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|
- Sun Oct 8 00:35:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
- -subjid 0050419 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_2/0050419/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
- subjid 0050419
- 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-586 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 55506200 10487648 1761292 0 52069704
- -/+ buffers/cache: 3436496 62557352
- 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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: 2017/10/07-22:35:27-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-586 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-6.0.0/0050419
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_2/0050419/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/orig/001.mgz
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_2/0050419/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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_2/0050419/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-6.0.0/0050419/mri/orig/001.mgz...
- #--------------------------------------------
- #@# MotionCor Sun Oct 8 00:35:29 CEST 2017
- Found 1 runs
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/rawavg.mgz
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/orig.mgz --conform
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/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-6.0.0/0050419/mri/orig.mgz...
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Sun Oct 8 00:35:38 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/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-586 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 00:35:38 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.25058
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25058/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.25058/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.25058/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sun Oct 8 00:35:40 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.25058/nu0.mnc ./tmp.mri_nu_correct.mni.25058/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25058/0/ -iterations 1000 -distance 50
- [ntraut@tars-586:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/] [2017-10-08 00:35:40] 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.25058/0/ ./tmp.mri_nu_correct.mni.25058/nu0.mnc ./tmp.mri_nu_correct.mni.25058/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 36
- CV of field change: 0.000992138
-
-
-
- mri_convert ./tmp.mri_nu_correct.mni.25058/nu1.mnc orig_nu.mgz --like orig.mgz --conform
- mri_convert.bin ./tmp.mri_nu_correct.mni.25058/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.25058/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 00:36:45 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 00:36:46 CEST 2017
- Ended at Sun Oct 8 00:37:20 CEST 2017
- talairach_avi done
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Sun Oct 8 00:37:22 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7488, pval=0.6675 >= threshold=0.0050)
- awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/transforms/talairach_avi.log
- tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/transforms/talairach_avi.log
- TalAviQA: 0.97480
- z-score: 0
- #--------------------------------------------
- #@# Nu Intensity Correction Sun Oct 8 00:37:23 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-6.0.0/0050419/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-586 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 00:37:23 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.25890
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25890/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.25890/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.25890/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sun Oct 8 00:37:25 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.25890/nu0.mnc ./tmp.mri_nu_correct.mni.25890/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25890/0/
- [ntraut@tars-586:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/] [2017-10-08 00:37:26] 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.25890/0/ ./tmp.mri_nu_correct.mni.25890/nu0.mnc ./tmp.mri_nu_correct.mni.25890/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 24
- CV of field change: 0.000974292
-
-
- --------------------------------------------------------
- Iteration 2 Sun Oct 8 00:38:09 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.25890/nu1.mnc ./tmp.mri_nu_correct.mni.25890/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.25890/1/
- [ntraut@tars-586:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/] [2017-10-08 00:38:09] 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.25890/1/ ./tmp.mri_nu_correct.mni.25890/nu1.mnc ./tmp.mri_nu_correct.mni.25890/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 16
- CV of field change: 0.000965661
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.25890/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25890/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-6.0.0/0050419/mri
- cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.25890/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25890/ones.mgz
- sysname Linux
- hostname tars-586
- machine x86_64
- user ntraut
- input ./tmp.mri_nu_correct.mni.25890/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.25890/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.25890/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25890/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25890/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.25890/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25890/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25890/input.mean.dat
- sysname Linux
- hostname tars-586
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.25890/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.25890/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25890/ones.mgz --i ./tmp.mri_nu_correct.mni.25890/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25890/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25890/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.25890/ones.mgz --i ./tmp.mri_nu_correct.mni.25890/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25890/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25890/output.mean.dat
- sysname Linux
- hostname tars-586
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.25890/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.25890/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.25890/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.25890/nu2.mnc ./tmp.mri_nu_correct.mni.25890/nu2.mnc mul 1.03326129391482660389
- Saving result to './tmp.mri_nu_correct.mni.25890/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.25890/nu2.mnc nu.mgz --like orig.mgz
- mri_convert.bin ./tmp.mri_nu_correct.mni.25890/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.25890/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -1)
- k_ras = (0, 1, 0)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 9 seconds.
- mapping (15, 106) to ( 3, 110)
-
-
- Sun Oct 8 00:39:33 CEST 2017
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Sun Oct 8 00:39:34 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri
- mri_normalize -g 1 -mprage nu.mgz T1.mgz
- using max gradient = 1.000
- assuming input volume is MGH (Van der Kouwe) MP-RAGE
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 0.96316 0.07798 -0.03653 2.75716;
- -0.07400 1.11691 0.18221 -1.32323;
- 0.03158 -0.20964 1.27227 -30.80481;
- 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 = 11
- Starting OpenSpline(): npoints = 11
- 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 110
- gm peak at 66 (66), valley at 30 (30)
- csf peak at 33, setting threshold to 55
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 110
- white matter peak found at 110
- gm peak at 63 (63), valley at 29 (29)
- csf peak at 32, setting threshold to 52
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 5 seconds.
- #--------------------------------------------
- #@# Skull Stripping Sun Oct 8 00:41:39 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- == Number of threads available to mri_em_register for OpenMP = 2 ==
- reading 1 input volumes...
- logging results to talairach_with_skull.log
- reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'...
- average std = 22.9 using min determinant for regularization = 52.6
- 0 singular and 9002 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- accounting for voxel sizes in initial transform
- bounding unknown intensity as < 8.7 or > 569.1
- total sample mean = 77.6 (1399 zeros)
- ************************************************
- spacing=8, using 3243 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3243, passno 0, spacing 8
- resetting wm mean[0]: 100 --> 108
- resetting gm mean[0]: 61 --> 61
- input volume #1 is the most T1-like
- using real data threshold=11.0
- skull bounding box = (42, 23, 18) --> (209, 167, 205)
- using (98, 71, 112) as brain centroid...
- mean wm in atlas = 108, using box (77,53,89) --> (118, 88,135) to find MRI wm
- before smoothing, mri peak at 105
- robust fit to distribution - 104 +- 7.7
- after smoothing, mri peak at 104, scaling input intensities by 1.038
- scaling channel 0 by 1.03846
- initial log_p = -4.570
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.550583 @ (-9.091, 27.273, -9.091)
- max log p = -4.430731 @ (4.545, -13.636, 13.636)
- max log p = -4.413496 @ (2.273, -2.273, -2.273)
- max log p = -4.391697 @ (3.409, 12.500, -5.682)
- max log p = -4.383786 @ (-1.705, 0.568, -0.568)
- max log p = -4.378005 @ (0.284, -0.852, -0.284)
- Found translation: (-0.3, 23.6, -4.3): log p = -4.378
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.022, old_max_log_p =-4.378 (thresh=-4.4)
- 1.00000 0.00000 0.00000 -0.28409;
- 0.00000 1.22567 0.16136 -21.77067;
- 0.00000 -0.15011 1.14016 4.89585;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.011, old_max_log_p =-4.022 (thresh=-4.0)
- 0.91709 0.01812 -0.13766 22.89470;
- 0.00000 1.31760 0.17347 -34.06654;
- 0.13053 -0.14882 1.13041 -10.53366;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.999, old_max_log_p =-4.011 (thresh=-4.0)
- 0.99575 -0.00157 0.01190 -0.85826;
- 0.00000 1.31760 0.17347 -34.06654;
- 0.00971 -0.14991 1.13870 3.81656;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.999, old_max_log_p =-3.999 (thresh=-4.0)
- 0.99575 -0.00157 0.01190 -0.85826;
- 0.00000 1.31760 0.17347 -34.06654;
- 0.00971 -0.14991 1.13870 3.81656;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.927, old_max_log_p =-3.999 (thresh=-4.0)
- 0.97323 -0.03434 -0.06568 12.43335;
- 0.02937 1.29584 0.13002 -28.54400;
- 0.07337 -0.10609 1.12049 -9.28000;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.918, old_max_log_p =-3.927 (thresh=-3.9)
- 0.99392 0.00158 -0.02310 0.88338;
- 0.00214 1.26263 0.20005 -30.75764;
- 0.03941 -0.18939 1.11114 5.88011;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.918, old_max_log_p =-3.918 (thresh=-3.9)
- 0.99392 0.00158 -0.02310 0.88338;
- 0.00214 1.26263 0.20005 -30.75764;
- 0.03941 -0.18939 1.11114 5.88011;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.897, old_max_log_p =-3.918 (thresh=-3.9)
- 0.99547 0.00469 -0.04138 2.33212;
- 0.00214 1.26559 0.20052 -31.16295;
- 0.05560 -0.18912 1.10931 3.99091;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.895, old_max_log_p =-3.897 (thresh=-3.9)
- 0.99664 0.00469 -0.04142 2.18852;
- 0.00259 1.26104 0.20912 -31.15697;
- 0.05552 -0.19921 1.10634 5.53291;
- 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
- 0.99664 0.00469 -0.04142 2.18852;
- 0.00259 1.26104 0.20912 -31.15697;
- 0.05552 -0.19921 1.10634 5.53291;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3243
- Quasinewton: input matrix
- 0.99664 0.00469 -0.04142 2.18852;
- 0.00259 1.26104 0.20912 -31.15697;
- 0.05552 -0.19921 1.10634 5.53291;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 0.99664 0.00469 -0.04142 2.18852;
- 0.00259 1.26104 0.20912 -31.15697;
- 0.05552 -0.19921 1.10634 5.53291;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.895 (old=-4.570)
- transform before final EM align:
- 0.99664 0.00469 -0.04142 2.18852;
- 0.00259 1.26104 0.20912 -31.15697;
- 0.05552 -0.19921 1.10634 5.53291;
- 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
- 0.99664 0.00469 -0.04142 2.18852;
- 0.00259 1.26104 0.20912 -31.15697;
- 0.05552 -0.19921 1.10634 5.53291;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 364799
- Quasinewton: input matrix
- 0.99664 0.00469 -0.04142 2.18852;
- 0.00259 1.26104 0.20912 -31.15697;
- 0.05552 -0.19921 1.10634 5.53291;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 013: -log(p) = 4.3 tol 0.000000
- final transform:
- 0.99664 0.00469 -0.04142 2.18852;
- 0.00259 1.26104 0.20912 -31.15697;
- 0.05552 -0.19921 1.10634 5.53291;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach_with_skull.lta...
- mri_em_register utimesec 1773.388403
- mri_em_register stimesec 1.638750
- 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 157572
- mri_em_register ru_majflt 0
- mri_em_register ru_nswap 0
- mri_em_register ru_inblock 0
- mri_em_register ru_oublock 32
- mri_em_register ru_msgsnd 0
- mri_em_register ru_msgrcv 0
- mri_em_register ru_nsignals 0
- mri_em_register ru_nvcsw 131
- mri_em_register ru_nivcsw 7623
- registration took 15 minutes and 15 seconds.
- mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
- Mode: T1 normalized volume
- Mode: Use the information of atlas (default parms, --help for details)
- *********************************************************
- The input file is T1.mgz
- The output file is brainmask.auto.mgz
- Weighting the input with atlas information before watershed
- *************************WATERSHED**************************
- Sorting...
- first estimation of the COG coord: x=126 y=96 z=109 r=68
- first estimation of the main basin volume: 1373526 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 16 found in the rest of the brain
- global maximum in x=152, y=94, z=76, Imax=255
- CSF=19, 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=8361039559 voxels, voxel volume =1.000
- = 8361039559 mmm3 = 8361039.360 cm3
- done.
- PostAnalyze...Basin Prior
- 175 basins merged thanks to atlas
- ***** 0 basin(s) merged in 1 iteration(s)
- ***** 0 voxel(s) added to the main basin
- done.
- Weighting the input with prior template
- ****************TEMPLATE DEFORMATION****************
- second estimation of the COG coord: x=127,y=101, z=104, r=8761 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 44917
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1043781280
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1044142717
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1045064877
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1074832338
- OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1071804068
- Problem with the least square interpolation in GM_MIN calculation.
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 3, 4, 34, 58
- after analyzing : 3, 24, 34, 32
- RIGHT_CER
- before analyzing : 3, 4, 42, 71
- after analyzing : 3, 29, 42, 39
- LEFT_CER
- before analyzing : 3, 4, 39, 60
- after analyzing : 3, 27, 39, 35
- RIGHT_BRAIN
- before analyzing : 4, 6, 34, 58
- after analyzing : 4, 24, 34, 32
- LEFT_BRAIN
- before analyzing : 3, 4, 34, 59
- after analyzing : 3, 24, 34, 32
- OTHER
- before analyzing : 4, 15, 83, 95
- after analyzing : 4, 60, 83, 68
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...71 iterations
- *********************VALIDATION*********************
- curvature mean = -0.014, std = 0.010
- curvature mean = 67.616, std = 8.264
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 4.57, sigma = 6.54
- after rotation: sse = 4.57, sigma = 6.54
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 6.57, its var is 8.19
- before Erosion-Dilatation 3.90% of inacurate vertices
- after Erosion-Dilatation 6.01% of inacurate vertices
- Validation of the shape of the surface done.
- Scaling of atlas fields onto current surface fields
- ********FINAL ITERATIVE TEMPLATE DEFORMATION********
- Compute Local values csf/gray
- Fine Segmentation...28 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1421250 voxels, voxel volume = 1.000 mm3
- = 1421250 mmm3 = 1421.250 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- mri_watershed utimesec 23.593413
- mri_watershed stimesec 0.428934
- mri_watershed ru_maxrss 818720
- mri_watershed ru_ixrss 0
- mri_watershed ru_idrss 0
- mri_watershed ru_isrss 0
- mri_watershed ru_minflt 211764
- mri_watershed ru_majflt 0
- mri_watershed ru_nswap 0
- mri_watershed ru_inblock 0
- mri_watershed ru_oublock 2248
- mri_watershed ru_msgsnd 0
- mri_watershed ru_msgrcv 0
- mri_watershed ru_nsignals 0
- mri_watershed ru_nvcsw 1878
- mri_watershed ru_nivcsw 74
- mri_watershed done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Sun Oct 8 00:57:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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=23.1
- skull bounding box = (53, 45, 35) --> (200, 149, 188)
- using (102, 80, 112) as brain centroid...
- mean wm in atlas = 107, using box (84,67,93) --> (120, 92,130) to find MRI wm
- before smoothing, mri peak at 103
- robust fit to distribution - 103 +- 6.6
- after smoothing, mri peak at 103, scaling input intensities by 1.039
- scaling channel 0 by 1.03883
- initial log_p = -4.248
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.130107 @ (-9.091, 9.091, -9.091)
- max log p = -3.981550 @ (4.545, 4.545, 4.545)
- max log p = -3.961359 @ (2.273, 2.273, 2.273)
- max log p = -3.917463 @ (1.136, 1.136, 3.409)
- max log p = -3.905686 @ (0.568, -0.568, -0.568)
- max log p = -3.902217 @ (-0.852, -0.852, -0.852)
- Found translation: (-1.4, 15.6, -0.3): log p = -3.902
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.660, old_max_log_p =-3.902 (thresh=-3.9)
- 1.00000 0.00000 0.00000 -1.42046;
- 0.00000 1.22567 0.14032 -22.60484;
- 0.00000 -0.16136 1.06580 9.48633;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.660, old_max_log_p =-3.660 (thresh=-3.7)
- 1.00000 0.00000 0.00000 -1.42046;
- 0.00000 1.22567 0.14032 -22.60484;
- 0.00000 -0.16136 1.06580 9.48633;
- 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=-3.556, old_max_log_p =-3.660 (thresh=-3.7)
- 0.97915 0.00778 -0.06866 7.69681;
- 0.00000 1.25337 0.10734 -20.04616;
- 0.06540 -0.12091 1.06753 -3.14915;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.556, old_max_log_p =-3.556 (thresh=-3.6)
- 0.97915 0.00778 -0.06866 7.69681;
- 0.00000 1.25337 0.10734 -20.04616;
- 0.06540 -0.12091 1.06753 -3.14915;
- 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=-3.535, old_max_log_p =-3.556 (thresh=-3.6)
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07348 -0.12099 1.06819 -3.77676;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.533, old_max_log_p =-3.535 (thresh=-3.5)
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07356 -0.12113 1.06944 -3.90476;
- 0.00000 0.00000 0.00000 1.00000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 2830 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07356 -0.12113 1.06944 -3.90476;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2830
- Quasinewton: input matrix
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07356 -0.12113 1.06944 -3.90476;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07356 -0.12113 1.06944 -3.90476;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.533 (old=-4.248)
- transform before final EM align:
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07356 -0.12113 1.06944 -3.90476;
- 0.00000 0.00000 0.00000 1.00000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 315557 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07356 -0.12113 1.06944 -3.90476;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 315557
- Quasinewton: input matrix
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07356 -0.12113 1.06944 -3.90476;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 010: -log(p) = 4.0 tol 0.000000
- final transform:
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07356 -0.12113 1.06944 -3.90476;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach.lta...
- mri_em_register utimesec 1048.429614
- mri_em_register stimesec 1.229813
- mri_em_register ru_maxrss 601048
- mri_em_register ru_ixrss 0
- mri_em_register ru_idrss 0
- mri_em_register ru_isrss 0
- mri_em_register ru_minflt 159454
- 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 168
- mri_em_register ru_nivcsw 4774
- registration took 9 minutes and 8 seconds.
- #--------------------------------------
- #@# CA Normalize Sun Oct 8 01:06:25 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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=23.1
- skull bounding box = (53, 45, 35) --> (200, 149, 188)
- using (102, 80, 112) as brain centroid...
- mean wm in atlas = 107, using box (84,67,93) --> (120, 92,130) to find MRI wm
- before smoothing, mri peak at 103
- robust fit to distribution - 103 +- 6.6
- after smoothing, mri peak at 103, scaling input intensities by 1.039
- scaling channel 0 by 1.03883
- using 246344 sample points...
- INFO: compute sample coordinates transform
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07356 -0.12113 1.06944 -3.90476;
- 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 (122, 49, 31) --> (195, 142, 187)
- Left_Cerebral_White_Matter: limiting intensities to 104.0 --> 132.0
- 119 of 510 (23.3%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 50, 33) --> (132, 142, 188)
- Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
- 0 of 305 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (127, 119, 54) --> (177, 153, 105)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 0 of 24 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (81, 119, 55) --> (126, 152, 108)
- Right_Cerebellum_White_Matter: limiting intensities to 112.0 --> 132.0
- 9 of 15 (60.0%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (111, 111, 89) --> (146, 167, 117)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 0 of 13 (0.0%) samples deleted
- using 867 total control points for intensity normalization...
- bias field = 0.982 +- 0.074
- 0 of 739 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (122, 49, 31) --> (195, 142, 187)
- Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 120.0
- 2 of 715 (0.3%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 50, 33) --> (132, 142, 188)
- Right_Cerebral_White_Matter: limiting intensities to 102.0 --> 132.0
- 232 of 440 (52.7%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (127, 119, 54) --> (177, 153, 105)
- Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0
- 40 of 71 (56.3%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (81, 119, 55) --> (126, 152, 108)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 2 of 48 (4.2%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (111, 111, 89) --> (146, 167, 117)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 62 of 79 (78.5%) samples deleted
- using 1353 total control points for intensity normalization...
- bias field = 1.008 +- 0.081
- 0 of 1000 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (122, 49, 31) --> (195, 142, 187)
- Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 9 of 838 (1.1%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 50, 33) --> (132, 142, 188)
- Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
- 240 of 583 (41.2%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (127, 119, 54) --> (177, 153, 105)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 60 of 107 (56.1%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (81, 119, 55) --> (126, 152, 108)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 9 of 62 (14.5%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (111, 111, 89) --> (146, 167, 117)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 123 of 133 (92.5%) samples deleted
- using 1723 total control points for intensity normalization...
- bias field = 1.027 +- 0.069
- 0 of 1250 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 1 minutes and 51 seconds.
