12841 12847 12853 12857) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 53
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.thresh.label 1542
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 1451
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.thresh.label 8410
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 136
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.thresh.label 1148
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 157
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.thresh.label 1335
- mri_label2label: Done
- PIDs (12841 12847 12853 12857) 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 0050379 --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 0050379 --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 0050379 --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 0050379 --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 0050379 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 12911 of (12911 12917 12923 12929 12933) to complete...
- Waiting for PID 12917 of (12911 12917 12923 12929 12933) to complete...
- Waiting for PID 12923 of (12911 12917 12923 12929 12933) to complete...
- Waiting for PID 12929 of (12911 12917 12923 12929 12933) to complete...
- Waiting for PID 12933 of (12911 12917 12923 12929 12933) 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 1244
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.thresh.label 4476
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 1336
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.thresh.label 4773
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 34
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.thresh.label 302
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 132
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.thresh.label 826
- 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 0050379 --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 = 0050379
- 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-6.0.0/0050379/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 134102
- Number of reverse mapping hits = 58
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.thresh.label 349
- mri_label2label: Done
- PIDs (12911 12917 12923 12929 12933) completed and logs appended.
- mris_label2annot --s 0050379 --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-6.0.0/0050379/label
- cmdline mris_label2annot --s 0050379 --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-598
- machine x86_64
- user ntraut
- subject 0050379
- 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-6.0.0/0050379/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 91133 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/label/rh.BA_exvivo.annot
- mris_label2annot --s 0050379 --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-6.0.0/0050379/label
- cmdline mris_label2annot --s 0050379 --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-598
- machine x86_64
- user ntraut
- subject 0050379
- 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-6.0.0/0050379/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 108967 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/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 0050379 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 266947
- Total vertex volume 263106 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 1013 583 1820 2.238 0.640 0.140 0.043 15 1.6 BA1_exvivo
- 3159 2132 4669 2.237 0.515 0.103 0.024 21 3.0 BA2_exvivo
- 1121 710 990 1.897 0.447 0.122 0.026 9 1.1 BA3a_exvivo
- 1832 1250 2393 1.705 0.588 0.095 0.029 14 1.9 BA3b_exvivo
- 1886 1084 3685 2.868 0.467 0.090 0.024 11 2.0 BA4a_exvivo
- 1149 794 2130 2.723 0.417 0.086 0.021 5 1.0 BA4p_exvivo
- 10134 6682 23535 2.998 0.669 0.127 0.040 124 17.0 BA6_exvivo
- 3389 2292 7210 2.715 0.586 0.115 0.034 36 4.3 BA44_exvivo
- 4107 2844 9629 2.721 0.707 0.139 0.039 58 6.4 BA45_exvivo
- 4197 2978 5653 1.760 0.498 0.149 0.041 62 7.0 V1_exvivo
- 8100 5394 11489 1.898 0.572 0.147 0.042 127 12.9 V2_exvivo
- 1768 1229 3637 2.647 0.652 0.131 0.032 19 2.3 MT_exvivo
- 676 414 1752 2.941 0.902 0.136 0.070 13 1.7 perirhinal_exvivo
- 438 276 1160 2.869 0.849 0.137 0.054 9 0.8 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 0050379 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050379/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 266947
- Total vertex volume 263106 (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) = 1459333 mm^3 (det: 1.334928 )
- lhCtxGM: 270594.696 270452.000 diff= 142.7 pctdiff= 0.053
- rhCtxGM: 260998.617 260632.000 diff= 366.6 pctdiff= 0.140
- lhCtxWM: 217865.953 218311.500 diff= -445.5 pctdiff=-0.205
- rhCtxWM: 211758.006 212169.500 diff= -411.5 pctdiff=-0.194
- SubCortGMVol 58627.000
- SupraTentVol 1031369.272 (1028334.000) diff=3035.272 pctdiff=0.294
- SupraTentVolNotVent 1023277.272 (1020242.000) diff=3035.272 pctdiff=0.297
- BrainSegVol 1154166.000 (1151331.000) diff=2835.000 pctdiff=0.246
- BrainSegVolNotVent 1142368.000 (1141816.272) diff=551.728 pctdiff=0.048
- BrainSegVolNotVent 1142368.000
- CerebellumVol 121922.000
- VentChorVol 8092.000
- 3rd4th5thCSF 3706.000
- CSFVol 871.000, OptChiasmVol 204.000
- MaskVol 1539640.000
- 747 418 1264 2.163 0.629 0.135 0.049 11 1.3 BA1_exvivo
- 1778 1197 2848 2.254 0.536 0.095 0.020 11 1.5 BA2_exvivo
- 1004 642 841 1.887 0.404 0.126 0.027 8 1.1 BA3a_exvivo
- 1412 1004 1515 1.500 0.393 0.080 0.019 7 1.0 BA3b_exvivo
- 1157 645 1997 2.756 0.515 0.106 0.035 10 1.6 BA4a_exvivo
- 971 664 1744 2.739 0.387 0.083 0.019 3 0.8 BA4p_exvivo
- 6869 4439 15271 2.967 0.630 0.124 0.042 83 12.1 BA6_exvivo
- 892 603 2306 2.810 0.648 0.127 0.044 12 1.5 BA44_exvivo
- 996 712 2973 2.915 0.585 0.154 0.044 16 1.7 BA45_exvivo
- 4007 2841 5353 1.759 0.499 0.147 0.040 58 6.5 V1_exvivo
- 4337 2982 6187 1.838 0.553 0.158 0.043 77 7.4 V2_exvivo
- 252 177 693 3.053 0.524 0.129 0.025 3 0.3 MT_exvivo
- 415 251 1059 2.908 0.903 0.119 0.077 7 1.2 perirhinal_exvivo
- 298 200 741 2.836 0.931 0.135 0.045 4 0.5 entorhinal_exvivo
- Started at Sun Oct 8 00:08:31 CEST 2017
- Ended at Sun Oct 8 09:27:12 CEST 2017
- #@#%# recon-all-run-time-hours 9.311
- recon-all -s 0050379 finished without error at Sun Oct 8 09:27:12 CEST 2017
|