- #--------------------------------------
- #@# CA Reg Sun Oct 8 01:08:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri
- mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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) = 1.33 (predicted orig area = 6.0)
- 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=0.913, neg=0, invalid=762
- 0001: dt=221.952000, rms=0.815 (10.717%), neg=0, invalid=762
- 0002: dt=248.865376, rms=0.793 (2.735%), neg=0, invalid=762
- 0003: dt=168.239521, rms=0.783 (1.212%), neg=0, invalid=762
- 0004: dt=369.920000, rms=0.775 (1.057%), neg=0, invalid=762
- 0005: dt=129.472000, rms=0.770 (0.612%), neg=0, invalid=762
- 0006: dt=887.808000, rms=0.763 (1.009%), neg=0, invalid=762
- 0007: dt=129.472000, rms=0.759 (0.431%), neg=0, invalid=762
- 0008: dt=443.904000, rms=0.758 (0.219%), neg=0, invalid=762
- 0009: dt=443.904000, rms=0.758 (-0.377%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.759, neg=0, invalid=762
- 0010: dt=129.472000, rms=0.755 (0.427%), neg=0, invalid=762
- 0011: dt=517.888000, rms=0.753 (0.366%), neg=0, invalid=762
- 0012: dt=517.888000, rms=0.750 (0.291%), neg=0, invalid=762
- 0013: dt=369.920000, rms=0.749 (0.157%), neg=0, invalid=762
- 0014: dt=369.920000, rms=0.748 (0.163%), neg=0, invalid=762
- 0015: dt=369.920000, rms=0.746 (0.271%), neg=0, invalid=762
- 0016: dt=369.920000, rms=0.743 (0.338%), neg=0, invalid=762
- 0017: dt=369.920000, rms=0.741 (0.350%), neg=0, invalid=762
- 0018: dt=369.920000, rms=0.738 (0.326%), neg=0, invalid=762
- 0019: dt=369.920000, rms=0.737 (0.218%), neg=0, invalid=762
- 0020: dt=369.920000, rms=0.735 (0.287%), neg=0, invalid=762
- 0021: dt=369.920000, rms=0.733 (0.178%), neg=0, invalid=762
- 0022: dt=369.920000, rms=0.732 (0.210%), neg=0, invalid=762
- 0023: dt=369.920000, rms=0.730 (0.207%), neg=0, invalid=762
- 0024: dt=369.920000, rms=0.729 (0.195%), neg=0, invalid=762
- 0025: dt=369.920000, rms=0.728 (0.150%), neg=0, invalid=762
- 0026: dt=369.920000, rms=0.726 (0.182%), neg=0, invalid=762
- 0027: dt=369.920000, rms=0.725 (0.166%), neg=0, invalid=762
- 0028: dt=369.920000, rms=0.724 (0.186%), neg=0, invalid=762
- 0029: dt=369.920000, rms=0.723 (0.143%), neg=0, invalid=762
- 0030: dt=369.920000, rms=0.722 (0.138%), neg=0, invalid=762
- 0031: dt=369.920000, rms=0.721 (0.117%), neg=0, invalid=762
- 0032: dt=369.920000, rms=0.720 (0.129%), neg=0, invalid=762
- 0033: dt=369.920000, rms=0.719 (0.177%), neg=0, invalid=762
- 0034: dt=369.920000, rms=0.718 (0.082%), neg=0, invalid=762
- 0035: dt=369.920000, rms=0.718 (0.062%), neg=0, invalid=762
- 0036: dt=221.952000, rms=0.718 (0.040%), neg=0, invalid=762
- 0037: dt=221.952000, rms=0.717 (0.021%), neg=0, invalid=762
- 0038: dt=221.952000, rms=0.717 (0.017%), neg=0, invalid=762
- 0039: dt=221.952000, rms=0.717 (0.035%), neg=0, invalid=762
- 0040: dt=221.952000, rms=0.717 (0.031%), neg=0, invalid=762
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.723, neg=0, invalid=762
- 0041: dt=98.714653, rms=0.719 (0.533%), neg=0, invalid=762
- 0042: dt=331.776000, rms=0.712 (1.058%), neg=0, invalid=762
- 0043: dt=63.689018, rms=0.707 (0.700%), neg=0, invalid=762
- 0044: dt=331.776000, rms=0.701 (0.762%), neg=0, invalid=762
- 0045: dt=36.288000, rms=0.699 (0.406%), neg=0, invalid=762
- 0046: dt=103.680000, rms=0.697 (0.208%), neg=0, invalid=762
- 0047: dt=103.680000, rms=0.696 (0.138%), neg=0, invalid=762
- 0048: dt=103.680000, rms=0.694 (0.300%), neg=0, invalid=762
- 0049: dt=103.680000, rms=0.691 (0.376%), neg=0, invalid=762
- 0050: dt=103.680000, rms=0.688 (0.522%), neg=0, invalid=762
- 0051: dt=103.680000, rms=0.684 (0.512%), neg=0, invalid=762
- 0052: dt=103.680000, rms=0.681 (0.523%), neg=0, invalid=762
- 0053: dt=103.680000, rms=0.678 (0.363%), neg=0, invalid=762
- 0054: dt=103.680000, rms=0.675 (0.406%), neg=0, invalid=762
- 0055: dt=103.680000, rms=0.673 (0.318%), neg=0, invalid=762
- 0056: dt=103.680000, rms=0.672 (0.240%), neg=0, invalid=762
- 0057: dt=103.680000, rms=0.670 (0.200%), neg=0, invalid=762
- 0058: dt=103.680000, rms=0.669 (0.270%), neg=0, invalid=762
- 0059: dt=103.680000, rms=0.667 (0.230%), neg=0, invalid=762
- 0060: dt=103.680000, rms=0.666 (0.158%), neg=0, invalid=762
- 0061: dt=103.680000, rms=0.665 (0.146%), neg=0, invalid=762
- 0062: dt=103.680000, rms=0.664 (0.142%), neg=0, invalid=762
- 0063: dt=103.680000, rms=0.663 (0.102%), neg=0, invalid=762
- 0064: dt=103.680000, rms=0.663 (0.098%), neg=0, invalid=762
- 0065: dt=103.680000, rms=0.662 (0.047%), neg=0, invalid=762
- 0066: dt=103.680000, rms=0.662 (-0.015%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.663, neg=0, invalid=762
- 0067: dt=94.199134, rms=0.660 (0.411%), neg=0, invalid=762
- 0068: dt=36.288000, rms=0.660 (0.080%), neg=0, invalid=762
- 0069: dt=36.288000, rms=0.660 (0.022%), neg=0, invalid=762
- 0070: dt=36.288000, rms=0.660 (0.031%), neg=0, invalid=762
- 0071: dt=36.288000, rms=0.659 (0.024%), neg=0, invalid=762
- 0072: dt=36.288000, rms=0.659 (-0.010%), neg=0, invalid=762
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.689, neg=0, invalid=762
- 0073: dt=4.800000, rms=0.688 (0.168%), neg=0, invalid=762
- 0074: dt=1.600000, rms=0.688 (0.005%), neg=0, invalid=762
- 0075: dt=1.600000, rms=0.688 (-0.002%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.689, neg=0, invalid=762
- 0076: dt=0.700000, rms=0.688 (0.122%), neg=0, invalid=762
- 0077: dt=0.700000, rms=0.688 (0.000%), neg=0, invalid=762
- 0078: dt=0.700000, rms=0.688 (0.001%), neg=0, invalid=762
- 0079: dt=0.700000, rms=0.688 (-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=0.765, neg=0, invalid=762
- 0080: dt=6.005571, rms=0.739 (3.330%), neg=0, invalid=762
- 0081: dt=4.867925, rms=0.737 (0.301%), neg=0, invalid=762
- 0082: dt=1.500000, rms=0.737 (0.018%), neg=0, invalid=762
- 0083: dt=1.500000, rms=0.737 (-0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.738, neg=0, invalid=762
- 0084: dt=0.000000, rms=0.737 (0.098%), neg=0, invalid=762
- 0085: dt=0.000000, rms=0.737 (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=0.796, neg=0, invalid=762
- 0086: dt=0.384000, rms=0.795 (0.133%), neg=0, invalid=762
- 0087: dt=0.448000, rms=0.795 (0.049%), neg=0, invalid=762
- 0088: dt=0.448000, rms=0.794 (0.069%), neg=0, invalid=762
- 0089: dt=0.448000, rms=0.794 (0.079%), neg=0, invalid=762
- 0090: dt=0.448000, rms=0.793 (0.030%), neg=0, invalid=762
- 0091: dt=0.448000, rms=0.793 (-0.035%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.794, neg=0, invalid=762
- 0092: dt=3.195046, rms=0.786 (0.963%), neg=0, invalid=762
- 0093: dt=0.000000, rms=0.786 (0.002%), neg=0, invalid=762
- 0094: dt=0.100000, rms=0.786 (-0.005%), 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=0.734, neg=0, invalid=762
- 0095: dt=0.916153, rms=0.711 (3.099%), neg=0, invalid=762
- 0096: dt=0.080000, rms=0.710 (0.147%), neg=0, invalid=762
- 0097: dt=0.080000, rms=0.710 (-0.071%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.711, neg=0, invalid=762
- 0098: dt=0.028000, rms=0.710 (0.126%), neg=0, invalid=762
- 0099: dt=0.020000, rms=0.710 (0.005%), neg=0, invalid=762
- 0100: dt=0.020000, rms=0.710 (-0.007%), neg=0, invalid=762
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.10027 (20)
- mri peak = 0.08397 (18)
- Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (1163 voxels, overlap=0.397)
- Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (1163 voxels, peak = 20), gca=20.5
- gca peak = 0.15565 (16)
- mri peak = 0.07483 (17)
- Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (453 voxels, overlap=0.818)
- Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (453 voxels, peak = 17), gca=16.6
- gca peak = 0.26829 (96)
- mri peak = 0.06017 (92)
- Right_Pallidum (52): linear fit = 0.96 x + 0.0 (765 voxels, overlap=0.724)
- Right_Pallidum (52): linear fit = 0.96 x + 0.0 (765 voxels, peak = 93), gca=92.6
- gca peak = 0.20183 (93)
- mri peak = 0.06038 (77)
- Left_Pallidum (13): linear fit = 0.81 x + 0.0 (718 voxels, overlap=0.412)
- Left_Pallidum (13): linear fit = 0.81 x + 0.0 (718 voxels, peak = 76), gca=75.8
- gca peak = 0.21683 (55)
- mri peak = 0.08924 (63)
- Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (421 voxels, overlap=0.514)
- Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (421 voxels, peak = 62), gca=62.4
- gca peak = 0.30730 (58)
- mri peak = 0.06107 (67)
- Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (424 voxels, overlap=0.792)
- Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (424 voxels, peak = 64), gca=63.5
- gca peak = 0.11430 (101)
- mri peak = 0.05240 (104)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52207 voxels, overlap=0.902)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52207 voxels, peak = 105), gca=104.5
- gca peak = 0.12076 (102)
- mri peak = 0.05757 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (50365 voxels, overlap=0.914)
- Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (50365 voxels, peak = 104), gca=103.5
- gca peak = 0.14995 (59)
- mri peak = 0.03875 (58)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (14848 voxels, overlap=0.986)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (14848 voxels, peak = 60), gca=60.5
- gca peak = 0.15082 (58)
- mri peak = 0.03398 (67)
- Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (15801 voxels, overlap=0.862)
- Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (15801 voxels, peak = 64), gca=63.5
- gca peak = 0.14161 (67)
- mri peak = 0.08020 (66)
- Right_Caudate (50): linear fit = 0.98 x + 0.0 (806 voxels, overlap=0.885)
- Right_Caudate (50): linear fit = 0.98 x + 0.0 (806 voxels, peak = 65), gca=65.3
- gca peak = 0.15243 (71)
- mri peak = 0.03720 (80)
- Left_Caudate (11): linear fit = 1.11 x + 0.0 (817 voxels, overlap=0.564)
- Left_Caudate (11): linear fit = 1.11 x + 0.0 (817 voxels, peak = 78), gca=78.5
- gca peak = 0.13336 (57)
- mri peak = 0.04096 (51)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (13417 voxels, overlap=0.987)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (13417 voxels, peak = 55), gca=55.0
- gca peak = 0.13252 (56)
- mri peak = 0.04435 (57)
- Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17126 voxels, overlap=0.979)
- Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17126 voxels, peak = 59), gca=58.5
- gca peak = 0.18181 (84)
- mri peak = 0.04078 (79)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6005 voxels, overlap=0.975)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6005 voxels, peak = 89), gca=88.6
- gca peak = 0.20573 (83)
- mri peak = 0.05537 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (5329 voxels, overlap=0.581)
- Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (5329 voxels, peak = 93), gca=92.5
- gca peak = 0.21969 (57)
- mri peak = 0.06859 (54)
- Left_Amygdala (18): linear fit = 1.10 x + 0.0 (303 voxels, overlap=1.004)
- Left_Amygdala (18): linear fit = 1.10 x + 0.0 (303 voxels, peak = 62), gca=62.4
- gca peak = 0.39313 (56)
- mri peak = 0.07162 (63)
- Right_Amygdala (54): linear fit = 1.13 x + 0.0 (418 voxels, overlap=0.591)
- Right_Amygdala (54): linear fit = 1.13 x + 0.0 (418 voxels, peak = 64), gca=63.6
- gca peak = 0.14181 (85)
- mri peak = 0.05099 (78)
- Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4810 voxels, overlap=0.995)
- Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4810 voxels, peak = 91), gca=90.5
- gca peak = 0.11978 (83)
- mri peak = 0.06674 (77)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4027 voxels, overlap=0.929)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4027 voxels, peak = 84), gca=84.2
- gca peak = 0.13399 (79)
- mri peak = 0.03843 (80)
- Left_Putamen (12): linear fit = 1.04 x + 0.0 (1638 voxels, overlap=0.695)
- Left_Putamen (12): linear fit = 1.04 x + 0.0 (1638 voxels, peak = 83), gca=82.6
- gca peak = 0.14159 (79)
- mri peak = 0.05129 (84)
- Right_Putamen (51): linear fit = 1.08 x + 0.0 (2099 voxels, overlap=0.450)
- Right_Putamen (51): linear fit = 1.08 x + 0.0 (2099 voxels, peak = 85), gca=84.9
- gca peak = 0.10025 (80)
- mri peak = 0.14701 (80)
- Brain_Stem (16): linear fit = 1.05 x + 0.0 (9463 voxels, overlap=0.401)
- Brain_Stem (16): linear fit = 1.05 x + 0.0 (9463 voxels, peak = 84), gca=84.4
- gca peak = 0.13281 (86)
- mri peak = 0.09903 (84)
- Right_VentralDC (60): linear fit = 0.96 x + 0.0 (822 voxels, overlap=0.724)
- Right_VentralDC (60): linear fit = 0.96 x + 0.0 (822 voxels, peak = 83), gca=83.0
- gca peak = 0.12801 (89)
- mri peak = 0.10850 (82)
- Left_VentralDC (28): linear fit = 0.93 x + 0.0 (908 voxels, overlap=0.657)
- Left_VentralDC (28): linear fit = 0.93 x + 0.0 (908 voxels, peak = 82), gca=82.3
- gca peak = 0.20494 (23)
- mri peak = 1.00000 (54)
- gca peak = 0.15061 (21)
- mri peak = 0.10260 (11)
- Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (217 voxels, overlap=0.020)
- Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (217 voxels, peak = 10), gca=10.0
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.18056 (32)
- gca peak Left_Thalamus = 0.64095 (94)
- gca peak Third_Ventricle = 0.20494 (23)
- gca peak Fourth_Ventricle = 0.15061 (21)
- gca peak CSF = 0.20999 (34)
- gca peak Left_Accumbens_area = 0.39030 (62)
- gca peak Left_undetermined = 0.95280 (25)
- gca peak Left_vessel = 0.67734 (53)
- gca peak Left_choroid_plexus = 0.09433 (44)
- gca peak Right_Inf_Lat_Vent = 0.23544 (26)
- gca peak Right_Accumbens_area = 0.30312 (64)
- gca peak Right_vessel = 0.46315 (51)
- gca peak Right_choroid_plexus = 0.14086 (44)
- gca peak Fifth_Ventricle = 0.51669 (36)
- gca peak WM_hypointensities = 0.09722 (76)
- gca peak non_WM_hypointensities = 0.11899 (47)
- gca peak Optic_Chiasm = 0.39033 (72)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.10 x + 0.0
- estimating mean wm scale to be 1.02 x + 0.0
- estimating mean csf scale to be 1.03 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=0.705, neg=0, invalid=762
- 0101: dt=110.976000, rms=0.699 (0.763%), neg=0, invalid=762
- 0102: dt=295.936000, rms=0.696 (0.462%), neg=0, invalid=762
- 0103: dt=369.920000, rms=0.694 (0.306%), neg=0, invalid=762
- 0104: dt=110.976000, rms=0.693 (0.130%), neg=0, invalid=762
- 0105: dt=129.472000, rms=0.693 (0.051%), neg=0, invalid=762
- 0106: dt=129.472000, rms=0.692 (0.051%), neg=0, invalid=762
- 0107: dt=295.936000, rms=0.692 (0.088%), neg=0, invalid=762
- 0108: dt=92.480000, rms=0.691 (0.048%), neg=0, invalid=762
- 0109: dt=92.480000, rms=0.691 (0.032%), neg=0, invalid=762
- 0110: dt=92.480000, rms=0.691 (0.047%), neg=0, invalid=762
- 0111: dt=92.480000, rms=0.690 (0.065%), neg=0, invalid=762
- 0112: dt=92.480000, rms=0.690 (0.069%), neg=0, invalid=762
- 0113: dt=92.480000, rms=0.689 (0.070%), neg=0, invalid=762
- 0114: dt=92.480000, rms=0.689 (0.062%), neg=0, invalid=762
- 0115: dt=92.480000, rms=0.689 (0.042%), neg=0, invalid=762
- 0116: dt=92.480000, rms=0.688 (0.031%), neg=0, invalid=762
- 0117: dt=92.480000, rms=0.688 (0.024%), neg=0, invalid=762
- 0118: dt=92.480000, rms=0.688 (0.020%), neg=0, invalid=762
- 0119: dt=2071.552000, rms=0.687 (0.193%), neg=0, invalid=762
- 0120: dt=55.488000, rms=0.687 (0.013%), neg=0, invalid=762
- 0121: dt=55.488000, rms=0.687 (0.002%), neg=0, invalid=762
- 0122: dt=55.488000, rms=0.687 (-0.009%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.687, neg=0, invalid=762
- 0123: dt=221.952000, rms=0.685 (0.312%), neg=0, invalid=762
- 0124: dt=369.920000, rms=0.684 (0.183%), neg=0, invalid=762
- 0125: dt=129.472000, rms=0.683 (0.053%), neg=0, invalid=762
- 0126: dt=369.920000, rms=0.683 (0.037%), neg=0, invalid=762
- 0127: dt=369.920000, rms=0.683 (-0.030%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.684, neg=0, invalid=762
- 0128: dt=87.100592, rms=0.679 (0.662%), neg=0, invalid=762
- 0129: dt=211.277108, rms=0.673 (1.000%), neg=0, invalid=762
- 0130: dt=70.981818, rms=0.669 (0.485%), neg=0, invalid=762
- 0131: dt=124.416000, rms=0.666 (0.464%), neg=0, invalid=762
- 0132: dt=36.288000, rms=0.665 (0.238%), neg=0, invalid=762
- 0133: dt=145.152000, rms=0.663 (0.323%), neg=0, invalid=762
- 0134: dt=124.416000, rms=0.660 (0.371%), neg=0, invalid=762
- 0135: dt=36.288000, rms=0.659 (0.141%), neg=0, invalid=762
- 0136: dt=331.776000, rms=0.657 (0.292%), neg=0, invalid=762
- 0137: dt=67.531629, rms=0.654 (0.527%), neg=0, invalid=762
- 0138: dt=62.208000, rms=0.653 (0.087%), neg=0, invalid=762
- 0139: dt=414.720000, rms=0.650 (0.469%), neg=0, invalid=762
- 0140: dt=36.288000, rms=0.649 (0.234%), neg=0, invalid=762
- 0141: dt=36.288000, rms=0.648 (0.065%), neg=0, invalid=762
- 0142: dt=414.720000, rms=0.647 (0.237%), neg=0, invalid=762
- 0143: dt=77.020057, rms=0.645 (0.334%), neg=0, invalid=762
- 0144: dt=36.288000, rms=0.644 (0.056%), neg=0, invalid=762
- 0145: dt=497.664000, rms=0.643 (0.252%), neg=0, invalid=762
- 0146: dt=74.735484, rms=0.641 (0.282%), neg=0, invalid=762
- 0147: dt=9.072000, rms=0.641 (0.014%), neg=0, invalid=762
- 0148: dt=9.072000, rms=0.641 (0.009%), neg=0, invalid=762
- 0149: dt=4.536000, rms=0.641 (0.005%), neg=0, invalid=762
- 0150: dt=0.070875, rms=0.641 (0.003%), neg=0, invalid=762
- 0151: dt=0.008859, rms=0.641 (-0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.641, neg=0, invalid=762
- 0152: dt=145.152000, rms=0.637 (0.734%), neg=0, invalid=762
- 0153: dt=69.260274, rms=0.635 (0.232%), neg=0, invalid=762
- 0154: dt=36.288000, rms=0.635 (0.078%), neg=0, invalid=762
- 0155: dt=36.288000, rms=0.634 (0.060%), neg=0, invalid=762
- 0156: dt=0.567000, rms=0.634 (0.003%), neg=0, invalid=762
- 0157: dt=0.567000, rms=0.634 (0.001%), neg=0, invalid=762
- 0158: dt=0.283500, rms=0.634 (0.002%), neg=0, invalid=762
- 0159: dt=0.008859, rms=0.634 (0.000%), neg=0, invalid=762
- 0160: dt=0.004430, rms=0.634 (0.000%), neg=0, invalid=762
- 0161: dt=0.002215, rms=0.634 (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=0.639, neg=0, invalid=762
- 0162: dt=44.800000, rms=0.628 (1.844%), neg=0, invalid=762
- 0163: dt=32.000000, rms=0.620 (1.247%), neg=0, invalid=762
- 0164: dt=2.800000, rms=0.619 (0.084%), neg=0, invalid=762
- 0165: dt=2.400000, rms=0.619 (0.061%), neg=0, invalid=762
- 0166: dt=0.175000, rms=0.619 (0.011%), neg=0, invalid=762
- 0167: dt=0.010937, rms=0.619 (0.000%), neg=0, invalid=762
- 0168: dt=0.002734, rms=0.619 (0.000%), neg=0, invalid=762
- 0169: dt=0.000342, rms=0.619 (0.000%), neg=0, invalid=762
- 0170: dt=0.000000, rms=0.619 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.620, neg=0, invalid=762
- 0171: dt=11.200000, rms=0.616 (0.627%), neg=0, invalid=762
- 0172: dt=2.800000, rms=0.615 (0.101%), neg=0, invalid=762
- 0173: dt=2.800000, rms=0.615 (0.095%), neg=0, invalid=762
- 0174: dt=0.031250, rms=0.615 (0.000%), neg=0, invalid=762
- 0175: dt=0.001953, rms=0.615 (0.000%), neg=0, invalid=762
- 0176: dt=0.000008, rms=0.615 (0.000%), neg=0, invalid=762
- 0177: dt=0.000002, rms=0.615 (0.000%), neg=0, invalid=762
- 0178: dt=0.000000, rms=0.615 (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=0.631, neg=0, invalid=762
- 0179: dt=0.000000, rms=0.630 (0.123%), neg=0, invalid=762
- 0180: dt=0.000000, rms=0.630 (0.000%), neg=0, invalid=762
- 0181: dt=0.000001, rms=0.630 (0.000%), neg=0, invalid=762
- 0182: dt=0.000000, rms=0.630 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.631, neg=0, invalid=762
- 0183: dt=0.000000, rms=0.630 (0.123%), neg=0, invalid=762
- 0184: dt=0.000000, rms=0.630 (0.000%), neg=0, invalid=762
- 0185: dt=0.000001, rms=0.630 (0.000%), neg=0, invalid=762
- 0186: dt=0.000001, rms=0.630 (0.000%), neg=0, invalid=762
- 0187: dt=0.000000, rms=0.630 (-0.000%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.662, neg=0, invalid=762
- 0188: dt=1.792000, rms=0.649 (1.980%), neg=0, invalid=762
- 0189: dt=5.120000, rms=0.635 (2.089%), neg=0, invalid=762
- 0190: dt=0.000000, rms=0.635 (0.002%), neg=0, invalid=762
- 0191: dt=0.100000, rms=0.635 (-0.005%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.636, neg=0, invalid=762
- 0192: dt=3.608696, rms=0.631 (0.711%), neg=0, invalid=762
- 0193: dt=1.792000, rms=0.629 (0.325%), neg=0, invalid=762
- 0194: dt=7.168000, rms=0.625 (0.737%), neg=0, invalid=762
- 0195: dt=1.792000, rms=0.624 (0.017%), neg=0, invalid=762
- 0196: dt=1.792000, rms=0.624 (0.052%), neg=0, invalid=762
- 0197: dt=1.792000, rms=0.624 (0.100%), neg=0, invalid=762
- 0198: dt=1.792000, rms=0.623 (0.133%), neg=0, invalid=762
- 0199: dt=1.792000, rms=0.622 (0.105%), neg=0, invalid=762
- 0200: dt=1.792000, rms=0.622 (0.036%), neg=0, invalid=762
- 0201: dt=1.792000, rms=0.622 (-0.066%), neg=0, invalid=762
- 0202: dt=0.000000, rms=0.622 (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=0.609, neg=0, invalid=762
- 0203: dt=0.448000, rms=0.590 (3.029%), neg=0, invalid=762
- 0204: dt=0.448000, rms=0.585 (0.913%), neg=0, invalid=762
- 0205: dt=0.448000, rms=0.582 (0.524%), neg=0, invalid=762
- 0206: dt=0.448000, rms=0.580 (0.331%), neg=0, invalid=762
- 0207: dt=0.448000, rms=0.578 (0.256%), neg=0, invalid=762
- 0208: dt=0.448000, rms=0.577 (0.190%), neg=0, invalid=762
- 0209: dt=0.448000, rms=0.576 (0.155%), neg=0, invalid=762
- 0210: dt=0.448000, rms=0.576 (0.127%), neg=0, invalid=762
- 0211: dt=0.448000, rms=0.575 (0.108%), neg=0, invalid=762
- 0212: dt=0.448000, rms=0.574 (0.088%), neg=0, invalid=762
- 0213: dt=0.448000, rms=0.574 (0.083%), neg=0, invalid=762
- 0214: dt=0.448000, rms=0.574 (0.062%), neg=0, invalid=762
- 0215: dt=0.448000, rms=0.573 (0.067%), neg=0, invalid=762
- 0216: dt=0.448000, rms=0.573 (0.048%), neg=0, invalid=762
- 0217: dt=0.448000, rms=0.573 (0.052%), neg=0, invalid=762
- 0218: dt=0.448000, rms=0.572 (0.077%), neg=0, invalid=762
- 0219: dt=0.448000, rms=0.572 (0.109%), neg=0, invalid=762
- 0220: dt=0.448000, rms=0.571 (0.114%), neg=0, invalid=762
- 0221: dt=0.448000, rms=0.571 (0.016%), neg=0, invalid=762
- 0222: dt=0.448000, rms=0.571 (0.018%), neg=0, invalid=762
- 0223: dt=0.448000, rms=0.571 (0.020%), neg=0, invalid=762
- 0224: dt=0.448000, rms=0.570 (0.024%), neg=0, invalid=762
- 0225: dt=0.448000, rms=0.570 (0.019%), neg=0, invalid=762
- 0226: dt=0.448000, rms=0.570 (0.020%), neg=0, invalid=762
- 0227: dt=0.320000, rms=0.570 (-0.004%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.571, neg=0, invalid=762
- 0228: dt=0.448000, rms=0.563 (1.447%), neg=0, invalid=762
- 0229: dt=0.448000, rms=0.562 (0.182%), neg=0, invalid=762
- 0230: dt=0.448000, rms=0.561 (0.035%), neg=0, invalid=762
- 0231: dt=0.448000, rms=0.561 (-0.005%), 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=0.559, neg=0, invalid=762
- 0232: dt=0.000000, rms=0.558 (0.126%), neg=0, invalid=762
- 0233: dt=0.000000, rms=0.558 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.559, neg=0, invalid=762
- 0234: dt=73.984000, rms=0.558 (0.146%), neg=0, invalid=762
- 0235: dt=129.472000, rms=0.558 (0.027%), neg=0, invalid=762
- 0236: dt=129.472000, rms=0.558 (-0.007%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.558, neg=0, invalid=762
- 0237: dt=23.148936, rms=0.557 (0.213%), neg=0, invalid=762
- 0238: dt=20.736000, rms=0.557 (0.028%), neg=0, invalid=762
- 0239: dt=20.736000, rms=0.557 (0.019%), neg=0, invalid=762
- 0240: dt=20.736000, rms=0.557 (-0.035%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.558, neg=0, invalid=762
- 0241: dt=88.533333, rms=0.555 (0.552%), neg=0, invalid=762
- 0242: dt=31.104000, rms=0.553 (0.330%), neg=0, invalid=762
- 0243: dt=62.208000, rms=0.552 (0.083%), neg=0, invalid=762
- 0244: dt=62.208000, rms=0.552 (0.041%), neg=0, invalid=762
- 0245: dt=62.208000, rms=0.551 (0.234%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0246: dt=62.208000, rms=0.550 (0.210%), neg=0, invalid=762
- 0247: dt=62.208000, rms=0.549 (0.073%), neg=0, invalid=762
- 0248: dt=62.208000, rms=0.548 (0.168%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0249: dt=62.208000, rms=0.548 (0.128%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0250: dt=62.208000, rms=0.547 (0.049%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 0 iterations, nbhd size=0, neg = 0
- 0251: dt=62.208000, rms=0.547 (0.117%), neg=0, invalid=762
- 0252: dt=62.208000, rms=0.546 (0.071%), neg=0, invalid=762
- 0253: dt=31.104000, rms=0.546 (0.060%), neg=0, invalid=762
- 0254: dt=31.104000, rms=0.546 (0.020%), neg=0, invalid=762
- 0255: dt=31.104000, rms=0.546 (0.032%), neg=0, invalid=762
- 0256: dt=31.104000, rms=0.546 (0.037%), neg=0, invalid=762
- 0257: dt=31.104000, rms=0.545 (0.040%), neg=0, invalid=762
- 0258: dt=31.104000, rms=0.545 (0.041%), neg=0, invalid=762
- 0259: dt=31.104000, rms=0.545 (0.043%), neg=0, invalid=762
- 0260: dt=31.104000, rms=0.545 (0.040%), neg=0, invalid=762
- 0261: dt=31.104000, rms=0.544 (0.042%), neg=0, invalid=762
- 0262: dt=31.104000, rms=0.544 (0.035%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.546, neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0263: dt=11.200000, rms=0.544 (0.302%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 1 iterations, nbhd size=0, neg = 0
- 0264: dt=11.200000, rms=0.544 (0.064%), neg=0, invalid=762
- 0265: dt=11.200000, rms=0.544 (0.047%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 0 iterations, nbhd size=0, neg = 0
- 0266: dt=11.200000, rms=0.543 (-0.009%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.544, neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0267: dt=38.400000, rms=0.538 (1.158%), neg=0, invalid=762
- 0268: dt=23.433628, rms=0.536 (0.446%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0269: dt=25.573770, rms=0.534 (0.233%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0270: dt=25.573770, rms=0.533 (0.299%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0271: dt=25.573770, rms=0.531 (0.394%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 0 iterations, nbhd size=0, neg = 0
- 0272: dt=25.573770, rms=0.528 (0.447%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 2 iterations, nbhd size=0, neg = 0
- 0273: dt=25.573770, rms=0.526 (0.510%), neg=0, invalid=762
- iter 0, gcam->neg = 8
- after 9 iterations, nbhd size=1, neg = 0
- 0274: dt=25.573770, rms=0.523 (0.503%), neg=0, invalid=762
- iter 0, gcam->neg = 10
- after 1 iterations, nbhd size=0, neg = 0
- 0275: dt=25.573770, rms=0.521 (0.428%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 4 iterations, nbhd size=0, neg = 0
- 0276: dt=25.573770, rms=0.519 (0.330%), neg=0, invalid=762
- iter 0, gcam->neg = 6
- after 1 iterations, nbhd size=0, neg = 0
- 0277: dt=25.573770, rms=0.517 (0.371%), neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 2 iterations, nbhd size=0, neg = 0
- 0278: dt=25.573770, rms=0.516 (0.264%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 8 iterations, nbhd size=1, neg = 0
- 0279: dt=25.573770, rms=0.514 (0.258%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 3 iterations, nbhd size=0, neg = 0
- 0280: dt=25.573770, rms=0.514 (0.134%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 7 iterations, nbhd size=1, neg = 0
- 0281: dt=25.573770, rms=0.512 (0.239%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 1 iterations, nbhd size=0, neg = 0
- 0282: dt=25.573770, rms=0.512 (0.090%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 4 iterations, nbhd size=0, neg = 0
- 0283: dt=25.573770, rms=0.511 (0.154%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0284: dt=25.573770, rms=0.511 (-0.024%), neg=0, invalid=762
- 0285: dt=11.200000, rms=0.511 (0.023%), neg=0, invalid=762
- 0286: dt=32.000000, rms=0.511 (0.029%), neg=0, invalid=762
- 0287: dt=11.200000, rms=0.511 (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=0.520, neg=0, invalid=762
- 0288: dt=1.008000, rms=0.519 (0.152%), neg=0, invalid=762
- 0289: dt=0.252000, rms=0.519 (-0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.520, neg=0, invalid=762
- 0290: dt=2.304000, rms=0.519 (0.163%), neg=0, invalid=762
- 0291: dt=1.008000, rms=0.519 (0.004%), neg=0, invalid=762
- 0292: dt=1.008000, rms=0.519 (-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=0.535, neg=0, invalid=762
- 0293: dt=0.768000, rms=0.534 (0.261%), neg=0, invalid=762
- 0294: dt=0.320000, rms=0.534 (0.013%), neg=0, invalid=762
- 0295: dt=0.320000, rms=0.533 (-0.004%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.534, neg=0, invalid=762
- 0296: dt=1.536000, rms=0.532 (0.403%), neg=0, invalid=762
- 0297: dt=0.768000, rms=0.532 (0.034%), neg=0, invalid=762
- 0298: dt=0.768000, rms=0.532 (0.003%), neg=0, invalid=762
- 0299: dt=0.768000, rms=0.532 (-0.082%), 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=0.520, neg=0, invalid=762
- iter 0, gcam->neg = 1203
- after 14 iterations, nbhd size=1, neg = 0
- 0300: dt=2.212488, rms=0.487 (6.398%), neg=0, invalid=762
- 0301: dt=0.096000, rms=0.487 (0.061%), neg=0, invalid=762
- 0302: dt=0.096000, rms=0.487 (-0.074%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.487, neg=0, invalid=762
- 0303: dt=0.112000, rms=0.486 (0.257%), neg=0, invalid=762
- 0304: dt=0.016000, rms=0.486 (0.006%), neg=0, invalid=762
- 0305: dt=0.016000, rms=0.486 (0.001%), neg=0, invalid=762
- 0306: dt=0.016000, rms=0.486 (-0.013%), 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=0.472, neg=0, invalid=762
- 0307: dt=0.000000, rms=0.472 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.472, neg=0, invalid=762
- 0308: dt=32.368000, rms=0.472 (0.005%), neg=0, invalid=762
- 0309: dt=18.496000, rms=0.472 (0.000%), neg=0, invalid=762
- 0310: dt=18.496000, rms=0.472 (-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=0.472, neg=0, invalid=762
- 0311: dt=0.000000, rms=0.472 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.472, neg=0, invalid=762
- 0312: dt=36.288000, rms=0.472 (0.047%), neg=0, invalid=762
- 0313: dt=124.416000, rms=0.472 (0.063%), neg=0, invalid=762
- 0314: dt=145.152000, rms=0.471 (0.071%), neg=0, invalid=762
- 0315: dt=36.288000, rms=0.471 (0.011%), neg=0, invalid=762
- 0316: dt=36.288000, rms=0.471 (0.008%), neg=0, invalid=762
- 0317: dt=36.288000, rms=0.471 (0.015%), neg=0, invalid=762
- 0318: dt=36.288000, rms=0.471 (0.020%), neg=0, invalid=762
- 0319: dt=36.288000, rms=0.471 (0.024%), neg=0, invalid=762
- 0320: dt=36.288000, rms=0.471 (0.023%), neg=0, invalid=762
- 0321: dt=36.288000, rms=0.471 (0.019%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.471, neg=0, invalid=762
- 0322: dt=2.800000, rms=0.471 (0.012%), neg=0, invalid=762
- 0323: dt=1.600000, rms=0.471 (0.002%), neg=0, invalid=762
- 0324: dt=1.600000, rms=0.471 (-0.002%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.471, neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0325: dt=98.381244, rms=0.467 (0.922%), neg=0, invalid=762
- 0326: dt=11.200000, rms=0.466 (0.230%), neg=0, invalid=762
- 0327: dt=11.200000, rms=0.466 (0.067%), neg=0, invalid=762
- 0328: dt=11.200000, rms=0.465 (0.060%), neg=0, invalid=762
- 0329: dt=11.200000, rms=0.465 (0.055%), neg=0, invalid=762
- 0330: dt=44.800000, rms=0.464 (0.188%), neg=0, invalid=762
- 0331: dt=25.600000, rms=0.464 (0.078%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.467, neg=0, invalid=762
- 0332: dt=2.545455, rms=0.467 (0.030%), neg=0, invalid=762
- 0333: dt=0.720000, rms=0.467 (0.002%), neg=0, invalid=762
- 0334: dt=0.720000, rms=0.467 (-0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.467, neg=0, invalid=762
- 0335: dt=20.480000, rms=0.464 (0.651%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0336: dt=13.521127, rms=0.462 (0.332%), neg=0, invalid=762
- 0337: dt=9.166667, rms=0.462 (0.135%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0338: dt=9.166667, rms=0.461 (0.112%), neg=0, invalid=762
- 0339: dt=9.166667, rms=0.461 (0.138%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 8 iterations, nbhd size=1, neg = 0
- 0340: dt=9.166667, rms=0.460 (0.157%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 4 iterations, nbhd size=0, neg = 0
- 0341: dt=9.166667, rms=0.459 (0.157%), neg=0, invalid=762
- 0342: dt=9.166667, rms=0.458 (0.183%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 1 iterations, nbhd size=0, neg = 0
- 0343: dt=9.166667, rms=0.458 (0.139%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0344: dt=9.166667, rms=0.457 (0.099%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0345: dt=9.166667, rms=0.457 (0.067%), neg=0, invalid=762
- 0346: dt=4.032000, rms=0.457 (0.011%), neg=0, invalid=762
- 0347: dt=4.032000, rms=0.457 (-0.001%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.464, neg=0, invalid=762
- 0348: dt=0.000000, rms=0.464 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.464, neg=0, invalid=762
- 0349: dt=0.000000, rms=0.464 (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=0.452, neg=0, invalid=762
- iter 0, gcam->neg = 765
- after 15 iterations, nbhd size=1, neg = 0
- 0350: dt=1.447805, rms=0.439 (2.802%), neg=0, invalid=762
- 0351: dt=0.000013, rms=0.439 (0.000%), neg=0, invalid=762
- 0352: dt=0.000013, rms=0.439 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.439, neg=0, invalid=762
- 0353: dt=0.112000, rms=0.439 (0.115%), neg=0, invalid=762
- 0354: dt=0.096000, rms=0.439 (0.035%), neg=0, invalid=762
- 0355: dt=0.096000, rms=0.439 (0.011%), neg=0, invalid=762
- 0356: dt=0.096000, rms=0.439 (-0.060%), neg=0, invalid=762
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- mri_ca_register took 2 hours, 1 minutes and 22 seconds.
- mri_ca_register utimesec 8126.246622
- mri_ca_register stimesec 8.648685
- mri_ca_register ru_maxrss 1332768
- mri_ca_register ru_ixrss 0
- mri_ca_register ru_idrss 0
- mri_ca_register ru_isrss 0
- mri_ca_register ru_minflt 4611411
- mri_ca_register ru_majflt 0
- mri_ca_register ru_nswap 0
- mri_ca_register ru_inblock 0
- mri_ca_register ru_oublock 63320
- mri_ca_register ru_msgsnd 0
- mri_ca_register ru_msgrcv 0
- mri_ca_register ru_nsignals 0
- mri_ca_register ru_nvcsw 3645
- mri_ca_register ru_nivcsw 16962
- FSRUNTIME@ mri_ca_register 2.0228 hours 2 threads
- #--------------------------------------
- #@# SubCort Seg Sun Oct 8 03:09:39 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-586
- 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-6.0.0/0050419/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 6.01
- 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 = 0.08137 (15)
- Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (227 voxels, overlap=0.443)
- Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (227 voxels, peak = 17), gca=17.3
- gca peak = 0.17677 (13)
- mri peak = 0.10346 (15)
- Right_Lateral_Ventricle (43): linear fit = 1.11 x + 0.0 (174 voxels, overlap=0.823)
- Right_Lateral_Ventricle (43): linear fit = 1.11 x + 0.0 (174 voxels, peak = 14), gca=14.4
- gca peak = 0.28129 (95)
- mri peak = 0.06980 (95)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (658 voxels, overlap=1.018)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (658 voxels, peak = 95), gca=94.5
- gca peak = 0.16930 (96)
- mri peak = 0.09955 (93)
- Left_Pallidum (13): linear fit = 0.95 x + 0.0 (553 voxels, overlap=0.846)
- Left_Pallidum (13): linear fit = 0.95 x + 0.0 (553 voxels, peak = 92), gca=91.7
- gca peak = 0.24553 (55)
- mri peak = 0.08704 (63)
- Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (565 voxels, overlap=1.015)
- Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (565 voxels, peak = 62), gca=62.4
- gca peak = 0.30264 (59)
- mri peak = 0.05941 (63)
- Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (317 voxels, overlap=1.015)
- Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (317 voxels, peak = 62), gca=61.7
- gca peak = 0.07580 (103)
- mri peak = 0.05175 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (37416 voxels, overlap=0.784)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (37416 voxels, peak = 107), gca=106.6
- gca peak = 0.07714 (104)
- mri peak = 0.06331 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41891 voxels, overlap=0.794)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41891 voxels, peak = 105), gca=104.5
- gca peak = 0.09712 (58)
- mri peak = 0.03765 (56)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19787 voxels, overlap=0.966)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19787 voxels, peak = 59), gca=59.4
- gca peak = 0.11620 (58)
- mri peak = 0.03590 (60)
- Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (17953 voxels, overlap=0.917)
- Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (17953 voxels, peak = 59), gca=59.4
- gca peak = 0.30970 (66)
- mri peak = 0.09249 (69)
- Right_Caudate (50): linear fit = 1.02 x + 0.0 (692 voxels, overlap=1.008)
- Right_Caudate (50): linear fit = 1.02 x + 0.0 (692 voxels, peak = 68), gca=67.7
- gca peak = 0.15280 (69)
- mri peak = 0.07303 (67)
- Left_Caudate (11): linear fit = 0.98 x + 0.0 (732 voxels, overlap=1.008)
- Left_Caudate (11): linear fit = 0.98 x + 0.0 (732 voxels, peak = 67), gca=67.3
- gca peak = 0.13902 (56)
- mri peak = 0.04233 (55)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (13997 voxels, overlap=1.000)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (13997 voxels, peak = 55), gca=55.2
- gca peak = 0.14777 (55)
- mri peak = 0.04865 (57)
- Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17125 voxels, overlap=0.993)
- Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17125 voxels, peak = 57), gca=57.5
- gca peak = 0.16765 (84)
- mri peak = 0.05033 (82)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4006 voxels, overlap=0.960)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4006 voxels, peak = 89), gca=89.5
- gca peak = 0.18739 (84)
- mri peak = 0.06469 (92)
- Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (3694 voxels, overlap=0.558)
- Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (3694 voxels, peak = 91), gca=91.1
- gca peak = 0.29869 (57)
- mri peak = 0.07639 (61)
- Left_Amygdala (18): linear fit = 1.10 x + 0.0 (289 voxels, overlap=1.036)
- Left_Amygdala (18): linear fit = 1.10 x + 0.0 (289 voxels, peak = 62), gca=62.4
- gca peak = 0.33601 (57)
- mri peak = 0.07421 (63)
- Right_Amygdala (54): linear fit = 1.12 x + 0.0 (269 voxels, overlap=0.933)
- Right_Amygdala (54): linear fit = 1.12 x + 0.0 (269 voxels, peak = 64), gca=63.6
- gca peak = 0.11131 (90)
- mri peak = 0.06804 (77)
- Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (4125 voxels, overlap=1.001)
- Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (4125 voxels, peak = 85), gca=85.1
- gca peak = 0.11793 (83)
- mri peak = 0.06598 (77)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3610 voxels, overlap=0.978)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3610 voxels, peak = 84), gca=84.2
- gca peak = 0.08324 (81)
- mri peak = 0.07202 (79)
- Left_Putamen (12): linear fit = 0.99 x + 0.0 (1758 voxels, overlap=0.855)
- Left_Putamen (12): linear fit = 0.99 x + 0.0 (1758 voxels, peak = 80), gca=79.8
- gca peak = 0.10360 (77)
- mri peak = 0.05988 (82)
- Right_Putamen (51): linear fit = 1.03 x + 0.0 (2291 voxels, overlap=0.785)
- Right_Putamen (51): linear fit = 1.03 x + 0.0 (2291 voxels, peak = 80), gca=79.7
- gca peak = 0.08424 (78)
- mri peak = 0.13666 (80)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (9693 voxels, overlap=0.476)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (9693 voxels, peak = 81), gca=80.7
- gca peak = 0.12631 (89)
- mri peak = 0.08538 (84)
- Right_VentralDC (60): linear fit = 0.96 x + 0.0 (893 voxels, overlap=0.823)
- Right_VentralDC (60): linear fit = 0.96 x + 0.0 (893 voxels, peak = 86), gca=85.9
- gca peak = 0.14500 (87)
- mri peak = 0.11417 (82)
- Left_VentralDC (28): linear fit = 0.95 x + 0.0 (837 voxels, overlap=0.899)
- Left_VentralDC (28): linear fit = 0.95 x + 0.0 (837 voxels, peak = 83), gca=83.1
- gca peak = 0.14975 (24)
- mri peak = 0.17396 (17)
- gca peak = 0.19357 (14)
- mri peak = 0.12165 (11)
- Fourth_Ventricle (15): linear fit = 0.43 x + 0.0 (89 voxels, overlap=0.216)
- Fourth_Ventricle (15): linear fit = 0.43 x + 0.0 (89 voxels, peak = 6), gca=6.0
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.16825 (27)
- gca peak Left_Thalamus = 1.00000 (94)
- gca peak Third_Ventricle = 0.14975 (24)
- gca peak Fourth_Ventricle = 0.19357 (14)
- gca peak CSF = 0.23379 (36)
- gca peak Left_Accumbens_area = 0.70037 (62)
- gca peak Left_undetermined = 1.00000 (26)
- gca peak Left_vessel = 0.75997 (52)
- gca peak Left_choroid_plexus = 0.12089 (35)
- gca peak Right_Inf_Lat_Vent = 0.24655 (23)
- gca peak Right_Accumbens_area = 0.45042 (65)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14516 (37)
- gca peak Fifth_Ventricle = 0.65475 (32)
- gca peak WM_hypointensities = 0.07854 (76)
- gca peak non_WM_hypointensities = 0.08491 (43)
- gca peak Optic_Chiasm = 0.71127 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.07 x + 0.0
- estimating mean wm scale to be 1.02 x + 0.0
- estimating mean csf scale to be 0.99 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.17217 (16)
- mri peak = 0.08137 (15)
- Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (227 voxels, overlap=0.811)
- Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (227 voxels, peak = 15), gca=15.4
- gca peak = 0.21357 (14)
- mri peak = 0.10346 (15)
- Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (174 voxels, overlap=0.743)
- Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (174 voxels, peak = 14), gca=14.5
- gca peak = 0.28681 (93)
- mri peak = 0.06980 (95)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (658 voxels, overlap=1.017)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (658 voxels, peak = 93), gca=92.5
- gca peak = 0.18417 (92)
- mri peak = 0.09955 (93)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (553 voxels, overlap=1.011)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (553 voxels, peak = 92), gca=91.5
- gca peak = 0.26476 (63)
- mri peak = 0.08704 (63)
- Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (565 voxels, overlap=0.956)
- Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (565 voxels, peak = 62), gca=62.1
- gca peak = 0.29363 (59)
- mri peak = 0.05941 (63)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (317 voxels, overlap=1.015)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (317 voxels, peak = 59), gca=59.0
- gca peak = 0.07498 (106)
- mri peak = 0.05175 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (37416 voxels, overlap=0.890)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (37416 voxels, peak = 107), gca=106.5
- gca peak = 0.07920 (105)
- mri peak = 0.06331 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41891 voxels, overlap=0.814)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41891 voxels, peak = 105), gca=105.0
- gca peak = 0.09504 (59)
- mri peak = 0.03765 (56)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19787 voxels, overlap=0.977)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19787 voxels, peak = 60), gca=60.5
- gca peak = 0.11322 (59)
- mri peak = 0.03590 (60)
- Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (17953 voxels, overlap=0.950)
- Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (17953 voxels, peak = 60), gca=60.5
- gca peak = 0.25451 (68)
- mri peak = 0.09249 (69)
- Right_Caudate (50): linear fit = 1.01 x + 0.0 (692 voxels, overlap=1.010)
- Right_Caudate (50): linear fit = 1.01 x + 0.0 (692 voxels, peak = 69), gca=69.0
- gca peak = 0.13721 (67)
- mri peak = 0.07303 (67)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (732 voxels, overlap=1.006)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (732 voxels, peak = 66), gca=66.0
- gca peak = 0.14491 (55)
- mri peak = 0.04233 (55)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (13997 voxels, overlap=1.000)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (13997 voxels, peak = 54), gca=54.2
- gca peak = 0.14311 (57)
- mri peak = 0.04865 (57)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (17125 voxels, overlap=0.998)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (17125 voxels, peak = 58), gca=58.4
- gca peak = 0.15873 (90)
- mri peak = 0.05033 (82)
- Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (4006 voxels, overlap=0.998)
- Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (4006 voxels, peak = 88), gca=87.8
- gca peak = 0.15055 (91)
- mri peak = 0.06469 (92)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3694 voxels, overlap=0.957)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3694 voxels, peak = 91), gca=90.5
- gca peak = 0.26686 (62)
- mri peak = 0.07639 (61)
- Left_Amygdala (18): linear fit = 0.99 x + 0.0 (289 voxels, overlap=1.020)
- Left_Amygdala (18): linear fit = 0.99 x + 0.0 (289 voxels, peak = 61), gca=61.1
- gca peak = 0.30423 (64)
- mri peak = 0.07421 (63)
- Right_Amygdala (54): linear fit = 0.99 x + 0.0 (269 voxels, overlap=1.025)
- Right_Amygdala (54): linear fit = 0.99 x + 0.0 (269 voxels, peak = 63), gca=63.0
- gca peak = 0.10664 (85)
- mri peak = 0.06804 (77)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4125 voxels, overlap=0.945)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4125 voxels, peak = 85), gca=84.6
- gca peak = 0.10968 (82)
- mri peak = 0.06598 (77)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3610 voxels, overlap=0.993)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3610 voxels, peak = 82), gca=81.6
- gca peak = 0.09216 (74)
- mri peak = 0.07202 (79)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1758 voxels, overlap=0.875)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1758 voxels, peak = 74), gca=73.6
- gca peak = 0.10883 (78)
- mri peak = 0.05988 (82)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (2291 voxels, overlap=0.788)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (2291 voxels, peak = 78), gca=77.6
- gca peak = 0.08850 (81)
- mri peak = 0.13666 (80)
- Brain_Stem: unreasonable value (79.8/80.0), not in range [80, 110] - rejecting
- gca peak = 0.12873 (86)
- mri peak = 0.08538 (84)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (893 voxels, overlap=0.781)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (893 voxels, peak = 88), gca=88.2
- gca peak = 0.15136 (83)
- mri peak = 0.11417 (82)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (837 voxels, overlap=0.849)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (837 voxels, peak = 83), gca=82.6
- gca peak = 0.17077 (25)
- mri peak = 0.17396 (17)
- gca peak = 0.16682 (15)
- mri peak = 0.12165 (11)
- Fourth_Ventricle (15): linear fit = 0.41 x + 0.0 (89 voxels, overlap=0.172)
- Fourth_Ventricle (15): linear fit = 0.41 x + 0.0 (89 voxels, peak = 6), gca=6.1
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.16503 (28)
- gca peak Left_Thalamus = 1.00000 (101)
- gca peak Third_Ventricle = 0.17077 (25)
- gca peak Fourth_Ventricle = 0.16682 (15)
- gca peak Brain_Stem = 0.08850 (81)
- gca peak CSF = 0.25860 (36)
- gca peak Left_Accumbens_area = 0.49175 (60)
- 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 = 0.21972 (26)
- gca peak Right_Accumbens_area = 0.41171 (66)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14516 (37)
- gca peak Fifth_Ventricle = 0.54107 (32)
- gca peak WM_hypointensities = 0.07269 (78)
- gca peak non_WM_hypointensities = 0.08683 (44)
- gca peak Optic_Chiasm = 0.71095 (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 1.00 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
- 76984 voxels changed in iteration 0 of unlikely voxel relabeling
- 300 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
- 41236 gm and wm labels changed (%22 to gray, %78 to white out of all changed labels)
- 314 hippocampal voxels changed.
- 0 amygdala voxels changed.
- pass 1: 72189 changed. image ll: -2.119, PF=0.500
- pass 2: 22096 changed. image ll: -2.119, PF=0.500
- pass 3: 7078 changed.
- pass 4: 2639 changed.
- 51365 voxels changed in iteration 0 of unlikely voxel relabeling
- 290 voxels changed in iteration 1 of unlikely voxel relabeling
- 10 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 7355 voxels changed in iteration 0 of unlikely voxel relabeling
- 114 voxels changed in iteration 1 of unlikely voxel relabeling
- 9 voxels changed in iteration 2 of unlikely voxel relabeling
- 1 voxels changed in iteration 3 of unlikely voxel relabeling
- 6 voxels changed in iteration 4 of unlikely voxel relabeling
- 6564 voxels changed in iteration 0 of unlikely voxel relabeling
- 48 voxels changed in iteration 1 of unlikely voxel relabeling
- 11 voxels changed in iteration 2 of unlikely voxel relabeling
- 3 voxels changed in iteration 3 of unlikely voxel relabeling
- 0 voxels changed in iteration 4 of unlikely voxel relabeling
- 5727 voxels changed in iteration 0 of unlikely voxel relabeling
- 24 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
- MRItoUCHAR: min=0, max=85
- MRItoUCHAR: converting to UCHAR
- writing labeled volume to aseg.auto_noCCseg.mgz
- mri_ca_label utimesec 3593.040774
- mri_ca_label stimesec 1.406786
- mri_ca_label ru_maxrss 2098688
- mri_ca_label ru_ixrss 0
- mri_ca_label ru_idrss 0
- mri_ca_label ru_isrss 0
- mri_ca_label ru_minflt 591419
- mri_ca_label ru_majflt 0
- mri_ca_label ru_nswap 0
- mri_ca_label ru_inblock 63312
- mri_ca_label ru_oublock 424
- mri_ca_label ru_msgsnd 0
- mri_ca_label ru_msgrcv 0
- mri_ca_label ru_nsignals 0
- mri_ca_label ru_nvcsw 278
- mri_ca_label ru_nivcsw 11229
- auto-labeling took 59 minutes and 5 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/transforms/cc_up.lta 0050419
- 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-6.0.0/0050419/mri/transforms/cc_up.lta
- reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/aseg.auto_noCCseg.mgz
- reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/norm.mgz
- 57880 voxels in left wm, 56493 in right wm, xrange [120, 135]
- searching rotation angles z=[-5 9], y=[-11 3]
-
searching scale 1 Z rot -5.1
searching scale 1 Z rot -4.9
searching scale 1 Z rot -4.6
searching scale 1 Z rot -4.4
searching scale 1 Z rot -4.1
searching scale 1 Z rot -3.9
searching scale 1 Z rot -3.6
searching scale 1 Z rot -3.4
searching scale 1 Z rot -3.1
searching scale 1 Z rot -2.9
searching scale 1 Z rot -2.6
searching scale 1 Z rot -2.4
searching scale 1 Z rot -2.1
searching scale 1 Z rot -1.9
searching scale 1 Z rot -1.6
searching scale 1 Z rot -1.4
searching scale 1 Z rot -1.1
searching scale 1 Z rot -0.9
searching scale 1 Z rot -0.6
searching scale 1 Z rot -0.4
searching scale 1 Z rot -0.1
searching scale 1 Z rot 0.1
searching scale 1 Z rot 0.4
searching scale 1 Z rot 0.6
searching scale 1 Z rot 0.9
searching scale 1 Z rot 1.1
searching scale 1 Z rot 1.4
searching scale 1 Z rot 1.6
searching scale 1 Z rot 1.9
searching scale 1 Z rot 2.1
searching scale 1 Z rot 2.4
searching scale 1 Z rot 2.6
searching scale 1 Z rot 2.9
searching scale 1 Z rot 3.1
searching scale 1 Z rot 3.4
searching scale 1 Z rot 3.6
searching scale 1 Z rot 3.9
searching scale 1 Z rot 4.1
searching scale 1 Z rot 4.4
searching scale 1 Z rot 4.6
searching scale 1 Z rot 4.9
searching scale 1 Z rot 5.1
searching scale 1 Z rot 5.4
searching scale 1 Z rot 5.6
searching scale 1 Z rot 5.9
searching scale 1 Z rot 6.1
searching scale 1 Z rot 6.4
searching scale 1 Z rot 6.6
searching scale 1 Z rot 6.9
searching scale 1 Z rot 7.1
searching scale 1 Z rot 7.4
searching scale 1 Z rot 7.6
searching scale 1 Z rot 7.9
searching scale 1 Z rot 8.1
searching scale 1 Z rot 8.4
searching scale 1 Z rot 8.6 global minimum found at slice 126.8, rotations (-4.16, 1.89)
- final transformation (x=126.8, yr=-4.157, zr=1.885):
- 0.99683 -0.03290 -0.07246 12.37405;
- 0.03281 0.99946 -0.00239 39.14775;
- 0.07250 0.00000 0.99737 9.09738;
- 0.00000 0.00000 0.00000 1.00000;
- updating x range to be [126, 131] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 85 110
- eigenvectors:
- 0.00023 -0.00923 0.99996;
- -0.01855 -0.99979 -0.00922;
- 0.99983 -0.01855 -0.00040;
- writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/aseg.auto.mgz...
- corpus callosum segmentation took 1.4 minutes
- #--------------------------------------
- #@# Merge ASeg Sun Oct 8 04:10:07 CEST 2017
- cp aseg.auto.mgz aseg.presurf.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Sun Oct 8 04:10:07 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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...
- 2669 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 101
- gm peak at 63 (63), valley at 22 (22)
- csf peak at 32, setting threshold to 52
- 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 61 (61), valley at 21 (21)
- csf peak at 31, setting threshold to 51
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 3 minutes and 18 seconds.
- #--------------------------------------------
- #@# Mask BFS Sun Oct 8 04:13:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1327682 voxels in mask (pct= 7.91)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Sun Oct 8 04:13:28 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 (104.0): 105.9 +- 6.0 [79.0 --> 125.0]
- GM (70.0) : 67.7 +- 10.5 [30.0 --> 95.0]
- setting bottom of white matter range to 78.2
- setting top of gray matter range to 88.7
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- using local geometry to label remaining ambiguous voxels...
- reclassifying voxels using Gaussian border classifier...
- removing voxels with positive offset direction...
- smoothing T1 volume with sigma = 0.250
- removing 1-dimensional structures...
- 6453 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 4462 filled
- 2774 bright non-wm voxels segmented.
- 3279 diagonally connected voxels added...
- white matter segmentation took 1.4 minutes
- writing output to wm.seg.mgz...
- assuming input volume is MGH (Van der Kouwe) MP-RAGE
- mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz
- preserving editing changes in input volume...
- auto filling took 0.55 minutes
- reading wm segmentation from wm.seg.mgz...
- 574 voxels added to wm to prevent paths from MTL structures to cortex
- 4180 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 37720 voxels turned on, 15140 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+): 42 found - 42 modified | TOTAL: 42
- pass 2 (xy+): 0 found - 42 modified | TOTAL: 42
- pass 1 (xy-): 26 found - 26 modified | TOTAL: 68
- pass 2 (xy-): 0 found - 26 modified | TOTAL: 68
- pass 1 (yz+): 34 found - 34 modified | TOTAL: 102
- pass 2 (yz+): 0 found - 34 modified | TOTAL: 102
- pass 1 (yz-): 47 found - 47 modified | TOTAL: 149
- pass 2 (yz-): 0 found - 47 modified | TOTAL: 149
- pass 1 (xz+): 33 found - 33 modified | TOTAL: 182
- pass 2 (xz+): 0 found - 33 modified | TOTAL: 182
- pass 1 (xz-): 30 found - 30 modified | TOTAL: 212
- pass 2 (xz-): 0 found - 30 modified | TOTAL: 212
- Iteration Number : 1
- pass 1 (+++): 38 found - 38 modified | TOTAL: 38
- pass 2 (+++): 0 found - 38 modified | TOTAL: 38
- pass 1 (+++): 31 found - 31 modified | TOTAL: 69
- pass 2 (+++): 0 found - 31 modified | TOTAL: 69
- pass 1 (+++): 44 found - 44 modified | TOTAL: 113
- pass 2 (+++): 0 found - 44 modified | TOTAL: 113
- pass 1 (+++): 30 found - 30 modified | TOTAL: 143
- pass 2 (+++): 0 found - 30 modified | TOTAL: 143
- Iteration Number : 1
- pass 1 (++): 105 found - 105 modified | TOTAL: 105
- pass 2 (++): 0 found - 105 modified | TOTAL: 105
- pass 1 (+-): 132 found - 132 modified | TOTAL: 237
- pass 2 (+-): 2 found - 134 modified | TOTAL: 239
- pass 3 (+-): 0 found - 134 modified | TOTAL: 239
- pass 1 (--): 108 found - 108 modified | TOTAL: 347
- pass 2 (--): 1 found - 109 modified | TOTAL: 348
- pass 3 (--): 0 found - 109 modified | TOTAL: 348
- pass 1 (-+): 117 found - 117 modified | TOTAL: 465
- pass 2 (-+): 0 found - 117 modified | TOTAL: 465
- Iteration Number : 2
- pass 1 (xy+): 10 found - 10 modified | TOTAL: 10
- pass 2 (xy+): 0 found - 10 modified | TOTAL: 10
- pass 1 (xy-): 7 found - 7 modified | TOTAL: 17
- pass 2 (xy-): 0 found - 7 modified | TOTAL: 17
- pass 1 (yz+): 8 found - 8 modified | TOTAL: 25
- pass 2 (yz+): 0 found - 8 modified | TOTAL: 25
- pass 1 (yz-): 10 found - 10 modified | TOTAL: 35
- pass 2 (yz-): 0 found - 10 modified | TOTAL: 35
- pass 1 (xz+): 5 found - 5 modified | TOTAL: 40
- pass 2 (xz+): 0 found - 5 modified | TOTAL: 40
- pass 1 (xz-): 10 found - 10 modified | TOTAL: 50
- pass 2 (xz-): 0 found - 10 modified | TOTAL: 50
- Iteration Number : 2
- pass 1 (+++): 4 found - 4 modified | TOTAL: 4
- pass 2 (+++): 0 found - 4 modified | TOTAL: 4
- pass 1 (+++): 1 found - 1 modified | TOTAL: 5
- pass 2 (+++): 0 found - 1 modified | TOTAL: 5
- pass 1 (+++): 2 found - 2 modified | TOTAL: 7
- pass 2 (+++): 0 found - 2 modified | TOTAL: 7
- pass 1 (+++): 0 found - 0 modified | TOTAL: 7
- Iteration Number : 2
- pass 1 (++): 5 found - 5 modified | TOTAL: 5
- pass 2 (++): 0 found - 5 modified | TOTAL: 5
- pass 1 (+-): 2 found - 2 modified | TOTAL: 7
- pass 2 (+-): 0 found - 2 modified | TOTAL: 7
- pass 1 (--): 4 found - 4 modified | TOTAL: 11
- pass 2 (--): 0 found - 4 modified | TOTAL: 11
- pass 1 (-+): 4 found - 4 modified | TOTAL: 15
- pass 2 (-+): 0 found - 4 modified | TOTAL: 15
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 2
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 3
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 3
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 3
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 4
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 4
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 0 found - 0 modified | TOTAL: 1
- pass 1 (--): 1 found - 1 modified | TOTAL: 2
- pass 2 (--): 0 found - 1 modified | TOTAL: 2
- pass 1 (-+): 1 found - 1 modified | TOTAL: 3
- pass 2 (-+): 0 found - 1 modified | TOTAL: 3
- Iteration Number : 4
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 2
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
- 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 (++): 3 found - 3 modified | TOTAL: 3
- pass 2 (++): 0 found - 3 modified | TOTAL: 3
- pass 1 (+-): 0 found - 0 modified | TOTAL: 3
- pass 1 (--): 0 found - 0 modified | TOTAL: 3
- pass 1 (-+): 0 found - 0 modified | TOTAL: 3
- Iteration Number : 5
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 5
- 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 : 5
- 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 : 6
- 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 : 6
- 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 : 6
- 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 = 905 (out of 454949: 0.198923)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Sun Oct 8 04:15:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri
- mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
- logging cutting plane coordinates to ../scripts/ponscc.cut.log...
- INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
- using segmentation aseg.auto_noCCseg.mgz...
- reading input volume...done.
- searching for cutting planes...voxel to talairach voxel transform
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07356 -0.12113 1.06944 -3.90477;
- 0.00000 0.00000 0.00000 1.00000;
- voxel to talairach voxel transform
- 0.97743 0.00876 -0.07732 8.26133;
- 0.00000 1.25483 0.10747 -20.20944;
- 0.07356 -0.12113 1.06944 -3.90477;
- 0.00000 0.00000 0.00000 1.00000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1234 (min = 350, max = 1400), aspect = 0.56 (min = 0.10, max = 0.75)
- no need to search
- using seed (125, 114, 94), TAL = (3.0, -34.0, 14.0)
- talairach voxel to voxel transform
- 1.01755 -0.00000 0.07357 -8.11911;
- 0.00594 0.78926 -0.07889 15.59348;
- -0.06932 0.08940 0.92107 5.97591;
- 0.00000 0.00000 0.00000 1.00000;
- segmentation indicates cc at (125, 114, 94) --> (3.0, -34.0, 14.0)
- done.
- writing output to filled.mgz...
- filling took 0.8 minutes
- talairach cc position changed to (3.00, -34.00, 14.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(21.00, -34.00, 14.00) SRC: (107.67, 98.79, 95.33)
- search lh wm seed point around talairach space (-15.00, -34.00, 14.00), SRC: (144.31, 99.00, 92.83)
- 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 04:16:18 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 2
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 4
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 4
- pass 1 (xz+): 3 found - 3 modified | TOTAL: 7
- pass 2 (xz+): 0 found - 3 modified | TOTAL: 7
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 7
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 3 found - 3 modified | TOTAL: 3
- pass 2 (++): 0 found - 3 modified | TOTAL: 3
- pass 1 (+-): 1 found - 1 modified | TOTAL: 4
- pass 2 (+-): 0 found - 1 modified | TOTAL: 4
- pass 1 (--): 1 found - 1 modified | TOTAL: 5
- pass 2 (--): 0 found - 1 modified | TOTAL: 5
- pass 1 (-+): 1 found - 1 modified | TOTAL: 6
- pass 2 (-+): 0 found - 1 modified | TOTAL: 6
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 13 (out of 220348: 0.005900)
- 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: 693 vertices, 790 faces
- slice 50: 5736 vertices, 5969 faces
- slice 60: 13849 vertices, 14208 faces
- slice 70: 24772 vertices, 25190 faces
- slice 80: 36996 vertices, 37490 faces
- slice 90: 49475 vertices, 50018 faces
- slice 100: 61612 vertices, 62129 faces
- slice 110: 73007 vertices, 73514 faces
- slice 120: 85192 vertices, 85786 faces
- slice 130: 96072 vertices, 96648 faces
- slice 140: 105755 vertices, 106293 faces
- slice 150: 114239 vertices, 114775 faces
- slice 160: 121504 vertices, 121989 faces
- slice 170: 127219 vertices, 127635 faces
- slice 180: 130642 vertices, 130997 faces
- slice 190: 131482 vertices, 131756 faces
- slice 200: 131482 vertices, 131756 faces
- slice 210: 131482 vertices, 131756 faces
- slice 220: 131482 vertices, 131756 faces
- slice 230: 131482 vertices, 131756 faces
- slice 240: 131482 vertices, 131756 faces
- slice 250: 131482 vertices, 131756 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...
- 131482 voxel in cpt #1: X=-274 [v=131482,e=395268,f=263512] located at (-29.335833, -23.566959, 30.893963)
- For the whole surface: X=-274 [v=131482,e=395268,f=263512]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Tessellate rh Sun Oct 8 04:16:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 4 found - 4 modified | TOTAL: 4
- pass 2 (yz-): 0 found - 4 modified | TOTAL: 4
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 5
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 5
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 5
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 1 found - 1 modified | TOTAL: 1
- pass 2 (--): 0 found - 1 modified | TOTAL: 1
- pass 1 (-+): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 2
- pass 1 (xy+): 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+): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 2
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
- 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 (--): 1 found - 1 modified | TOTAL: 1
- pass 2 (--): 0 found - 1 modified | TOTAL: 1
- pass 1 (-+): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 11 (out of 229330: 0.004797)
- 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: 675 vertices, 754 faces
- slice 50: 5034 vertices, 5265 faces
- slice 60: 12726 vertices, 13047 faces
- slice 70: 22474 vertices, 22886 faces
- slice 80: 33654 vertices, 34043 faces
- slice 90: 44526 vertices, 44945 faces
- slice 100: 55940 vertices, 56384 faces
- slice 110: 67152 vertices, 67629 faces
- slice 120: 78473 vertices, 78963 faces
- slice 130: 89870 vertices, 90372 faces
- slice 140: 99547 vertices, 99990 faces
- slice 150: 107548 vertices, 107990 faces
- slice 160: 115456 vertices, 115900 faces
- slice 170: 122221 vertices, 122606 faces
- slice 180: 126889 vertices, 127195 faces
- slice 190: 128484 vertices, 128676 faces
- slice 200: 128484 vertices, 128676 faces
- slice 210: 128484 vertices, 128676 faces
- slice 220: 128484 vertices, 128676 faces
- slice 230: 128484 vertices, 128676 faces
- slice 240: 128484 vertices, 128676 faces
- slice 250: 128484 vertices, 128676 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...
- 128484 voxel in cpt #1: X=-192 [v=128484,e=386028,f=257352] located at (31.502375, -20.414465, 30.071417)
- For the whole surface: X=-192 [v=128484,e=386028,f=257352]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Sun Oct 8 04:16:29 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- #--------------------------------------------
- #@# Smooth1 rh Sun Oct 8 04:16:29 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- Waiting for PID 6438 of (6438 6441) to complete...
- Waiting for PID 6441 of (6438 6441) 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 (6438 6441) completed and logs appended.
- #--------------------------------------------
- #@# Inflation1 lh Sun Oct 8 04:16:35 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- #--------------------------------------------
- #@# Inflation1 rh Sun Oct 8 04:16:35 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Waiting for PID 6487 of (6487 6490) to complete...
- Waiting for PID 6490 of (6487 6490) 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 = 43.7 mm, total surface area = 66609 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.7 minutes
-
step 000: RMS=0.187 (target=0.015)
step 005: RMS=0.149 (target=0.015)
step 010: RMS=0.124 (target=0.015)
step 015: RMS=0.113 (target=0.015)
step 020: RMS=0.106 (target=0.015)
step 025: RMS=0.101 (target=0.015)
step 030: RMS=0.098 (target=0.015)
step 035: RMS=0.095 (target=0.015)
step 040: RMS=0.094 (target=0.015)
step 045: RMS=0.093 (target=0.015)
step 050: RMS=0.092 (target=0.015)
step 055: RMS=0.092 (target=0.015)
step 060: RMS=0.092 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 41.614673
- mris_inflate stimesec 0.094985
- mris_inflate ru_maxrss 193396
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 28357
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 9280
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2174
- mris_inflate ru_nivcsw 3377
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Not saving sulc
- Reading ../surf/rh.smoothwm.nofix
- avg radius = 44.1 mm, total surface area = 65811 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.7 minutes
-
step 000: RMS=0.176 (target=0.015)
step 005: RMS=0.138 (target=0.015)
step 010: RMS=0.112 (target=0.015)
step 015: RMS=0.099 (target=0.015)
step 020: RMS=0.092 (target=0.015)
step 025: RMS=0.085 (target=0.015)
step 030: RMS=0.080 (target=0.015)
step 035: RMS=0.078 (target=0.015)
step 040: RMS=0.074 (target=0.015)
step 045: RMS=0.072 (target=0.015)
step 050: RMS=0.072 (target=0.015)
step 055: RMS=0.072 (target=0.015)
step 060: RMS=0.072 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 40.807796
- mris_inflate stimesec 0.104984
- mris_inflate ru_maxrss 188912
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 27745
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 9064
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2232
- mris_inflate ru_nivcsw 3168
- PIDs (6487 6490) completed and logs appended.
- #--------------------------------------------
- #@# QSphere lh Sun Oct 8 04:17:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- #--------------------------------------------
- #@# QSphere rh Sun Oct 8 04:17:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- Waiting for PID 6585 of (6585 6589) to complete...
- Waiting for PID 6589 of (6585 6589) 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 1.01 +- 0.67 (0.00-->10.59) (max @ vno 88121 --> 88122)
- face area 0.03 +- 0.04 (-0.41-->0.75)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.344...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.379, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.119, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.563, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.832, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.000, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.110, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.188, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.249, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.300, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.349, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.399, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.451, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.506, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.568, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.634, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.705, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.782, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.863, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.949, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.039, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.135, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.235, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.340, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.450, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.565, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.685, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.810, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.939, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.074, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.213, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.356, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.505, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.658, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.816, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.979, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.146, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.318, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.495, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.676, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.862, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.053, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.248, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.447, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.652, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.860, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.073, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.291, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.512, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.739, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.969, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.204, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.443, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.687, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.935, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.187, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.443, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.704, avgs=0
- 285/300: dt: 0.9000, rms radial error=128.969, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.238, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.511, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.788, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 15128.33
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
- epoch 2 (K=40.0), pass 1, starting sse = 2597.40
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00041
- epoch 3 (K=160.0), pass 1, starting sse = 361.91
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.03/10 = 0.00316
- epoch 4 (K=640.0), pass 1, starting sse = 71.08
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.09/12 = 0.00768
- final distance error %26.54
- writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.07 hours
- mris_sphere utimesec 240.383456
- mris_sphere stimesec 0.148977
- mris_sphere ru_maxrss 193596
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 28404
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 9304
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 9980
- mris_sphere ru_nivcsw 17993
- FSRUNTIME@ mris_sphere 0.0651 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 1.02 +- 0.63 (0.00-->8.89) (max @ vno 86035 --> 86036)
- face area 0.03 +- 0.03 (-0.25-->1.22)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.333...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.395, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.138, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.583, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.851, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.018, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.129, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.208, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.269, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.323, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.376, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.430, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.487, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.547, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.611, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.680, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.753, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.832, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.915, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.002, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.095, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.193, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.297, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.406, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.520, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.638, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.762, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.890, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.022, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.160, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.302, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.449, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.600, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.756, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.917, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.083, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.252, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.427, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.606, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.789, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.977, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.169, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.366, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.567, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.773, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.983, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.198, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.417, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.640, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.868, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.100, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.336, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.577, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.822, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.071, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.324, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.581, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.842, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.108, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.378, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.652, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.929, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 14769.00
- 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 = 2428.04
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00022
- epoch 3 (K=160.0), pass 1, starting sse = 286.62
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.03/10 = 0.00265
- epoch 4 (K=640.0), pass 1, starting sse = 36.65
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.04/10 = 0.00412
- final distance error %26.68
- writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.06 hours
- mris_sphere utimesec 224.441879
- mris_sphere stimesec 0.165974
- mris_sphere ru_maxrss 189124
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 27801
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 9088
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 8977
- mris_sphere ru_nivcsw 18171
- FSRUNTIME@ mris_sphere 0.0624 hours 1 threads
- PIDs (6585 6589) completed and logs appended.
- #--------------------------------------------
- #@# Fix Topology Copy lh Sun Oct 8 04:21:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- #--------------------------------------------
- #@# Fix Topology Copy rh Sun Oct 8 04:21:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- #@# Fix Topology lh Sun Oct 8 04:21:12 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050419 lh
- #@# Fix Topology rh Sun Oct 8 04:21:12 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050419 rh
- Waiting for PID 6888 of (6888 6891) to complete...
- Waiting for PID 6891 of (6888 6891) to complete...
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050419 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=-274 (nv=131482, nf=263512, ne=395268, g=138)
- 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 8 iterations
- marking ambiguous vertices...
- 36439 ambiguous faces found in tessellation
- segmenting defects...
- 106 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 19 into 10
- -merging segment 29 into 16
- -merging segment 28 into 22
- -merging segment 94 into 47
- -merging segment 80 into 78
- 101 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.4825 (-4.7413)
- -vertex loglikelihood: -6.6302 (-3.3151)
- -normal dot loglikelihood: -3.4106 (-3.4106)
- -quad curv loglikelihood: -6.0785 (-3.0392)
- Total Loglikelihood : -25.6018
- CORRECTING DEFECT 0 (vertices=41, convex hull=32, v0=87)
- After retessellation of defect 0 (v0=87), euler #=-95 (110752,326854,216007) : difference with theory (-98) = -3
- CORRECTING DEFECT 1 (vertices=22, convex hull=20, v0=97)
- After retessellation of defect 1 (v0=97), euler #=-94 (110752,326862,216016) : difference with theory (-97) = -3
- CORRECTING DEFECT 2 (vertices=49, convex hull=48, v0=117)
- After retessellation of defect 2 (v0=117), euler #=-93 (110756,326891,216042) : difference with theory (-96) = -3
- CORRECTING DEFECT 3 (vertices=50, convex hull=62, v0=218)
- After retessellation of defect 3 (v0=218), euler #=-92 (110768,326955,216095) : difference with theory (-95) = -3
- CORRECTING DEFECT 4 (vertices=36, convex hull=31, v0=246)
- After retessellation of defect 4 (v0=246), euler #=-91 (110769,326969,216109) : difference with theory (-94) = -3
- CORRECTING DEFECT 5 (vertices=69, convex hull=87, v0=369)
- After retessellation of defect 5 (v0=369), euler #=-90 (110793,327076,216193) : difference with theory (-93) = -3
- CORRECTING DEFECT 6 (vertices=37, convex hull=69, v0=811)
- After retessellation of defect 6 (v0=811), euler #=-89 (110814,327169,216266) : difference with theory (-92) = -3
- CORRECTING DEFECT 7 (vertices=61, convex hull=105, v0=1453)
- After retessellation of defect 7 (v0=1453), euler #=-88 (110848,327314,216378) : difference with theory (-91) = -3
- CORRECTING DEFECT 8 (vertices=66, convex hull=36, v0=1672)
- After retessellation of defect 8 (v0=1672), euler #=-87 (110852,327341,216402) : difference with theory (-90) = -3
- CORRECTING DEFECT 9 (vertices=30, convex hull=20, v0=1685)
- After retessellation of defect 9 (v0=1685), euler #=-86 (110854,327354,216414) : difference with theory (-89) = -3
- CORRECTING DEFECT 10 (vertices=197, convex hull=224, v0=1757)
- After retessellation of defect 10 (v0=1757), euler #=-84 (110945,327741,216712) : difference with theory (-88) = -4
- CORRECTING DEFECT 11 (vertices=47, convex hull=45, v0=2223)
- After retessellation of defect 11 (v0=2223), euler #=-83 (110952,327779,216744) : difference with theory (-87) = -4
- CORRECTING DEFECT 12 (vertices=41, convex hull=68, v0=2280)
- After retessellation of defect 12 (v0=2280), euler #=-82 (110971,327867,216814) : difference with theory (-86) = -4
- CORRECTING DEFECT 13 (vertices=245, convex hull=161, v0=2334)
- After retessellation of defect 13 (v0=2334), euler #=-81 (111055,328190,217054) : difference with theory (-85) = -4
- CORRECTING DEFECT 14 (vertices=189, convex hull=150, v0=4931)
- After retessellation of defect 14 (v0=4931), euler #=-80 (111119,328466,217267) : difference with theory (-84) = -4
- CORRECTING DEFECT 15 (vertices=231, convex hull=176, v0=5178)
- After retessellation of defect 15 (v0=5178), euler #=-79 (111190,328760,217491) : difference with theory (-83) = -4
- CORRECTING DEFECT 16 (vertices=2114, convex hull=874, v0=5625)
- XL defect detected...
- After retessellation of defect 16 (v0=5625), euler #=-80 (111786,331013,219147) : difference with theory (-82) = -2
- CORRECTING DEFECT 17 (vertices=26, convex hull=29, v0=5710)
- After retessellation of defect 17 (v0=5710), euler #=-79 (111789,331030,219162) : difference with theory (-81) = -2
- CORRECTING DEFECT 18 (vertices=112, convex hull=160, v0=6461)
- After retessellation of defect 18 (v0=6461), euler #=-78 (111869,331349,219402) : difference with theory (-80) = -2
- CORRECTING DEFECT 19 (vertices=111, convex hull=171, v0=8023)
- After retessellation of defect 19 (v0=8023), euler #=-77 (111937,331638,219624) : difference with theory (-79) = -2
- CORRECTING DEFECT 20 (vertices=39, convex hull=28, v0=8354)
- After retessellation of defect 20 (v0=8354), euler #=-76 (111941,331660,219643) : difference with theory (-78) = -2
- CORRECTING DEFECT 21 (vertices=181, convex hull=132, v0=8510)
- After retessellation of defect 21 (v0=8510), euler #=-74 (111986,331861,219801) : difference with theory (-77) = -3
- CORRECTING DEFECT 22 (vertices=66, convex hull=113, v0=10503)
- After retessellation of defect 22 (v0=10503), euler #=-73 (112023,332026,219930) : difference with theory (-76) = -3
- CORRECTING DEFECT 23 (vertices=736, convex hull=506, v0=12458)
- L defect detected...
- After retessellation of defect 23 (v0=12458), euler #=-73 (112263,333026,220690) : difference with theory (-75) = -2
- CORRECTING DEFECT 24 (vertices=119, convex hull=99, v0=13085)
- After retessellation of defect 24 (v0=13085), euler #=-72 (112315,333226,220839) : difference with theory (-74) = -2
- CORRECTING DEFECT 25 (vertices=187, convex hull=121, v0=13749)
- After retessellation of defect 25 (v0=13749), euler #=-71 (112365,333434,220998) : difference with theory (-73) = -2
- CORRECTING DEFECT 26 (vertices=148, convex hull=162, v0=14456)
- After retessellation of defect 26 (v0=14456), euler #=-70 (112414,333649,221165) : difference with theory (-72) = -2
- CORRECTING DEFECT 27 (vertices=5, convex hull=14, v0=20422)
- After retessellation of defect 27 (v0=20422), euler #=-69 (112414,333654,221171) : difference with theory (-71) = -2
- CORRECTING DEFECT 28 (vertices=28, convex hull=68, v0=22234)
- After retessellation of defect 28 (v0=22234), euler #=-68 (112424,333710,221218) : difference with theory (-70) = -2
- CORRECTING DEFECT 29 (vertices=46, convex hull=107, v0=22822)
- After retessellation of defect 29 (v0=22822), euler #=-67 (112456,333846,221323) : difference with theory (-69) = -2
- CORRECTING DEFECT 30 (vertices=56, convex hull=53, v0=24784)
- After retessellation of defect 30 (v0=24784), euler #=-66 (112462,333885,221357) : difference with theory (-68) = -2
- CORRECTING DEFECT 31 (vertices=45, convex hull=84, v0=31821)
- After retessellation of defect 31 (v0=31821), euler #=-65 (112480,333976,221431) : difference with theory (-67) = -2
- CORRECTING DEFECT 32 (vertices=66, convex hull=98, v0=32898)
- After retessellation of defect 32 (v0=32898), euler #=-64 (112519,334141,221558) : difference with theory (-66) = -2
- CORRECTING DEFECT 33 (vertices=9, convex hull=27, v0=40256)
- After retessellation of defect 33 (v0=40256), euler #=-63 (112520,334153,221570) : difference with theory (-65) = -2
- CORRECTING DEFECT 34 (vertices=60, convex hull=51, v0=40614)
- After retessellation of defect 34 (v0=40614), euler #=-62 (112528,334199,221609) : difference with theory (-64) = -2
- CORRECTING DEFECT 35 (vertices=46, convex hull=36, v0=41194)
- After retessellation of defect 35 (v0=41194), euler #=-61 (112534,334231,221636) : difference with theory (-63) = -2
- CORRECTING DEFECT 36 (vertices=152, convex hull=107, v0=41347)
- After retessellation of defect 36 (v0=41347), euler #=-60 (112569,334382,221753) : difference with theory (-62) = -2
- CORRECTING DEFECT 37 (vertices=105, convex hull=56, v0=41743)
- After retessellation of defect 37 (v0=41743), euler #=-59 (112576,334425,221790) : difference with theory (-61) = -2
- CORRECTING DEFECT 38 (vertices=698, convex hull=215, v0=42517)
- After retessellation of defect 38 (v0=42517), euler #=-58 (112693,334884,222133) : difference with theory (-60) = -2
- CORRECTING DEFECT 39 (vertices=9, convex hull=22, v0=44662)
- After retessellation of defect 39 (v0=44662), euler #=-57 (112693,334891,222141) : difference with theory (-59) = -2
- CORRECTING DEFECT 40 (vertices=130, convex hull=143, v0=46626)
- After retessellation of defect 40 (v0=46626), euler #=-56 (112753,335130,222321) : difference with theory (-58) = -2
- CORRECTING DEFECT 41 (vertices=24, convex hull=64, v0=47146)
- After retessellation of defect 41 (v0=47146), euler #=-55 (112765,335192,222372) : difference with theory (-57) = -2
- CORRECTING DEFECT 42 (vertices=25, convex hull=43, v0=47874)
- After retessellation of defect 42 (v0=47874), euler #=-54 (112772,335230,222404) : difference with theory (-56) = -2
- CORRECTING DEFECT 43 (vertices=103, convex hull=97, v0=48185)
- After retessellation of defect 43 (v0=48185), euler #=-53 (112793,335336,222490) : difference with theory (-55) = -2
- CORRECTING DEFECT 44 (vertices=6184, convex hull=1813, v0=52434)
- XL defect detected...
- After retessellation of defect 44 (v0=52434), euler #=-54 (114179,340445,226212) : difference with theory (-54) = 0
- CORRECTING DEFECT 45 (vertices=35, convex hull=60, v0=54451)
- After retessellation of defect 45 (v0=54451), euler #=-53 (114197,340522,226272) : difference with theory (-53) = 0
- CORRECTING DEFECT 46 (vertices=24, convex hull=51, v0=54504)
- After retessellation of defect 46 (v0=54504), euler #=-52 (114211,340586,226323) : difference with theory (-52) = 0
- CORRECTING DEFECT 47 (vertices=83, convex hull=32, v0=57947)
- After retessellation of defect 47 (v0=57947), euler #=-51 (114218,340618,226349) : difference with theory (-51) = 0
- CORRECTING DEFECT 48 (vertices=58, convex hull=65, v0=57963)
- After retessellation of defect 48 (v0=57963), euler #=-51 (114231,340688,226406) : difference with theory (-50) = 1
- CORRECTING DEFECT 49 (vertices=51, convex hull=81, v0=61113)
- After retessellation of defect 49 (v0=61113), euler #=-50 (114262,340814,226502) : difference with theory (-49) = 1
- CORRECTING DEFECT 50 (vertices=147, convex hull=60, v0=62359)
- After retessellation of defect 50 (v0=62359), euler #=-49 (114294,340931,226588) : difference with theory (-48) = 1
- CORRECTING DEFECT 51 (vertices=50, convex hull=65, v0=65963)
- After retessellation of defect 51 (v0=65963), euler #=-48 (114321,341040,226671) : difference with theory (-47) = 1
- CORRECTING DEFECT 52 (vertices=25, convex hull=30, v0=67434)
- After retessellation of defect 52 (v0=67434), euler #=-47 (114321,341051,226683) : difference with theory (-46) = 1
- CORRECTING DEFECT 53 (vertices=10, convex hull=34, v0=70627)
- After retessellation of defect 53 (v0=70627), euler #=-46 (114326,341076,226704) : difference with theory (-45) = 1
- CORRECTING DEFECT 54 (vertices=590, convex hull=147, v0=74039)
- After retessellation of defect 54 (v0=74039), euler #=-45 (114336,341180,226799) : difference with theory (-44) = 1
- CORRECTING DEFECT 55 (vertices=51, convex hull=50, v0=74812)
- After retessellation of defect 55 (v0=74812), euler #=-44 (114350,341239,226845) : difference with theory (-43) = 1
- CORRECTING DEFECT 56 (vertices=179, convex hull=157, v0=75181)
- After retessellation of defect 56 (v0=75181), euler #=-43 (114399,341459,227017) : difference with theory (-42) = 1
- CORRECTING DEFECT 57 (vertices=27, convex hull=56, v0=76159)
- After retessellation of defect 57 (v0=76159), euler #=-42 (114407,341501,227052) : difference with theory (-41) = 1
- CORRECTING DEFECT 58 (vertices=153, convex hull=84, v0=76956)
- After retessellation of defect 58 (v0=76956), euler #=-41 (114448,341665,227176) : difference with theory (-40) = 1
- CORRECTING DEFECT 59 (vertices=36, convex hull=85, v0=78226)
- After retessellation of defect 59 (v0=78226), euler #=-40 (114466,341751,227245) : difference with theory (-39) = 1
- CORRECTING DEFECT 60 (vertices=1293, convex hull=369, v0=78234)
- L defect detected...
- After retessellation of defect 60 (v0=78234), euler #=-39 (114694,342621,227888) : difference with theory (-38) = 1
- CORRECTING DEFECT 61 (vertices=5, convex hull=28, v0=78412)
- After retessellation of defect 61 (v0=78412), euler #=-38 (114695,342632,227899) : difference with theory (-37) = 1
- CORRECTING DEFECT 62 (vertices=521, convex hull=335, v0=79937)
- After retessellation of defect 62 (v0=79937), euler #=-37 (114785,343057,228235) : difference with theory (-36) = 1
- CORRECTING DEFECT 63 (vertices=403, convex hull=264, v0=82150)
- After retessellation of defect 63 (v0=82150), euler #=-36 (114975,343768,228757) : difference with theory (-35) = 1
- CORRECTING DEFECT 64 (vertices=64, convex hull=54, v0=82268)
- After retessellation of defect 64 (v0=82268), euler #=-35 (114984,343819,228800) : difference with theory (-34) = 1
- CORRECTING DEFECT 65 (vertices=17, convex hull=16, v0=84583)
- After retessellation of defect 65 (v0=84583), euler #=-34 (114987,343832,228811) : difference with theory (-33) = 1
- CORRECTING DEFECT 66 (vertices=15, convex hull=25, v0=87915)
- After retessellation of defect 66 (v0=87915), euler #=-33 (114991,343852,228828) : difference with theory (-32) = 1
- CORRECTING DEFECT 67 (vertices=83, convex hull=67, v0=89020)
- After retessellation of defect 67 (v0=89020), euler #=-32 (115005,343923,228886) : difference with theory (-31) = 1
- CORRECTING DEFECT 68 (vertices=39, convex hull=54, v0=89111)
- After retessellation of defect 68 (v0=89111), euler #=-31 (115014,343974,228929) : difference with theory (-30) = 1
- CORRECTING DEFECT 69 (vertices=618, convex hull=151, v0=90413)
- After retessellation of defect 69 (v0=90413), euler #=-30 (115030,344092,229032) : difference with theory (-29) = 1
- CORRECTING DEFECT 70 (vertices=24, convex hull=53, v0=91091)
- After retessellation of defect 70 (v0=91091), euler #=-29 (115043,344153,229081) : difference with theory (-28) = 1
- CORRECTING DEFECT 71 (vertices=67, convex hull=113, v0=92549)
- After retessellation of defect 71 (v0=92549), euler #=-28 (115077,344306,229201) : difference with theory (-27) = 1
- CORRECTING DEFECT 72 (vertices=42, convex hull=35, v0=95728)
- After retessellation of defect 72 (v0=95728), euler #=-27 (115077,344317,229213) : difference with theory (-26) = 1
- CORRECTING DEFECT 73 (vertices=16, convex hull=14, v0=97756)
- After retessellation of defect 73 (v0=97756), euler #=-26 (115079,344326,229221) : difference with theory (-25) = 1
- CORRECTING DEFECT 74 (vertices=9, convex hull=20, v0=97831)
- After retessellation of defect 74 (v0=97831), euler #=-25 (115079,344333,229229) : difference with theory (-24) = 1
- CORRECTING DEFECT 75 (vertices=556, convex hull=283, v0=98918)
- After retessellation of defect 75 (v0=98918), euler #=-23 (115208,344870,229639) : difference with theory (-23) = 0
- CORRECTING DEFECT 76 (vertices=43, convex hull=29, v0=99666)
- After retessellation of defect 76 (v0=99666), euler #=-22 (115210,344885,229653) : difference with theory (-22) = 0
- CORRECTING DEFECT 77 (vertices=15, convex hull=32, v0=102460)
- After retessellation of defect 77 (v0=102460), euler #=-21 (115212,344900,229667) : difference with theory (-21) = 0
- CORRECTING DEFECT 78 (vertices=24, convex hull=52, v0=102990)
- After retessellation of defect 78 (v0=102990), euler #=-20 (115224,344956,229712) : difference with theory (-20) = 0
- CORRECTING DEFECT 79 (vertices=23, convex hull=27, v0=103525)
- After retessellation of defect 79 (v0=103525), euler #=-19 (115224,344964,229721) : difference with theory (-19) = 0
- CORRECTING DEFECT 80 (vertices=28, convex hull=35, v0=107277)
- After retessellation of defect 80 (v0=107277), euler #=-18 (115230,344992,229744) : difference with theory (-18) = 0
- CORRECTING DEFECT 81 (vertices=31, convex hull=35, v0=110607)
- After retessellation of defect 81 (v0=110607), euler #=-17 (115235,345019,229767) : difference with theory (-17) = 0
- CORRECTING DEFECT 82 (vertices=22, convex hull=49, v0=112159)
- After retessellation of defect 82 (v0=112159), euler #=-16 (115248,345076,229812) : difference with theory (-16) = 0
- CORRECTING DEFECT 83 (vertices=24, convex hull=25, v0=113184)
- After retessellation of defect 83 (v0=113184), euler #=-15 (115251,345095,229829) : difference with theory (-15) = 0
- CORRECTING DEFECT 84 (vertices=72, convex hull=134, v0=115302)
- After retessellation of defect 84 (v0=115302), euler #=-14 (115305,345314,229995) : difference with theory (-14) = 0
- CORRECTING DEFECT 85 (vertices=183, convex hull=58, v0=116509)
- After retessellation of defect 85 (v0=116509), euler #=-13 (115327,345406,230066) : difference with theory (-13) = 0
- CORRECTING DEFECT 86 (vertices=341, convex hull=188, v0=117088)
- After retessellation of defect 86 (v0=117088), euler #=-12 (115419,345777,230346) : difference with theory (-12) = 0
- CORRECTING DEFECT 87 (vertices=49, convex hull=67, v0=117168)
- After retessellation of defect 87 (v0=117168), euler #=-11 (115452,345905,230442) : difference with theory (-11) = 0
- CORRECTING DEFECT 88 (vertices=321, convex hull=83, v0=117174)
- After retessellation of defect 88 (v0=117174), euler #=-10 (115491,346059,230558) : difference with theory (-10) = 0
- CORRECTING DEFECT 89 (vertices=352, convex hull=163, v0=117769)
- After retessellation of defect 89 (v0=117769), euler #=-9 (115526,346237,230702) : difference with theory (-9) = 0
- CORRECTING DEFECT 90 (vertices=45, convex hull=92, v0=120263)
- After retessellation of defect 90 (v0=120263), euler #=-8 (115554,346358,230796) : difference with theory (-8) = 0
- CORRECTING DEFECT 91 (vertices=75, convex hull=123, v0=120318)
- After retessellation of defect 91 (v0=120318), euler #=-7 (115599,346548,230942) : difference with theory (-7) = 0
- CORRECTING DEFECT 92 (vertices=38, convex hull=75, v0=123974)
- After retessellation of defect 92 (v0=123974), euler #=-6 (115619,346637,231012) : difference with theory (-6) = 0
- CORRECTING DEFECT 93 (vertices=73, convex hull=56, v0=126329)
- After retessellation of defect 93 (v0=126329), euler #=-5 (115626,346683,231052) : difference with theory (-5) = 0
- CORRECTING DEFECT 94 (vertices=81, convex hull=67, v0=127159)
- After retessellation of defect 94 (v0=127159), euler #=-4 (115635,346741,231102) : difference with theory (-4) = 0
- CORRECTING DEFECT 95 (vertices=39, convex hull=50, v0=127333)
- After retessellation of defect 95 (v0=127333), euler #=-3 (115643,346788,231142) : difference with theory (-3) = 0
- CORRECTING DEFECT 96 (vertices=89, convex hull=106, v0=127776)
- After retessellation of defect 96 (v0=127776), euler #=-2 (115694,346988,231292) : difference with theory (-2) = 0
- CORRECTING DEFECT 97 (vertices=26, convex hull=15, v0=127919)
- After retessellation of defect 97 (v0=127919), euler #=-1 (115696,346997,231300) : difference with theory (-1) = 0
- CORRECTING DEFECT 98 (vertices=240, convex hull=114, v0=128717)
- After retessellation of defect 98 (v0=128717), euler #=0 (115728,347143,231415) : difference with theory (0) = 0
- CORRECTING DEFECT 99 (vertices=112, convex hull=46, v0=129697)
- After retessellation of defect 99 (v0=129697), euler #=1 (115737,347189,231453) : difference with theory (1) = 0
- CORRECTING DEFECT 100 (vertices=43, convex hull=42, v0=131347)
- After retessellation of defect 100 (v0=131347), euler #=2 (115741,347217,231478) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.90 +- 0.34 (0.02-->21.92) (max @ vno 98839 --> 119296)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.90 +- 0.34 (0.02-->21.92) (max @ vno 98839 --> 119296)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 313 mutations (32.9%), 638 crossovers (67.1%), 1569 vertices were eliminated
- building final representation...
- 15741 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=115741, nf=231478, ne=347217, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 300.5 minutes
- 0 defective edges
- removing intersecting faces
- 000: 1789 intersecting
- 001: 166 intersecting
- 002: 78 intersecting
- 003: 48 intersecting
- 004: 18 intersecting
- 005: 12 intersecting
- 006: 4 intersecting
- 007: 2 intersecting
- mris_fix_topology utimesec 18037.870826
- mris_fix_topology stimesec 1.468776
- mris_fix_topology ru_maxrss 753844
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 103726
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 0
- mris_fix_topology ru_oublock 11784
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 584
- mris_fix_topology ru_nivcsw 51791
- FSRUNTIME@ mris_fix_topology lh 5.0086 hours 1 threads
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050419 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=-192 (nv=128484, nf=257352, ne=386028, g=97)
- 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 8 iterations
- marking ambiguous vertices...
- 17493 ambiguous faces found in tessellation
- segmenting defects...
- 110 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 64 into 57
- -merging segment 90 into 85
- -merging segment 105 into 106
- 107 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.5391 (-4.7696)
- -vertex loglikelihood: -6.5495 (-3.2748)
- -normal dot loglikelihood: -3.5227 (-3.5227)
- -quad curv loglikelihood: -6.0236 (-3.0118)
- Total Loglikelihood : -25.6349
- CORRECTING DEFECT 0 (vertices=84, convex hull=84, v0=0)
- After retessellation of defect 0 (v0=0), euler #=-99 (118087,350624,232438) : difference with theory (-104) = -5
- CORRECTING DEFECT 1 (vertices=63, convex hull=50, v0=71)
- After retessellation of defect 1 (v0=71), euler #=-98 (118094,350662,232470) : difference with theory (-103) = -5
- CORRECTING DEFECT 2 (vertices=233, convex hull=183, v0=180)
- After retessellation of defect 2 (v0=180), euler #=-97 (118185,351024,232742) : difference with theory (-102) = -5
- CORRECTING DEFECT 3 (vertices=64, convex hull=75, v0=243)
- After retessellation of defect 3 (v0=243), euler #=-96 (118189,351070,232785) : difference with theory (-101) = -5
- CORRECTING DEFECT 4 (vertices=14, convex hull=28, v0=280)
- After retessellation of defect 4 (v0=280), euler #=-95 (118190,351080,232795) : difference with theory (-100) = -5
- CORRECTING DEFECT 5 (vertices=6, convex hull=27, v0=569)
- After retessellation of defect 5 (v0=569), euler #=-94 (118190,351088,232804) : difference with theory (-99) = -5
- CORRECTING DEFECT 6 (vertices=47, convex hull=80, v0=685)
- After retessellation of defect 6 (v0=685), euler #=-93 (118199,351149,232857) : difference with theory (-98) = -5
- CORRECTING DEFECT 7 (vertices=5, convex hull=26, v0=713)
- After retessellation of defect 7 (v0=713), euler #=-92 (118199,351153,232862) : difference with theory (-97) = -5
- CORRECTING DEFECT 8 (vertices=50, convex hull=108, v0=766)
- After retessellation of defect 8 (v0=766), euler #=-91 (118231,351290,232968) : difference with theory (-96) = -5
- CORRECTING DEFECT 9 (vertices=36, convex hull=74, v0=977)
- After retessellation of defect 9 (v0=977), euler #=-90 (118247,351372,233035) : difference with theory (-95) = -5
- CORRECTING DEFECT 10 (vertices=42, convex hull=31, v0=2118)
- After retessellation of defect 10 (v0=2118), euler #=-89 (118247,351387,233051) : difference with theory (-94) = -5
- CORRECTING DEFECT 11 (vertices=33, convex hull=60, v0=2913)
- After retessellation of defect 11 (v0=2913), euler #=-88 (118264,351460,233108) : difference with theory (-93) = -5
- CORRECTING DEFECT 12 (vertices=40, convex hull=86, v0=2930)
- After retessellation of defect 12 (v0=2930), euler #=-87 (118275,351526,233164) : difference with theory (-92) = -5
- CORRECTING DEFECT 13 (vertices=232, convex hull=174, v0=3871)
- After retessellation of defect 13 (v0=3871), euler #=-86 (118339,351802,233377) : difference with theory (-91) = -5
- CORRECTING DEFECT 14 (vertices=21, convex hull=55, v0=4199)
- After retessellation of defect 14 (v0=4199), euler #=-85 (118350,351852,233417) : difference with theory (-90) = -5
- CORRECTING DEFECT 15 (vertices=23, convex hull=19, v0=6584)
- After retessellation of defect 15 (v0=6584), euler #=-84 (118351,351862,233427) : difference with theory (-89) = -5
- CORRECTING DEFECT 16 (vertices=30, convex hull=63, v0=6893)
- After retessellation of defect 16 (v0=6893), euler #=-83 (118366,351931,233482) : difference with theory (-88) = -5
- CORRECTING DEFECT 17 (vertices=48, convex hull=96, v0=8038)
- After retessellation of defect 17 (v0=8038), euler #=-82 (118390,352041,233569) : difference with theory (-87) = -5
- CORRECTING DEFECT 18 (vertices=52, convex hull=81, v0=8638)
- After retessellation of defect 18 (v0=8638), euler #=-81 (118415,352153,233657) : difference with theory (-86) = -5
- CORRECTING DEFECT 19 (vertices=191, convex hull=126, v0=9741)
- After retessellation of defect 19 (v0=9741), euler #=-80 (118476,352390,233834) : difference with theory (-85) = -5
- CORRECTING DEFECT 20 (vertices=27, convex hull=54, v0=14058)
- After retessellation of defect 20 (v0=14058), euler #=-79 (118490,352452,233883) : difference with theory (-84) = -5
- CORRECTING DEFECT 21 (vertices=5, convex hull=20, v0=14280)
- After retessellation of defect 21 (v0=14280), euler #=-78 (118491,352459,233890) : difference with theory (-83) = -5
- CORRECTING DEFECT 22 (vertices=11, convex hull=27, v0=15422)
- After retessellation of defect 22 (v0=15422), euler #=-77 (118493,352474,233904) : difference with theory (-82) = -5
- CORRECTING DEFECT 23 (vertices=29, convex hull=65, v0=15428)
- After retessellation of defect 23 (v0=15428), euler #=-76 (118502,352526,233948) : difference with theory (-81) = -5
- CORRECTING DEFECT 24 (vertices=112, convex hull=123, v0=15531)
- After retessellation of defect 24 (v0=15531), euler #=-75 (118563,352762,234124) : difference with theory (-80) = -5
- CORRECTING DEFECT 25 (vertices=49, convex hull=77, v0=15688)
- After retessellation of defect 25 (v0=15688), euler #=-74 (118597,352895,234224) : difference with theory (-79) = -5
- CORRECTING DEFECT 26 (vertices=24, convex hull=39, v0=15878)
- After retessellation of defect 26 (v0=15878), euler #=-73 (118601,352919,234245) : difference with theory (-78) = -5
- CORRECTING DEFECT 27 (vertices=95, convex hull=110, v0=17480)
- After retessellation of defect 27 (v0=17480), euler #=-72 (118634,353066,234360) : difference with theory (-77) = -5
- CORRECTING DEFECT 28 (vertices=41, convex hull=48, v0=20131)
- After retessellation of defect 28 (v0=20131), euler #=-71 (118644,353114,234399) : difference with theory (-76) = -5
- CORRECTING DEFECT 29 (vertices=20, convex hull=34, v0=24443)
- After retessellation of defect 29 (v0=24443), euler #=-70 (118651,353147,234426) : difference with theory (-75) = -5
- CORRECTING DEFECT 30 (vertices=25, convex hull=55, v0=26029)
- After retessellation of defect 30 (v0=26029), euler #=-69 (118660,353194,234465) : difference with theory (-74) = -5
- CORRECTING DEFECT 31 (vertices=15, convex hull=51, v0=28614)
- After retessellation of defect 31 (v0=28614), euler #=-68 (118666,353231,234497) : difference with theory (-73) = -5
- CORRECTING DEFECT 32 (vertices=5, convex hull=38, v0=28885)
- After retessellation of defect 32 (v0=28885), euler #=-67 (118667,353247,234513) : difference with theory (-72) = -5
- CORRECTING DEFECT 33 (vertices=964, convex hull=195, v0=30296)
- After retessellation of defect 33 (v0=30296), euler #=-68 (118727,353528,234733) : difference with theory (-71) = -3
- CORRECTING DEFECT 34 (vertices=30, convex hull=84, v0=38818)
- After retessellation of defect 34 (v0=38818), euler #=-67 (118747,353619,234805) : difference with theory (-70) = -3
- CORRECTING DEFECT 35 (vertices=11, convex hull=42, v0=39137)
- After retessellation of defect 35 (v0=39137), euler #=-66 (118749,353639,234824) : difference with theory (-69) = -3
- CORRECTING DEFECT 36 (vertices=20, convex hull=36, v0=41173)
- After retessellation of defect 36 (v0=41173), euler #=-65 (118751,353656,234840) : difference with theory (-68) = -3
- CORRECTING DEFECT 37 (vertices=27, convex hull=59, v0=41565)
- After retessellation of defect 37 (v0=41565), euler #=-64 (118768,353729,234897) : difference with theory (-67) = -3
- CORRECTING DEFECT 38 (vertices=46, convex hull=64, v0=44550)
- After retessellation of defect 38 (v0=44550), euler #=-63 (118784,353802,234955) : difference with theory (-66) = -3
- CORRECTING DEFECT 39 (vertices=277, convex hull=170, v0=45200)
- After retessellation of defect 39 (v0=45200), euler #=-62 (118831,354023,235130) : difference with theory (-65) = -3
- CORRECTING DEFECT 40 (vertices=16, convex hull=30, v0=47211)
- After retessellation of defect 40 (v0=47211), euler #=-61 (118833,354040,235146) : difference with theory (-64) = -3
- CORRECTING DEFECT 41 (vertices=53, convex hull=66, v0=52402)
- After retessellation of defect 41 (v0=52402), euler #=-60 (118855,354136,235221) : difference with theory (-63) = -3
- CORRECTING DEFECT 42 (vertices=29, convex hull=52, v0=54189)
- After retessellation of defect 42 (v0=54189), euler #=-59 (118871,354205,235275) : difference with theory (-62) = -3
- CORRECTING DEFECT 43 (vertices=18, convex hull=25, v0=55175)
- After retessellation of defect 43 (v0=55175), euler #=-58 (118874,354222,235290) : difference with theory (-61) = -3
- CORRECTING DEFECT 44 (vertices=72, convex hull=105, v0=55940)
- After retessellation of defect 44 (v0=55940), euler #=-57 (118923,354417,235437) : difference with theory (-60) = -3
- CORRECTING DEFECT 45 (vertices=38, convex hull=94, v0=59482)
- After retessellation of defect 45 (v0=59482), euler #=-56 (118948,354528,235524) : difference with theory (-59) = -3
- CORRECTING DEFECT 46 (vertices=88, convex hull=113, v0=59690)
- After retessellation of defect 46 (v0=59690), euler #=-55 (119006,354758,235697) : difference with theory (-58) = -3
- CORRECTING DEFECT 47 (vertices=923, convex hull=355, v0=61512)
- After retessellation of defect 47 (v0=61512), euler #=-56 (119145,355356,236155) : difference with theory (-57) = -1
- CORRECTING DEFECT 48 (vertices=168, convex hull=128, v0=63799)
- After retessellation of defect 48 (v0=63799), euler #=-55 (119163,355476,236258) : difference with theory (-56) = -1
- CORRECTING DEFECT 49 (vertices=35, convex hull=57, v0=64472)
- After retessellation of defect 49 (v0=64472), euler #=-54 (119183,355556,236319) : difference with theory (-55) = -1
- CORRECTING DEFECT 50 (vertices=106, convex hull=115, v0=65764)
- After retessellation of defect 50 (v0=65764), euler #=-53 (119219,355710,236438) : difference with theory (-54) = -1
- CORRECTING DEFECT 51 (vertices=66, convex hull=105, v0=67802)
- After retessellation of defect 51 (v0=67802), euler #=-52 (119261,355886,236573) : difference with theory (-53) = -1
- CORRECTING DEFECT 52 (vertices=5, convex hull=31, v0=70441)
- After retessellation of defect 52 (v0=70441), euler #=-51 (119262,355898,236585) : difference with theory (-52) = -1
- CORRECTING DEFECT 53 (vertices=14, convex hull=35, v0=75865)
- After retessellation of defect 53 (v0=75865), euler #=-50 (119264,355917,236603) : difference with theory (-51) = -1
- CORRECTING DEFECT 54 (vertices=19, convex hull=29, v0=76784)
- After retessellation of defect 54 (v0=76784), euler #=-49 (119268,355937,236620) : difference with theory (-50) = -1
- CORRECTING DEFECT 55 (vertices=86, convex hull=46, v0=77926)
- After retessellation of defect 55 (v0=77926), euler #=-48 (119281,355992,236663) : difference with theory (-49) = -1
- CORRECTING DEFECT 56 (vertices=61, convex hull=89, v0=80473)
- After retessellation of defect 56 (v0=80473), euler #=-47 (119293,356065,236725) : difference with theory (-48) = -1
- CORRECTING DEFECT 57 (vertices=430, convex hull=124, v0=80644)
- After retessellation of defect 57 (v0=80644), euler #=-45 (119343,356271,236883) : difference with theory (-47) = -2
- CORRECTING DEFECT 58 (vertices=64, convex hull=60, v0=81047)
- After retessellation of defect 58 (v0=81047), euler #=-44 (119369,356370,236957) : difference with theory (-46) = -2
- CORRECTING DEFECT 59 (vertices=18, convex hull=39, v0=81487)
- After retessellation of defect 59 (v0=81487), euler #=-43 (119378,356409,236988) : difference with theory (-45) = -2
- CORRECTING DEFECT 60 (vertices=462, convex hull=297, v0=82400)
- After retessellation of defect 60 (v0=82400), euler #=-43 (119566,357124,237515) : difference with theory (-44) = -1
- CORRECTING DEFECT 61 (vertices=85, convex hull=102, v0=83440)
- After retessellation of defect 61 (v0=83440), euler #=-42 (119620,357334,237672) : difference with theory (-43) = -1
- CORRECTING DEFECT 62 (vertices=27, convex hull=65, v0=83610)
- After retessellation of defect 62 (v0=83610), euler #=-41 (119638,357411,237732) : difference with theory (-42) = -1
- CORRECTING DEFECT 63 (vertices=306, convex hull=229, v0=83621)
- After retessellation of defect 63 (v0=83621), euler #=-40 (119683,357664,237941) : difference with theory (-41) = -1
- CORRECTING DEFECT 64 (vertices=50, convex hull=37, v0=85157)
- After retessellation of defect 64 (v0=85157), euler #=-39 (119690,357697,237968) : difference with theory (-40) = -1
- CORRECTING DEFECT 65 (vertices=8, convex hull=27, v0=88379)
- After retessellation of defect 65 (v0=88379), euler #=-38 (119693,357713,237982) : difference with theory (-39) = -1
- CORRECTING DEFECT 66 (vertices=35, convex hull=72, v0=89453)
- After retessellation of defect 66 (v0=89453), euler #=-37 (119702,357767,238028) : difference with theory (-38) = -1
- CORRECTING DEFECT 67 (vertices=22, convex hull=15, v0=90631)
- After retessellation of defect 67 (v0=90631), euler #=-36 (119704,357776,238036) : difference with theory (-37) = -1
- CORRECTING DEFECT 68 (vertices=28, convex hull=70, v0=90840)
- After retessellation of defect 68 (v0=90840), euler #=-35 (119718,357844,238091) : difference with theory (-36) = -1
- CORRECTING DEFECT 69 (vertices=42, convex hull=47, v0=91781)
- After retessellation of defect 69 (v0=91781), euler #=-34 (119721,357871,238116) : difference with theory (-35) = -1
- CORRECTING DEFECT 70 (vertices=33, convex hull=31, v0=92677)
- After retessellation of defect 70 (v0=92677), euler #=-33 (119728,357901,238140) : difference with theory (-34) = -1
- CORRECTING DEFECT 71 (vertices=430, convex hull=328, v0=93685)
- After retessellation of defect 71 (v0=93685), euler #=-33 (119865,358483,238585) : difference with theory (-33) = 0
- CORRECTING DEFECT 72 (vertices=7, convex hull=29, v0=93732)
- After retessellation of defect 72 (v0=93732), euler #=-32 (119866,358492,238594) : difference with theory (-32) = 0
- CORRECTING DEFECT 73 (vertices=40, convex hull=79, v0=94001)
- After retessellation of defect 73 (v0=94001), euler #=-31 (119885,358581,238665) : difference with theory (-31) = 0
- CORRECTING DEFECT 74 (vertices=22, convex hull=27, v0=97355)
- After retessellation of defect 74 (v0=97355), euler #=-30 (119892,358609,238687) : difference with theory (-30) = 0
- CORRECTING DEFECT 75 (vertices=83, convex hull=87, v0=98408)
- After retessellation of defect 75 (v0=98408), euler #=-29 (119907,358690,238754) : difference with theory (-29) = 0
- CORRECTING DEFECT 76 (vertices=184, convex hull=89, v0=101880)
- After retessellation of defect 76 (v0=101880), euler #=-28 (119942,358837,238867) : difference with theory (-28) = 0
- CORRECTING DEFECT 77 (vertices=26, convex hull=43, v0=103310)
- After retessellation of defect 77 (v0=103310), euler #=-27 (119954,358890,238909) : difference with theory (-27) = 0
- CORRECTING DEFECT 78 (vertices=27, convex hull=44, v0=104429)
- After retessellation of defect 78 (v0=104429), euler #=-26 (119963,358935,238946) : difference with theory (-26) = 0
- CORRECTING DEFECT 79 (vertices=44, convex hull=62, v0=105234)
- After retessellation of defect 79 (v0=105234), euler #=-25 (119975,359000,239000) : difference with theory (-25) = 0
- CORRECTING DEFECT 80 (vertices=72, convex hull=56, v0=105703)
- After retessellation of defect 80 (v0=105703), euler #=-24 (120002,359104,239078) : difference with theory (-24) = 0
- CORRECTING DEFECT 81 (vertices=566, convex hull=223, v0=107239)
- After retessellation of defect 81 (v0=107239), euler #=-23 (120033,359316,239260) : difference with theory (-23) = 0
- CORRECTING DEFECT 82 (vertices=38, convex hull=45, v0=107447)
- After retessellation of defect 82 (v0=107447), euler #=-22 (120041,359354,239291) : difference with theory (-22) = 0
- CORRECTING DEFECT 83 (vertices=94, convex hull=100, v0=107901)
- After retessellation of defect 83 (v0=107901), euler #=-21 (120067,359475,239387) : difference with theory (-21) = 0
- CORRECTING DEFECT 84 (vertices=446, convex hull=275, v0=109179)
- After retessellation of defect 84 (v0=109179), euler #=-19 (120190,359992,239783) : difference with theory (-20) = -1
- CORRECTING DEFECT 85 (vertices=350, convex hull=99, v0=109241)
- After retessellation of defect 85 (v0=109241), euler #=-18 (120227,360149,239904) : difference with theory (-19) = -1
- CORRECTING DEFECT 86 (vertices=30, convex hull=31, v0=110598)
- After retessellation of defect 86 (v0=110598), euler #=-17 (120228,360167,239922) : difference with theory (-18) = -1
- CORRECTING DEFECT 87 (vertices=36, convex hull=19, v0=110854)
- After retessellation of defect 87 (v0=110854), euler #=-16 (120230,360177,239931) : difference with theory (-17) = -1
- CORRECTING DEFECT 88 (vertices=11, convex hull=24, v0=110986)
- After retessellation of defect 88 (v0=110986), euler #=-15 (120231,360187,239941) : difference with theory (-16) = -1
- CORRECTING DEFECT 89 (vertices=161, convex hull=148, v0=112984)
- After retessellation of defect 89 (v0=112984), euler #=-14 (120293,360440,240133) : difference with theory (-15) = -1
- CORRECTING DEFECT 90 (vertices=24, convex hull=22, v0=113151)
- After retessellation of defect 90 (v0=113151), euler #=-13 (120296,360456,240147) : difference with theory (-14) = -1
- CORRECTING DEFECT 91 (vertices=69, convex hull=99, v0=113401)
- After retessellation of defect 91 (v0=113401), euler #=-12 (120329,360601,240260) : difference with theory (-13) = -1
- CORRECTING DEFECT 92 (vertices=25, convex hull=56, v0=113464)
- After retessellation of defect 92 (v0=113464), euler #=-11 (120341,360658,240306) : difference with theory (-12) = -1
- CORRECTING DEFECT 93 (vertices=20, convex hull=55, v0=113573)
- After retessellation of defect 93 (v0=113573), euler #=-10 (120352,360712,240350) : difference with theory (-11) = -1
- CORRECTING DEFECT 94 (vertices=264, convex hull=84, v0=114606)
- After retessellation of defect 94 (v0=114606), euler #=-10 (120398,360891,240483) : difference with theory (-10) = 0
- CORRECTING DEFECT 95 (vertices=6, convex hull=16, v0=115291)
- After retessellation of defect 95 (v0=115291), euler #=-9 (120399,360898,240490) : difference with theory (-9) = 0
- CORRECTING DEFECT 96 (vertices=103, convex hull=125, v0=118381)
- After retessellation of defect 96 (v0=118381), euler #=-8 (120448,361097,240641) : difference with theory (-8) = 0
- CORRECTING DEFECT 97 (vertices=6, convex hull=24, v0=120593)
- After retessellation of defect 97 (v0=120593), euler #=-7 (120450,361110,240653) : difference with theory (-7) = 0
- CORRECTING DEFECT 98 (vertices=38, convex hull=74, v0=121034)
- After retessellation of defect 98 (v0=121034), euler #=-6 (120477,361222,240739) : difference with theory (-6) = 0
- CORRECTING DEFECT 99 (vertices=8, convex hull=25, v0=122977)
- After retessellation of defect 99 (v0=122977), euler #=-5 (120479,361237,240753) : difference with theory (-5) = 0
- CORRECTING DEFECT 100 (vertices=36, convex hull=32, v0=123087)
- After retessellation of defect 100 (v0=123087), euler #=-4 (120480,361253,240769) : difference with theory (-4) = 0
- CORRECTING DEFECT 101 (vertices=19, convex hull=25, v0=124178)
- After retessellation of defect 101 (v0=124178), euler #=-3 (120482,361268,240783) : difference with theory (-3) = 0
- CORRECTING DEFECT 102 (vertices=153, convex hull=44, v0=124282)
- After retessellation of defect 102 (v0=124282), euler #=-2 (120491,361314,240821) : difference with theory (-2) = 0
- CORRECTING DEFECT 103 (vertices=277, convex hull=157, v0=126775)
- After retessellation of defect 103 (v0=126775), euler #=0 (120540,361539,240999) : difference with theory (-1) = -1
- CORRECTING DEFECT 104 (vertices=45, convex hull=43, v0=127187)
- After retessellation of defect 104 (v0=127187), euler #=1 (120543,361564,241022) : difference with theory (0) = -1
- CORRECTING DEFECT 105 (vertices=41, convex hull=71, v0=127304)
- After retessellation of defect 105 (v0=127304), euler #=2 (120564,361654,241092) : difference with theory (1) = -1
- CORRECTING DEFECT 106 (vertices=47, convex hull=59, v0=128162)
- After retessellation of defect 106 (v0=128162), euler #=2 (120570,361704,241136) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.89 +- 0.29 (0.05-->15.13) (max @ vno 101566 --> 105691)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.89 +- 0.29 (0.05-->15.13) (max @ vno 101566 --> 105691)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 382 mutations (34.9%), 712 crossovers (65.1%), 650 vertices were eliminated
- building final representation...
- 7914 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=120570, nf=241136, ne=361704, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 62.0 minutes
- 0 defective edges
- removing intersecting faces
- 000: 787 intersecting
- 001: 17 intersecting
- 002: 8 intersecting
- expanding nbhd size to 2
- 003: 8 intersecting
- expanding nbhd size to 3
- 004: 8 intersecting
- expanding nbhd size to 4
- 005: 9 intersecting
- expanding nbhd size to 5
- 006: 9 intersecting
- 007: 8 intersecting
- expanding nbhd size to 6
- 008: 8 intersecting
- expanding nbhd size to 7
- 009: 9 intersecting
- 010: 8 intersecting
- mris_fix_topology utimesec 3722.196140
- mris_fix_topology stimesec 0.421935
- mris_fix_topology ru_maxrss 407520
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 54104
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 16728
- mris_fix_topology ru_oublock 12032
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 644
- mris_fix_topology ru_nivcsw 15323
- FSRUNTIME@ mris_fix_topology rh 1.0339 hours 1 threads
- PIDs (6888 6891) completed and logs appended.
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 115741 - 347217 + 231478 = 2 --> 0 holes
- F =2V-4: 231478 = 231482-4 (0)
- 2E=3F: 694434 = 694434 (0)
- total defect index = 0
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 120570 - 361704 + 241136 = 2 --> 0 holes
- F =2V-4: 241136 = 241140-4 (0)
- 2E=3F: 723408 = 723408 (0)
- total defect index = 0
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 693 intersecting
- 001: 101 intersecting
- 002: 81 intersecting
- 003: 50 intersecting
- 004: 12 intersecting
- 005: 9 intersecting
- 006: 5 intersecting
- 007: 3 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 118 intersecting
- 001: 27 intersecting
- 002: 11 intersecting
- 003: 8 intersecting
- expanding nbhd size to 2
- 004: 8 intersecting
- expanding nbhd size to 3
- 005: 9 intersecting
- expanding nbhd size to 4
- 006: 9 intersecting
- expanding nbhd size to 5
- 007: 14 intersecting
- 008: 8 intersecting
- expanding nbhd size to 6
- 009: 8 intersecting
- expanding nbhd size to 7
- 010: 9 intersecting
- expanding nbhd size to 8
- 011: 11 intersecting
- 012: 2 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Sun Oct 8 09:22:04 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050419 lh
- #--------------------------------------------
- #@# Make White Surf rh Sun Oct 8 09:22:04 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050419 rh
- Waiting for PID 22354 of (22354 22357) to complete...
- Waiting for PID 22357 of (22354 22357) to complete...
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050419 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-6.0.0/0050419/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- 16765 bright wm thresholded.
- 3914 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.orig...
- computing class statistics...
- border white: 227339 voxels (1.36%)
- border gray 284070 voxels (1.69%)
- WM (94.0): 94.9 +- 9.0 [70.0 --> 110.0]
- GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 52.9 (was 70)
- setting MAX_BORDER_WHITE to 105.0 (was 105)
- setting MIN_BORDER_WHITE to 64.0 (was 85)
- setting MAX_CSF to 41.8 (was 40)
- setting MAX_GRAY to 87.0 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.9 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 30.7 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.27 (0.02-->9.11) (max @ vno 98839 --> 113193)
- face area 0.28 +- 0.16 (0.00-->7.49)
- mean absolute distance = 0.77 +- 0.98
- 3326 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=96+-9.6, GM=64+-8.7
- mean inside = 89.9, mean outside = 72.1
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- mean border=76.0, 517 (517) missing vertices, mean dist 0.3 [0.7 (%31.7)->0.8 (%68.3))]
- %66 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.93 +- 0.31 (0.07-->8.58) (max @ vno 98839 --> 113193)
- face area 0.28 +- 0.16 (0.00-->7.23)
- mean absolute distance = 0.38 +- 0.69
- 3342 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3144658.5, rms=10.903
- 001: dt: 0.5000, sse=1916638.2, rms=8.129 (25.442%)
- 002: dt: 0.5000, sse=1364355.1, rms=6.424 (20.977%)
- 003: dt: 0.5000, sse=1094688.6, rms=5.350 (16.724%)
- 004: dt: 0.5000, sse=942958.0, rms=4.688 (12.373%)
- 005: dt: 0.5000, sse=883262.2, rms=4.332 (7.593%)
- 006: dt: 0.5000, sse=841250.3, rms=4.123 (4.812%)
- 007: dt: 0.5000, sse=825469.2, rms=4.044 (1.913%)
- 008: dt: 0.5000, sse=822050.8, rms=3.977 (1.674%)
- rms = 3.95, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=822618.0, rms=3.953 (0.602%)
- 010: dt: 0.2500, sse=668265.3, rms=2.962 (25.056%)
- 011: dt: 0.2500, sse=639670.2, rms=2.722 (8.128%)
- 012: dt: 0.2500, sse=637707.1, rms=2.669 (1.933%)
- rms = 2.64, time step reduction 2 of 3 to 0.125...
- 013: dt: 0.2500, sse=628825.6, rms=2.636 (1.226%)
- 014: dt: 0.1250, sse=618400.4, rms=2.555 (3.079%)
- rms = 2.54, time step reduction 3 of 3 to 0.062...
- 015: dt: 0.1250, sse=616306.2, rms=2.539 (0.613%)
- positioning took 1.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=78.4, 423 (161) missing vertices, mean dist -0.2 [0.4 (%65.5)->0.3 (%34.5))]
- %72 local maxima, %22 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 0.92 +- 0.30 (0.08-->8.59) (max @ vno 73280 --> 113057)
- face area 0.36 +- 0.21 (0.00-->10.45)
- mean absolute distance = 0.30 +- 0.51
- 3322 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1022776.4, rms=4.345
- 016: dt: 0.5000, sse=858608.1, rms=3.279 (24.527%)
- rms = 3.38, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.2500, sse=791910.7, rms=2.683 (18.177%)
- 018: dt: 0.2500, sse=736769.9, rms=2.353 (12.298%)
- 019: dt: 0.2500, sse=731852.9, rms=2.255 (4.168%)
- rms = 2.21, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=732245.4, rms=2.208 (2.081%)
- 021: dt: 0.1250, sse=712746.2, rms=2.143 (2.977%)
- rms = 2.11, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=710021.9, rms=2.111 (1.478%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=79.8, 407 (98) missing vertices, mean dist -0.1 [0.3 (%59.6)->0.3 (%40.4))]
- %77 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.92 +- 0.30 (0.08-->8.59) (max @ vno 73280 --> 113057)
- face area 0.35 +- 0.21 (0.00-->11.01)
- mean absolute distance = 0.28 +- 0.43
- 2984 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=793683.0, rms=2.958
- 023: dt: 0.5000, sse=785225.9, rms=2.867 (3.070%)
- rms = 3.11, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=711587.4, rms=2.247 (21.614%)
- 025: dt: 0.2500, sse=694499.0, rms=2.003 (10.859%)
- 026: dt: 0.2500, sse=685749.1, rms=1.939 (3.185%)
- rms = 1.92, time step reduction 2 of 3 to 0.125...
- 027: dt: 0.2500, sse=681350.0, rms=1.920 (0.979%)
- 028: dt: 0.1250, sse=672554.9, rms=1.855 (3.381%)
- rms = 1.83, time step reduction 3 of 3 to 0.062...
- 029: dt: 0.1250, sse=673168.1, rms=1.830 (1.391%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=80.5, 429 (64) missing vertices, mean dist -0.0 [0.3 (%52.8)->0.3 (%47.2))]
- %80 local maxima, %13 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-6.0.0/0050419/surf/lh.white.preaparc...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=688305.8, rms=2.078
- rms = 2.15, time step reduction 1 of 3 to 0.250...
- 030: dt: 0.2500, sse=657376.2, rms=1.716 (17.432%)
- 031: dt: 0.2500, sse=657937.7, rms=1.529 (10.879%)
- rms = 1.53, time step reduction 2 of 3 to 0.125...
- rms = 1.51, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=640548.7, rms=1.508 (1.397%)
- positioning took 0.4 minutes
- generating cortex label...
- 10 non-cortical segments detected
- only using segment with 6602 vertices
- erasing segment 0 (vno[0] = 27858)
- erasing segment 2 (vno[0] = 61703)
- erasing segment 3 (vno[0] = 80829)
- erasing segment 4 (vno[0] = 82264)
- erasing segment 5 (vno[0] = 82451)
- erasing segment 6 (vno[0] = 83220)
- erasing segment 7 (vno[0] = 84830)
- erasing segment 8 (vno[0] = 93890)
- erasing segment 9 (vno[0] = 115006)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.area
- vertex spacing 0.91 +- 0.31 (0.02-->8.64) (max @ vno 73280 --> 113057)
- face area 0.35 +- 0.21 (0.00-->10.85)
- refinement took 4.4 minutes
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050419 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-6.0.0/0050419/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- 16765 bright wm thresholded.
- 3914 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.orig...
- computing class statistics...
- border white: 227339 voxels (1.36%)
- border gray 284070 voxels (1.69%)
- WM (94.0): 94.9 +- 9.0 [70.0 --> 110.0]
- GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 53.9 (was 70)
- setting MAX_BORDER_WHITE to 107.0 (was 105)
- setting MIN_BORDER_WHITE to 65.0 (was 85)
- setting MAX_CSF to 42.8 (was 40)
- setting MAX_GRAY to 89.0 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.9 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 31.7 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.24 (0.03-->5.77) (max @ vno 60351 --> 119029)
- face area 0.28 +- 0.14 (0.00-->3.73)
- mean absolute distance = 0.71 +- 0.87
- 3699 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=98+-7.8, GM=65+-8.7
- mean inside = 90.9, mean outside = 72.7
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=77.5, 123 (123) missing vertices, mean dist 0.3 [0.6 (%35.4)->0.8 (%64.6))]
- %69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.09-->5.94) (max @ vno 60351 --> 119029)
- face area 0.28 +- 0.14 (0.00-->3.60)
- mean absolute distance = 0.34 +- 0.62
- 3038 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3058668.8, rms=10.522
- 001: dt: 0.5000, sse=1789492.8, rms=7.579 (27.966%)
- 002: dt: 0.5000, sse=1254803.6, rms=5.850 (22.820%)
- 003: dt: 0.5000, sse=1004687.3, rms=4.825 (17.518%)
- 004: dt: 0.5000, sse=889956.9, rms=4.278 (11.328%)
- 005: dt: 0.5000, sse=838337.2, rms=3.971 (7.181%)
- 006: dt: 0.5000, sse=810723.8, rms=3.811 (4.026%)
- 007: dt: 0.5000, sse=792770.8, rms=3.726 (2.249%)
- 008: dt: 0.5000, sse=784591.6, rms=3.668 (1.554%)
- rms = 3.63, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=778661.9, rms=3.629 (1.047%)
- 010: dt: 0.2500, sse=621459.5, rms=2.457 (32.295%)
- 011: dt: 0.2500, sse=591889.1, rms=2.154 (12.329%)
- 012: dt: 0.2500, sse=585776.1, rms=2.084 (3.279%)
- rms = 2.04, time step reduction 2 of 3 to 0.125...
- 013: dt: 0.2500, sse=581292.9, rms=2.043 (1.952%)
- 014: dt: 0.1250, sse=580102.3, rms=1.951 (4.510%)
- rms = 1.94, time step reduction 3 of 3 to 0.062...
- 015: dt: 0.1250, sse=571021.1, rms=1.937 (0.723%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=79.9, 158 (22) missing vertices, mean dist -0.2 [0.4 (%66.7)->0.3 (%33.3))]
- %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.27 (0.07-->5.96) (max @ vno 60351 --> 119029)
- face area 0.35 +- 0.18 (0.00-->5.04)
- mean absolute distance = 0.27 +- 0.44
- 2929 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=996010.7, rms=4.071
- 016: dt: 0.5000, sse=820012.0, rms=2.950 (27.534%)
- rms = 3.12, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.2500, sse=732321.5, rms=2.245 (23.900%)
- 018: dt: 0.2500, sse=698609.1, rms=1.857 (17.290%)
- 019: dt: 0.2500, sse=689437.5, rms=1.723 (7.202%)
- rms = 1.69, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=681548.4, rms=1.690 (1.956%)
- 021: dt: 0.1250, sse=678484.8, rms=1.604 (5.055%)
- rms = 1.59, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=674957.6, rms=1.589 (0.943%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=81.5, 174 (20) missing vertices, mean dist -0.1 [0.3 (%61.9)->0.2 (%38.1))]
- %80 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 0.91 +- 0.27 (0.06-->6.02) (max @ vno 45001 --> 44976)
- face area 0.35 +- 0.18 (0.00-->5.14)
- mean absolute distance = 0.25 +- 0.38
- 2859 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=767836.4, rms=2.685
- 023: dt: 0.5000, sse=765362.6, rms=2.606 (2.948%)
- rms = 2.95, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=683773.8, rms=1.866 (28.367%)
- 025: dt: 0.2500, sse=663477.4, rms=1.590 (14.807%)
- 026: dt: 0.2500, sse=659064.1, rms=1.528 (3.905%)
- rms = 1.53, time step reduction 2 of 3 to 0.125...
- 027: dt: 0.2500, sse=664424.2, rms=1.527 (0.079%)
- 028: dt: 0.1250, sse=650001.8, rms=1.443 (5.469%)
- rms = 1.44, time step reduction 3 of 3 to 0.062...
- 029: dt: 0.1250, sse=648552.3, rms=1.435 (0.541%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=82.2, 201 (16) missing vertices, mean dist -0.0 [0.3 (%53.6)->0.2 (%46.4))]
- %83 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-6.0.0/0050419/surf/rh.white.preaparc...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=666528.9, rms=1.772
- rms = 1.88, time step reduction 1 of 3 to 0.250...
- 030: dt: 0.2500, sse=635652.4, rms=1.358 (23.362%)
- 031: dt: 0.2500, sse=625720.8, rms=1.150 (15.334%)
- rms = 1.17, time step reduction 2 of 3 to 0.125...
- rms = 1.13, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=623070.8, rms=1.134 (1.417%)
- positioning took 0.4 minutes
- generating cortex label...
- 8 non-cortical segments detected
- only using segment with 6551 vertices
- erasing segment 1 (vno[0] = 51399)
- erasing segment 2 (vno[0] = 82598)
- erasing segment 3 (vno[0] = 85775)
- erasing segment 4 (vno[0] = 86579)
- erasing segment 5 (vno[0] = 87505)
- erasing segment 6 (vno[0] = 89836)
- erasing segment 7 (vno[0] = 92564)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.area
- vertex spacing 0.90 +- 0.27 (0.03-->5.99) (max @ vno 44976 --> 45001)
- face area 0.34 +- 0.17 (0.00-->5.01)
- refinement took 4.6 minutes
- PIDs (22354 22357) completed and logs appended.
- #--------------------------------------------
- #@# Smooth2 lh Sun Oct 8 09:26:39 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
- #--------------------------------------------
- #@# Smooth2 rh Sun Oct 8 09:26:39 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
- Waiting for PID 22551 of (22551 22554) to complete...
- Waiting for PID 22554 of (22551 22554) 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 (22551 22554) completed and logs appended.
- #--------------------------------------------
- #@# Inflation2 lh Sun Oct 8 09:26:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- #--------------------------------------------
- #@# Inflation2 rh Sun Oct 8 09:26:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Waiting for PID 22603 of (22603 22606) to complete...
- Waiting for PID 22606 of (22603 22606) to complete...
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- Reading ../surf/lh.smoothwm
- avg radius = 43.8 mm, total surface area = 71639 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.198 (target=0.015)
step 005: RMS=0.143 (target=0.015)
step 010: RMS=0.114 (target=0.015)
step 015: RMS=0.096 (target=0.015)
step 020: RMS=0.082 (target=0.015)
step 025: RMS=0.071 (target=0.015)
step 030: RMS=0.062 (target=0.015)
step 035: RMS=0.055 (target=0.015)
step 040: RMS=0.048 (target=0.015)
step 045: RMS=0.044 (target=0.015)
step 050: RMS=0.041 (target=0.015)
step 055: RMS=0.039 (target=0.015)
step 060: RMS=0.037 (target=0.015)
- inflation complete.
- inflation took 0.6 minutes
- mris_inflate utimesec 37.590285
- mris_inflate stimesec 0.089986
- mris_inflate ru_maxrss 171420
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 25543
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 9072
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2246
- mris_inflate ru_nivcsw 2865
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Reading ../surf/rh.smoothwm
- avg radius = 43.9 mm, total surface area = 73879 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.190 (target=0.015)
step 005: RMS=0.136 (target=0.015)
step 010: RMS=0.105 (target=0.015)
step 015: RMS=0.086 (target=0.015)
step 020: RMS=0.072 (target=0.015)
step 025: RMS=0.062 (target=0.015)
step 030: RMS=0.054 (target=0.015)
step 035: RMS=0.047 (target=0.015)
step 040: RMS=0.041 (target=0.015)
step 045: RMS=0.038 (target=0.015)
step 050: RMS=0.035 (target=0.015)
step 055: RMS=0.033 (target=0.015)
step 060: RMS=0.031 (target=0.015)
- inflation complete.
- inflation took 0.6 minutes
- mris_inflate utimesec 38.565137
- mris_inflate stimesec 0.087986
- mris_inflate ru_maxrss 177796
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 26627
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 9448
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2222
- mris_inflate ru_nivcsw 3057
- PIDs (22603 22606) completed and logs appended.
- #--------------------------------------------
- #@# Curv .H and .K lh Sun Oct 8 09:27:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 09:27:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/surf
- reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 22690 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- Waiting for PID 22693 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- Waiting for PID 22696 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- Waiting for PID 22699 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- Waiting for PID 22702 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- Waiting for PID 22705 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- Waiting for PID 22708 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- Waiting for PID 22711 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- Waiting for PID 22714 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- Waiting for PID 22717 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- Waiting for PID 22722 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- Waiting for PID 22725 of (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) to complete...
- mris_curvature -w lh.white.preaparc
- total integrated curvature = 23.563*4pi (296.101) --> -23 handles
- ICI = 207.5, FI = 1801.8, variation=29309.119
- 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
- 146 vertices thresholded to be in k1 ~ [-0.52 0.75], k2 ~ [-0.32 0.19]
- total integrated curvature = 0.048*4pi (0.604) --> 1 handles
- ICI = 1.4, FI = 7.6, variation=143.367
- 118 vertices thresholded to be in [-0.14 0.04]
- writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.004
- 92 vertices thresholded to be in [-0.26 0.25]
- done.
- writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.025
- done.
- mris_curvature -w rh.white.preaparc
- total integrated curvature = 2.889*4pi (36.306) --> -2 handles
- ICI = 192.0, FI = 1755.0, variation=28549.882
- 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
- 139 vertices thresholded to be in k1 ~ [-0.31 1.92], k2 ~ [-0.18 0.15]
- total integrated curvature = 0.139*4pi (1.752) --> 1 handles
- ICI = 1.4, FI = 8.3, variation=151.735
- 128 vertices thresholded to be in [-0.11 0.03]
- writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.002
- 99 vertices thresholded to be in [-0.18 0.59]
- done.
- writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.026
- done.
- PIDs (22690 22693 22696 22699 22702 22705 22708 22711 22714 22717 22722 22725) completed and logs appended.
- #-----------------------------------------
- #@# Curvature Stats lh Sun Oct 8 09:28:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050419 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 [ 0050419/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 [ 228 ]
- Gb_filter = 0
- WARN: S lookup min: -1.297643
- WARN: S explicit min: 0.000000 vertex = 107
- #-----------------------------------------
- #@# Curvature Stats rh Sun Oct 8 09:28:40 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050419 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 [ 0050419/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 [ 229 ]
- Gb_filter = 0
- WARN: S lookup min: -1.077199
- WARN: S explicit min: 0.000000 vertex = 110
- #--------------------------------------------
- #@# Sphere lh Sun Oct 8 09:28:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- #--------------------------------------------
- #@# Sphere rh Sun Oct 8 09:28:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- Waiting for PID 22874 of (22874 22878) to complete...
- Waiting for PID 22878 of (22874 22878) to complete...
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0.322...
- 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 %22.56
- pass 1: epoch 2 of 3 starting distance error %22.40
- unfolding complete - removing small folds...
- starting distance error %21.82
- removing remaining folds...
- final distance error %21.87
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 339 negative triangles
- 359: dt=0.9900, 339 negative triangles
- 360: dt=0.9900, 159 negative triangles
- 361: dt=0.9900, 120 negative triangles
- 362: dt=0.9900, 97 negative triangles
- 363: dt=0.9900, 97 negative triangles
- 364: dt=0.9900, 86 negative triangles
- 365: dt=0.9900, 73 negative triangles
- 366: dt=0.9900, 78 negative triangles
- 367: dt=0.9900, 80 negative triangles
- 368: dt=0.9900, 79 negative triangles
- 369: dt=0.9900, 71 negative triangles
- 370: dt=0.9900, 80 negative triangles
- 371: dt=0.9900, 67 negative triangles
- 372: dt=0.9900, 62 negative triangles
- 373: dt=0.9900, 56 negative triangles
- 374: dt=0.9900, 65 negative triangles
- 375: dt=0.9900, 57 negative triangles
- 376: dt=0.9900, 56 negative triangles
- 377: dt=0.9900, 54 negative triangles
- 378: dt=0.9900, 47 negative triangles
- 379: dt=0.9900, 45 negative triangles
- 380: dt=0.9900, 37 negative triangles
- 381: dt=0.9900, 36 negative triangles
- 382: dt=0.9900, 39 negative triangles
- 383: dt=0.9900, 36 negative triangles
- 384: dt=0.9900, 27 negative triangles
- 385: dt=0.9900, 21 negative triangles
- 386: dt=0.9900, 29 negative triangles
- 387: dt=0.9900, 24 negative triangles
- 388: dt=0.9900, 20 negative triangles
- 389: dt=0.9900, 18 negative triangles
- 390: dt=0.9900, 18 negative triangles
- 391: dt=0.9900, 15 negative triangles
- 392: dt=0.9900, 10 negative triangles
- 393: dt=0.9900, 12 negative triangles
- 394: dt=0.9900, 8 negative triangles
- 395: dt=0.9900, 10 negative triangles
- 396: dt=0.9900, 10 negative triangles
- 397: dt=0.9900, 7 negative triangles
- 398: dt=0.9900, 10 negative triangles
- 399: dt=0.9900, 6 negative triangles
- 400: dt=0.9900, 5 negative triangles
- 401: dt=0.9900, 4 negative triangles
- 402: dt=0.9900, 2 negative triangles
- 403: dt=0.9900, 2 negative triangles
- 404: dt=0.9900, 1 negative triangles
- 405: dt=0.9900, 2 negative triangles
- 406: dt=0.9900, 1 negative triangles
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 1.01 hours
- mris_sphere utimesec 3932.188216
- mris_sphere stimesec 0.962853
- mris_sphere ru_maxrss 239076
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 42602
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 8176
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 147251
- mris_sphere ru_nivcsw 288537
- FSRUNTIME@ mris_sphere 1.0107 hours 1 threads
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0.315...
- 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 %21.53
- pass 1: epoch 2 of 3 starting distance error %21.38
- unfolding complete - removing small folds...
- starting distance error %21.20
- removing remaining folds...
- final distance error %21.23
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 197 negative triangles
- 266: dt=0.9900, 197 negative triangles
- 267: dt=0.9900, 107 negative triangles
- 268: dt=0.9900, 89 negative triangles
- 269: dt=0.9900, 76 negative triangles
- 270: dt=0.9900, 68 negative triangles
- 271: dt=0.9900, 57 negative triangles
- 272: dt=0.9900, 54 negative triangles
- 273: dt=0.9900, 51 negative triangles
- 274: dt=0.9900, 41 negative triangles
- 275: dt=0.9900, 41 negative triangles
- 276: dt=0.9900, 43 negative triangles
- 277: dt=0.9900, 38 negative triangles
- 278: dt=0.9900, 31 negative triangles
- 279: dt=0.9900, 27 negative triangles
- 280: dt=0.9900, 28 negative triangles
- 281: dt=0.9900, 27 negative triangles
- 282: dt=0.9900, 27 negative triangles
- 283: dt=0.9900, 24 negative triangles
- 284: dt=0.9900, 16 negative triangles
- 285: dt=0.9900, 10 negative triangles
- 286: dt=0.9900, 15 negative triangles
- 287: dt=0.9900, 9 negative triangles
- 288: dt=0.9900, 8 negative triangles
- 289: dt=0.9900, 10 negative triangles
- 290: dt=0.9900, 6 negative triangles
- 291: dt=0.9900, 3 negative triangles
- 292: dt=0.9900, 5 negative triangles
- 293: dt=0.9900, 4 negative triangles
- 294: dt=0.9900, 1 negative triangles
- 295: dt=0.9900, 4 negative triangles
- 296: dt=0.9900, 2 negative triangles
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.90 hours
- mris_sphere utimesec 3234.569270
- mris_sphere stimesec 1.011846
- mris_sphere ru_maxrss 248900
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 44036
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 8528
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 126126
- mris_sphere ru_nivcsw 281201
- FSRUNTIME@ mris_sphere 0.8984 hours 1 threads
- PIDs (22874 22878) completed and logs appended.
- #--------------------------------------------
- #@# Surf Reg lh Sun Oct 8 10:29:22 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 10:29:22 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 25373 of (25373 25376) to complete...
- Waiting for PID 25376 of (25373 25376) to complete...
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 = 5.303
- curvature mean = 0.005, std = 0.800
- curvature mean = 0.012, std = 0.865
- Starting MRISrigidBodyAlignGlobal()
- d=32.00 min @ (8.00, -8.00, 0.00) sse = 247803.0, tmin=1.7799
- d=16.00 min @ (-4.00, 4.00, 4.00) sse = 237704.4, tmin=2.6897
- d=8.00 min @ (0.00, 0.00, 2.00) sse = 236927.2, tmin=3.6406
- d=4.00 min @ (0.00, 0.00, -1.00) sse = 236769.7, tmin=4.5991
- d=2.00 min @ (0.50, -0.50, 0.00) sse = 236377.4, tmin=5.5583
- d=0.50 min @ (0.00, 0.12, 0.00) sse = 236373.9, tmin=7.4470
- 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 7.45 min
- curvature mean = -0.013, std = 0.830
- curvature mean = 0.004, std = 0.943
- curvature mean = -0.016, std = 0.840
- curvature mean = 0.002, std = 0.975
- curvature mean = -0.016, std = 0.843
- curvature mean = 0.000, std = 0.989
- 2 Reading smoothwm
- curvature mean = -0.043, std = 0.380
- curvature mean = 0.038, std = 0.248
- curvature mean = 0.061, std = 0.286
- curvature mean = 0.028, std = 0.309
- curvature mean = 0.053, std = 0.429
- curvature mean = 0.026, std = 0.338
- curvature mean = 0.032, std = 0.549
- curvature mean = 0.025, std = 0.350
- curvature mean = 0.012, std = 0.658
- MRISregister() return, current seed 0
- -01: dt=0.0000, 225 negative triangles
- 135: dt=0.9900, 225 negative triangles
- expanding nbhd size to 1
- 136: dt=0.9900, 296 negative triangles
- 137: dt=0.9900, 229 negative triangles
- 138: dt=0.9900, 218 negative triangles
- 139: dt=0.9900, 220 negative triangles
- 140: dt=0.9900, 208 negative triangles
- 141: dt=0.9900, 199 negative triangles
- 142: dt=0.9900, 195 negative triangles
- 143: dt=0.9900, 177 negative triangles
- 144: dt=0.9900, 167 negative triangles
- 145: dt=0.9900, 148 negative triangles
- 146: dt=0.9900, 147 negative triangles
- 147: dt=0.9900, 131 negative triangles
- 148: dt=0.9900, 118 negative triangles
- 149: dt=0.9900, 122 negative triangles
- 150: dt=0.9900, 114 negative triangles
- 151: dt=0.9900, 109 negative triangles
- 152: dt=0.9900, 93 negative triangles
- 153: dt=0.9900, 91 negative triangles
- 154: dt=0.9900, 82 negative triangles
- 155: dt=0.9900, 73 negative triangles
- 156: dt=0.9900, 73 negative triangles
- 157: dt=0.9900, 77 negative triangles
- 158: dt=0.9900, 71 negative triangles
- 159: dt=0.9900, 64 negative triangles
- 160: dt=0.9900, 56 negative triangles
- 161: dt=0.9900, 49 negative triangles
- 162: dt=0.9900, 47 negative triangles
- 163: dt=0.9900, 42 negative triangles
- 164: dt=0.9900, 44 negative triangles
- 165: dt=0.9900, 34 negative triangles
- 166: dt=0.9900, 31 negative triangles
- 167: dt=0.9900, 26 negative triangles
- 168: dt=0.9900, 33 negative triangles
- 169: dt=0.9900, 28 negative triangles
- 170: dt=0.9900, 23 negative triangles
- 171: dt=0.9900, 21 negative triangles
- 172: dt=0.9900, 20 negative triangles
- 173: dt=0.9900, 20 negative triangles
- 174: dt=0.9900, 17 negative triangles
- 175: dt=0.9900, 13 negative triangles
- 176: dt=0.9900, 13 negative triangles
- 177: dt=0.9900, 11 negative triangles
- 178: dt=0.9900, 10 negative triangles
- 179: dt=0.9900, 10 negative triangles
- 180: dt=0.9900, 11 negative triangles
- 181: dt=0.9900, 9 negative triangles
- 182: dt=0.9900, 9 negative triangles
- 183: dt=0.9900, 9 negative triangles
- 184: dt=0.9900, 11 negative triangles
- 185: dt=0.9900, 9 negative triangles
- 186: dt=0.9900, 9 negative triangles
- 187: dt=0.9900, 9 negative triangles
- 188: dt=0.9900, 6 negative triangles
- 189: dt=0.9900, 6 negative triangles
- 190: dt=0.9900, 7 negative triangles
- 191: dt=0.9900, 8 negative triangles
- 192: dt=0.9900, 6 negative triangles
- 193: dt=0.9900, 6 negative triangles
- 194: dt=0.9900, 6 negative triangles
- 195: dt=0.9900, 8 negative triangles
- 196: dt=0.9900, 8 negative triangles
- 197: dt=0.9900, 6 negative triangles
- 198: dt=0.9900, 5 negative triangles
- 199: dt=0.9900, 6 negative triangles
- 200: dt=0.9900, 7 negative triangles
- 201: dt=0.9900, 5 negative triangles
- 202: dt=0.9900, 4 negative triangles
- 203: dt=0.9900, 2 negative triangles
- 204: dt=0.9900, 3 negative triangles
- 205: dt=0.9900, 2 negative triangles
- 206: dt=0.9900, 3 negative triangles
- 207: dt=0.9900, 2 negative triangles
- 208: dt=0.9900, 2 negative triangles
- 209: dt=0.9900, 1 negative triangles
- 210: dt=0.9900, 2 negative triangles
- 211: dt=0.9900, 1 negative triangles
- writing registered surface to ../surf/lh.sphere.reg...
- registration took 0.98 hours
- mris_register utimesec 3531.979057
- mris_register stimesec 1.398787
- mris_register ru_maxrss 225452
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 32711
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 8240
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 254853
- mris_register ru_nivcsw 199701
- FSRUNTIME@ mris_register 0.9811 hours 1 threads
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 = 5.387
- curvature mean = 0.022, std = 0.809
- curvature mean = 0.015, std = 0.867
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 0.00) sse = 263048.0, tmin=0.9218
- d=32.00 min @ (0.00, -8.00, 8.00) sse = 241894.2, tmin=1.8620
- d=16.00 min @ (-4.00, 4.00, -4.00) sse = 212184.3, tmin=2.8162
- d=8.00 min @ (2.00, 0.00, 2.00) sse = 206636.9, tmin=3.8101
- d=4.00 min @ (0.00, -1.00, 0.00) sse = 204520.3, tmin=4.8129
- d=2.00 min @ (-0.50, 0.00, 0.00) sse = 204235.4, tmin=5.8158
- d=1.00 min @ (0.25, 0.00, 0.25) sse = 204184.9, tmin=6.8099
- d=0.50 min @ (-0.12, -0.12, 0.00) sse = 204158.2, tmin=7.8001
- 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 7.80 min
- curvature mean = -0.007, std = 0.830
- curvature mean = 0.006, std = 0.951
- curvature mean = -0.010, std = 0.841
- curvature mean = 0.002, std = 0.980
- curvature mean = -0.012, std = 0.843
- curvature mean = 0.000, std = 0.992
- 2 Reading smoothwm
- curvature mean = -0.040, std = 0.336
- curvature mean = 0.033, std = 0.242
- curvature mean = 0.071, std = 0.325
- curvature mean = 0.028, std = 0.301
- curvature mean = 0.052, std = 0.481
- curvature mean = 0.027, std = 0.327
- curvature mean = 0.031, std = 0.610
- curvature mean = 0.027, std = 0.337
- curvature mean = 0.012, std = 0.722
- MRISregister() return, current seed 0
- -01: dt=0.0000, 118 negative triangles
- 118: dt=0.9900, 118 negative triangles
- expanding nbhd size to 1
- 119: dt=0.9900, 132 negative triangles
- 120: dt=0.9900, 116 negative triangles
- 121: dt=0.9900, 108 negative triangles
- 122: dt=0.9900, 111 negative triangles
- 123: dt=0.9900, 108 negative triangles
- 124: dt=0.9900, 90 negative triangles
- 125: dt=0.9900, 84 negative triangles
- 126: dt=0.9900, 80 negative triangles
- 127: dt=0.9900, 71 negative triangles
- 128: dt=0.9900, 69 negative triangles
- 129: dt=0.9900, 64 negative triangles
- 130: dt=0.9900, 69 negative triangles
- 131: dt=0.9900, 54 negative triangles
- 132: dt=0.9900, 56 negative triangles
- 133: dt=0.9900, 51 negative triangles
- 134: dt=0.9900, 54 negative triangles
- 135: dt=0.9900, 50 negative triangles
- 136: dt=0.9900, 48 negative triangles
- 137: dt=0.9900, 46 negative triangles
- 138: dt=0.9900, 45 negative triangles
- 139: dt=0.9900, 43 negative triangles
- 140: dt=0.9900, 37 negative triangles
- 141: dt=0.9900, 36 negative triangles
- 142: dt=0.9900, 35 negative triangles
- 143: dt=0.9900, 35 negative triangles
- 144: dt=0.9900, 34 negative triangles
- 145: dt=0.9900, 29 negative triangles
- 146: dt=0.9900, 25 negative triangles
- 147: dt=0.9900, 25 negative triangles
- 148: dt=0.9900, 22 negative triangles
- 149: dt=0.9900, 20 negative triangles
- 150: dt=0.9900, 19 negative triangles
- 151: dt=0.9900, 18 negative triangles
- 152: dt=0.9900, 18 negative triangles
- 153: dt=0.9900, 20 negative triangles
- 154: dt=0.9900, 15 negative triangles
- 155: dt=0.9900, 11 negative triangles
- 156: dt=0.9900, 12 negative triangles
- 157: dt=0.9900, 8 negative triangles
- 158: dt=0.9900, 11 negative triangles
- 159: dt=0.9900, 9 negative triangles
- 160: dt=0.9900, 7 negative triangles
- 161: dt=0.9900, 5 negative triangles
- 162: dt=0.9900, 5 negative triangles
- 163: dt=0.9900, 4 negative triangles
- 164: dt=0.9900, 6 negative triangles
- 165: dt=0.9900, 5 negative triangles
- 166: dt=0.9900, 5 negative triangles
- 167: dt=0.9900, 3 negative triangles
- 168: dt=0.9900, 4 negative triangles
- writing registered surface to ../surf/rh.sphere.reg...
- registration took 1.03 hours
- mris_register utimesec 3811.513561
- mris_register stimesec 1.879714
- mris_register ru_maxrss 232376
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 33172
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 8584
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 295132
- mris_register ru_nivcsw 196077
- FSRUNTIME@ mris_register 1.0300 hours 1 threads
- PIDs (25373 25376) completed and logs appended.
- #--------------------------------------------
- #@# Jacobian white lh Sun Oct 8 11:31:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# Jacobian white rh Sun Oct 8 11:31:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- Waiting for PID 29077 of (29077 29080) to complete...
- Waiting for PID 29080 of (29077 29080) 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 (29077 29080) completed and logs appended.
- #--------------------------------------------
- #@# AvgCurv lh Sun Oct 8 11:31:12 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
- #--------------------------------------------
- #@# AvgCurv rh Sun Oct 8 11:31:12 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 29121 of (29121 29124) to complete...
- Waiting for PID 29124 of (29121 29124) 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 (29121 29124) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc lh Sun Oct 8 11:31:14 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot
- #-----------------------------------------
- #@# Cortical Parc rh Sun Oct 8 11:31:14 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 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 29170 of (29170 29173) to complete...
- Waiting for PID 29173 of (29170 29173) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 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...
- 1223 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2789 changed, 115741 examined...
- 001: 666 changed, 11899 examined...
- 002: 162 changed, 3714 examined...
- 003: 56 changed, 955 examined...
- 004: 24 changed, 324 examined...
- 005: 12 changed, 134 examined...
- 006: 3 changed, 81 examined...
- 007: 0 changed, 13 examined...
- 202 labels changed using aseg
- 000: 108 total segments, 64 labels (329 vertices) changed
- 001: 46 total segments, 5 labels (11 vertices) changed
- 002: 40 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 10 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1725 vertices marked for relabeling...
- 1725 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 13 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 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...
- 1248 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2544 changed, 120570 examined...
- 001: 596 changed, 10868 examined...
- 002: 136 changed, 3351 examined...
- 003: 38 changed, 855 examined...
- 004: 19 changed, 218 examined...
- 005: 6 changed, 123 examined...
- 006: 2 changed, 38 examined...
- 007: 0 changed, 9 examined...
- 146 labels changed using aseg
- 000: 101 total segments, 64 labels (334 vertices) changed
- 001: 38 total segments, 1 labels (2 vertices) changed
- 002: 37 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 11 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1197 vertices marked for relabeling...
- 1197 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 13 seconds.
- PIDs (29170 29173) completed and logs appended.
- #--------------------------------------------
- #@# Make Pial Surf lh Sun Oct 8 11:31:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050419 lh
- #--------------------------------------------
- #@# Make Pial Surf rh Sun Oct 8 11:31:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050419 rh
- Waiting for PID 29217 of (29217 29220) to complete...
- Waiting for PID 29220 of (29217 29220) to complete...
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050419 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-6.0.0/0050419/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- 16765 bright wm thresholded.
- 3914 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.orig...
- computing class statistics...
- border white: 227339 voxels (1.36%)
- border gray 284070 voxels (1.69%)
- WM (94.0): 94.9 +- 9.0 [70.0 --> 110.0]
- GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 52.9 (was 70)
- setting MAX_BORDER_WHITE to 105.0 (was 105)
- setting MIN_BORDER_WHITE to 64.0 (was 85)
- setting MAX_CSF to 41.8 (was 40)
- setting MAX_GRAY to 87.0 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.9 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 30.7 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=96+-9.6, GM=64+-8.7
- mean inside = 89.9, mean outside = 72.1
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.91 +- 0.31 (0.02-->8.64) (max @ vno 73280 --> 113057)
- face area 0.35 +- 0.21 (0.00-->10.82)
- mean absolute distance = 0.58 +- 0.94
- 2658 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 53 points - only 0.00% unknown
- deleting segment 1 with 33 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- deleting segment 4 with 53 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 62 points - only 0.00% unknown
- deleting segment 7 with 49 points - only 0.00% unknown
- deleting segment 8 with 156 points - only 0.00% unknown
- deleting segment 9 with 68 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- mean border=75.8, 488 (472) missing vertices, mean dist 0.2 [0.8 (%21.7)->0.5 (%78.3))]
- %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.94 +- 0.31 (0.08-->8.49) (max @ vno 73280 --> 113057)
- face area 0.35 +- 0.21 (0.00-->11.06)
- mean absolute distance = 0.37 +- 0.68
- 3252 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1573624.4, rms=6.699
- 001: dt: 0.5000, sse=1042869.8, rms=4.441 (33.708%)
- 002: dt: 0.5000, sse=902940.9, rms=3.762 (15.297%)
- rms = 3.77, time step reduction 1 of 3 to 0.250...
- 003: dt: 0.2500, sse=804296.1, rms=3.113 (17.240%)
- 004: dt: 0.2500, sse=763211.3, rms=2.786 (10.516%)
- 005: dt: 0.2500, sse=750426.8, rms=2.644 (5.084%)
- 006: dt: 0.2500, sse=742081.2, rms=2.574 (2.644%)
- 007: dt: 0.2500, sse=738756.6, rms=2.524 (1.956%)
- rms = 2.49, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=735273.8, rms=2.494 (1.198%)
- 009: dt: 0.1250, sse=724974.4, rms=2.432 (2.467%)
- rms = 2.41, time step reduction 3 of 3 to 0.062...
- 010: dt: 0.1250, sse=723872.8, rms=2.412 (0.816%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 66 points - only 0.00% unknown
- deleting segment 1 with 34 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- deleting segment 3 with 57 points - only 0.00% unknown
- deleting segment 4 with 51 points - only 0.00% unknown
- deleting segment 5 with 38 points - only 0.00% unknown
- deleting segment 6 with 143 points - only 0.00% unknown
- deleting segment 7 with 21 points - only 0.00% unknown
- deleting segment 8 with 66 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- mean border=78.3, 487 (204) missing vertices, mean dist -0.2 [0.4 (%65.0)->0.3 (%35.0))]
- %72 local maxima, %22 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 0.92 +- 0.31 (0.03-->8.46) (max @ vno 73280 --> 113057)
- face area 0.36 +- 0.22 (0.00-->11.81)
- mean absolute distance = 0.30 +- 0.51
- 3233 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=994124.2, rms=4.104
- 011: dt: 0.5000, sse=841973.9, rms=3.079 (24.974%)
- rms = 3.21, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.2500, sse=763922.4, rms=2.500 (18.797%)
- 013: dt: 0.2500, sse=742191.4, rms=2.188 (12.499%)
- 014: dt: 0.2500, sse=724216.0, rms=2.087 (4.588%)
- rms = 2.07, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=728996.2, rms=2.070 (0.839%)
- 016: dt: 0.1250, sse=730963.6, rms=1.999 (3.406%)
- rms = 1.99, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=713597.2, rms=1.988 (0.560%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 71 points - only 0.00% unknown
- deleting segment 1 with 28 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 67 points - only 0.00% unknown
- deleting segment 5 with 54 points - only 0.00% unknown
- deleting segment 6 with 39 points - only 0.00% unknown
- deleting segment 7 with 144 points - only 0.00% unknown
- deleting segment 8 with 82 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- mean border=79.7, 387 (102) missing vertices, mean dist -0.1 [0.3 (%60.0)->0.3 (%40.0))]
- %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.92 +- 0.31 (0.03-->8.46) (max @ vno 73280 --> 113057)
- face area 0.36 +- 0.22 (0.00-->11.57)
- mean absolute distance = 0.28 +- 0.43
- 3073 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=790881.8, rms=2.856
- 018: dt: 0.5000, sse=787143.9, rms=2.768 (3.074%)
- rms = 2.99, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=710054.4, rms=2.117 (23.526%)
- 020: dt: 0.2500, sse=718674.8, rms=1.886 (10.896%)
- 021: dt: 0.2500, sse=694899.4, rms=1.828 (3.072%)
- rms = 1.82, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=684932.7, rms=1.819 (0.510%)
- 023: dt: 0.1250, sse=680116.7, rms=1.733 (4.757%)
- rms = 1.72, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=671961.2, rms=1.718 (0.865%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 65 points - only 0.00% unknown
- deleting segment 1 with 26 points - only 0.00% unknown
- deleting segment 2 with 5 points - only 0.00% unknown
- deleting segment 3 with 67 points - only 0.00% unknown
- deleting segment 4 with 51 points - only 0.00% unknown
- deleting segment 5 with 40 points - only 0.00% unknown
- deleting segment 6 with 136 points - only 0.00% unknown
- deleting segment 7 with 82 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- deleting segment 9 with 6 points - only 0.00% unknown
- mean border=80.4, 388 (73) missing vertices, mean dist -0.0 [0.3 (%53.1)->0.3 (%46.9))]
- %81 local maxima, %13 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-6.0.0/0050419/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=686268.7, rms=1.979
- rms = 2.07, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=656894.3, rms=1.603 (19.021%)
- 026: dt: 0.2500, sse=648569.0, rms=1.400 (12.643%)
- rms = 1.44, time step reduction 2 of 3 to 0.125...
- rms = 1.38, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=642158.9, rms=1.379 (1.525%)
- positioning took 0.4 minutes
- generating cortex label...
- 11 non-cortical segments detected
- only using segment with 6588 vertices
- erasing segment 0 (vno[0] = 26670)
- erasing segment 2 (vno[0] = 61703)
- erasing segment 3 (vno[0] = 80103)
- erasing segment 4 (vno[0] = 80829)
- erasing segment 5 (vno[0] = 82264)
- erasing segment 6 (vno[0] = 82451)
- erasing segment 7 (vno[0] = 83220)
- erasing segment 8 (vno[0] = 84830)
- erasing segment 9 (vno[0] = 93890)
- erasing segment 10 (vno[0] = 115006)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.area
- vertex spacing 0.92 +- 0.31 (0.02-->8.50) (max @ vno 73280 --> 113057)
- face area 0.35 +- 0.21 (0.00-->11.35)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 36 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 8 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 5 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 9 with 23 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- deleting segment 11 with 13 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=51.7, 340 (340) missing vertices, mean dist 1.5 [1.2 (%0.1)->2.8 (%99.9))]
- %10 local maxima, %42 large gradients and %42 min vals, 519 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=19630168.0, rms=29.482
- 001: dt: 0.0500, sse=17387126.0, rms=27.691 (6.077%)
- 002: dt: 0.0500, sse=15758014.0, rms=26.313 (4.976%)
- 003: dt: 0.0500, sse=14496229.0, rms=25.193 (4.253%)
- 004: dt: 0.0500, sse=13471548.0, rms=24.246 (3.759%)
- 005: dt: 0.0500, sse=12606994.0, rms=23.418 (3.419%)
- 006: dt: 0.0500, sse=11858036.0, rms=22.675 (3.171%)
- 007: dt: 0.0500, sse=11196928.0, rms=21.998 (2.983%)
- 008: dt: 0.0500, sse=10604977.0, rms=21.374 (2.836%)
- 009: dt: 0.0500, sse=10068800.0, rms=20.793 (2.720%)
- 010: dt: 0.0500, sse=9580162.0, rms=20.249 (2.619%)
- positioning took 0.8 minutes
- mean border=51.5, 280 (165) missing vertices, mean dist 1.3 [0.2 (%0.2)->2.3 (%99.8))]
- %11 local maxima, %43 large gradients and %41 min vals, 485 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=10297617.0, rms=21.033
- 011: dt: 0.0500, sse=9841284.0, rms=20.532 (2.384%)
- 012: dt: 0.0500, sse=9421435.0, rms=20.059 (2.301%)
- 013: dt: 0.0500, sse=9033505.0, rms=19.613 (2.227%)
- 014: dt: 0.0500, sse=8674583.0, rms=19.190 (2.155%)
- 015: dt: 0.0500, sse=8341930.0, rms=18.790 (2.086%)
- 016: dt: 0.0500, sse=8034539.5, rms=18.412 (2.011%)
- 017: dt: 0.0500, sse=7748905.5, rms=18.054 (1.946%)
- 018: dt: 0.0500, sse=7484414.5, rms=17.715 (1.874%)
- 019: dt: 0.0500, sse=7238236.0, rms=17.394 (1.811%)
- 020: dt: 0.0500, sse=7009122.5, rms=17.090 (1.749%)
- positioning took 0.8 minutes
- mean border=51.3, 331 (124) missing vertices, mean dist 1.2 [0.1 (%2.3)->2.1 (%97.7))]
- %11 local maxima, %43 large gradients and %41 min vals, 473 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=7107461.5, rms=17.224
- 021: dt: 0.0500, sse=6884532.0, rms=16.926 (1.735%)
- 022: dt: 0.0500, sse=6678257.5, rms=16.644 (1.663%)
- 023: dt: 0.0500, sse=6484737.5, rms=16.376 (1.613%)
- 024: dt: 0.0500, sse=6304946.0, rms=16.122 (1.548%)
- 025: dt: 0.0500, sse=6137856.5, rms=15.883 (1.485%)
- 026: dt: 0.0500, sse=5982241.0, rms=15.656 (1.425%)
- 027: dt: 0.0500, sse=5836094.0, rms=15.441 (1.378%)
- 028: dt: 0.0500, sse=5697504.0, rms=15.233 (1.344%)
- 029: dt: 0.0500, sse=5566292.0, rms=15.034 (1.307%)
- 030: dt: 0.0500, sse=5441540.0, rms=14.842 (1.277%)
- positioning took 0.8 minutes
- mean border=51.3, 374 (95) missing vertices, mean dist 1.0 [0.1 (%12.7)->2.0 (%87.3))]
- %11 local maxima, %43 large gradients and %40 min vals, 453 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=5532633.0, rms=14.978
- 031: dt: 0.5000, sse=4621209.0, rms=13.511 (9.794%)
- 032: dt: 0.5000, sse=4029144.8, rms=12.456 (7.805%)
- 033: dt: 0.5000, sse=3583968.8, rms=11.603 (6.852%)
- 034: dt: 0.5000, sse=3249384.0, rms=10.911 (5.964%)
- 035: dt: 0.5000, sse=2963605.5, rms=10.286 (5.727%)
- 036: dt: 0.5000, sse=2723710.5, rms=9.728 (5.424%)
- 037: dt: 0.5000, sse=2501331.0, rms=9.186 (5.572%)
- 038: dt: 0.5000, sse=2317739.0, rms=8.709 (5.186%)
- 039: dt: 0.5000, sse=2157220.8, rms=8.275 (4.989%)
- 040: dt: 0.5000, sse=2039194.5, rms=7.937 (4.081%)
- 041: dt: 0.5000, sse=1938488.8, rms=7.640 (3.744%)
- 042: dt: 0.5000, sse=1873119.1, rms=7.437 (2.656%)
- 043: dt: 0.5000, sse=1814863.4, rms=7.255 (2.449%)
- 044: dt: 0.5000, sse=1779083.9, rms=7.138 (1.618%)
- 045: dt: 0.5000, sse=1741096.2, rms=7.013 (1.744%)
- 046: dt: 0.5000, sse=1722352.2, rms=6.949 (0.921%)
- 047: dt: 0.5000, sse=1697874.8, rms=6.867 (1.170%)
- rms = 6.83, time step reduction 1 of 3 to 0.250...
- 048: dt: 0.5000, sse=1687387.9, rms=6.829 (0.554%)
- 049: dt: 0.2500, sse=1615109.8, rms=6.553 (4.047%)
- 050: dt: 0.2500, sse=1590691.2, rms=6.465 (1.336%)
- rms = 6.46, time step reduction 2 of 3 to 0.125...
- 051: dt: 0.2500, sse=1590276.9, rms=6.462 (0.053%)
- 052: dt: 0.1250, sse=1567841.5, rms=6.377 (1.311%)
- rms = 6.35, time step reduction 3 of 3 to 0.062...
- 053: dt: 0.1250, sse=1561502.4, rms=6.354 (0.369%)
- positioning took 2.6 minutes
- mean border=50.2, 2719 (41) missing vertices, mean dist 0.2 [0.2 (%47.6)->0.9 (%52.4))]
- %19 local maxima, %36 large gradients and %37 min vals, 275 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=1754123.9, rms=6.325
- 054: dt: 0.5000, sse=1683664.5, rms=6.080 (3.876%)
- 055: dt: 0.5000, sse=1607073.6, rms=5.807 (4.492%)
- rms = 5.86, time step reduction 1 of 3 to 0.250...
- 056: dt: 0.2500, sse=1527654.1, rms=5.454 (6.073%)
- 057: dt: 0.2500, sse=1507545.6, rms=5.356 (1.793%)
- rms = 5.37, time step reduction 2 of 3 to 0.125...
- 058: dt: 0.1250, sse=1495354.4, rms=5.300 (1.045%)
- 059: dt: 0.1250, sse=1479099.4, rms=5.225 (1.417%)
- rms = 5.19, time step reduction 3 of 3 to 0.062...
- 060: dt: 0.1250, sse=1470539.8, rms=5.187 (0.729%)
- positioning took 1.1 minutes
- mean border=49.5, 3212 (36) missing vertices, mean dist 0.2 [0.2 (%48.3)->0.7 (%51.7))]
- %28 local maxima, %28 large gradients and %37 min vals, 292 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=1529688.6, rms=5.389
- rms = 5.65, time step reduction 1 of 3 to 0.250...
- 061: dt: 0.2500, sse=1499352.0, rms=5.257 (2.448%)
- 062: dt: 0.2500, sse=1484348.2, rms=5.201 (1.070%)
- rms = 5.21, time step reduction 2 of 3 to 0.125...
- rms = 5.16, time step reduction 3 of 3 to 0.062...
- 063: dt: 0.1250, sse=1475908.0, rms=5.161 (0.757%)
- positioning took 0.6 minutes
- mean border=49.0, 5508 (35) missing vertices, mean dist 0.1 [0.2 (%47.8)->0.5 (%52.2))]
- %32 local maxima, %23 large gradients and %36 min vals, 310 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-6.0.0/0050419/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1496372.1, rms=5.228
- rms = 5.44, time step reduction 1 of 3 to 0.250...
- 064: dt: 0.2500, sse=1465147.6, rms=5.091 (2.628%)
- 065: dt: 0.2500, sse=1440592.5, rms=5.000 (1.787%)
- rms = 4.98, time step reduction 2 of 3 to 0.125...
- 066: dt: 0.2500, sse=1433773.5, rms=4.981 (0.371%)
- 067: dt: 0.1250, sse=1396058.9, rms=4.801 (3.612%)
- 068: dt: 0.1250, sse=1381200.6, rms=4.735 (1.371%)
- rms = 4.70, time step reduction 3 of 3 to 0.062...
- 069: dt: 0.1250, sse=1372894.9, rms=4.699 (0.760%)
- positioning took 0.9 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.area.pial
- vertex spacing 1.08 +- 0.53 (0.07-->9.41) (max @ vno 112594 --> 112592)
- face area 0.45 +- 0.41 (0.00-->13.78)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 115741 vertices processed
- 25000 of 115741 vertices processed
- 50000 of 115741 vertices processed
- 75000 of 115741 vertices processed
- 100000 of 115741 vertices processed
- 0 of 115741 vertices processed
- 25000 of 115741 vertices processed
- 50000 of 115741 vertices processed
- 75000 of 115741 vertices processed
- 100000 of 115741 vertices processed
- thickness calculation complete, 391:1236 truncations.
- 21022 vertices at 0 distance
- 71923 vertices at 1 distance
- 72256 vertices at 2 distance
- 35044 vertices at 3 distance
- 12273 vertices at 4 distance
- 4172 vertices at 5 distance
- 1554 vertices at 6 distance
- 672 vertices at 7 distance
- 271 vertices at 8 distance
- 129 vertices at 9 distance
- 96 vertices at 10 distance
- 73 vertices at 11 distance
- 55 vertices at 12 distance
- 44 vertices at 13 distance
- 38 vertices at 14 distance
- 24 vertices at 15 distance
- 12 vertices at 16 distance
- 6 vertices at 17 distance
- 9 vertices at 18 distance
- 8 vertices at 19 distance
- 13 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.thickness
- positioning took 13.6 minutes
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050419 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-6.0.0/0050419/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- 16765 bright wm thresholded.
- 3914 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.orig...
- computing class statistics...
- border white: 227339 voxels (1.36%)
- border gray 284070 voxels (1.69%)
- WM (94.0): 94.9 +- 9.0 [70.0 --> 110.0]
- GM (69.0) : 68.1 +- 11.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 53.9 (was 70)
- setting MAX_BORDER_WHITE to 107.0 (was 105)
- setting MIN_BORDER_WHITE to 65.0 (was 85)
- setting MAX_CSF to 42.8 (was 40)
- setting MAX_GRAY to 89.0 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.9 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 31.7 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=98+-7.8, GM=65+-8.7
- mean inside = 90.9, mean outside = 72.7
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.27 (0.03-->5.99) (max @ vno 44976 --> 45001)
- face area 0.34 +- 0.17 (0.00-->5.00)
- mean absolute distance = 0.54 +- 0.84
- 2700 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 41 points - only 0.00% unknown
- deleting segment 1 with 114 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- deleting segment 5 with 240 points - only 0.00% unknown
- deleting segment 6 with 129 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- deleting segment 9 with 143 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- deleting segment 12 with 90 points - only 0.00% unknown
- deleting segment 13 with 37 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- mean border=77.3, 144 (143) missing vertices, mean dist 0.3 [0.7 (%20.5)->0.5 (%79.5))]
- %66 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 0.93 +- 0.28 (0.09-->6.21) (max @ vno 45001 --> 44976)
- face area 0.34 +- 0.18 (0.00-->4.71)
- mean absolute distance = 0.35 +- 0.62
- 3091 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1669381.2, rms=6.828
- 001: dt: 0.5000, sse=1035593.2, rms=4.362 (36.107%)
- 002: dt: 0.5000, sse=894456.6, rms=3.616 (17.106%)
- rms = 3.58, time step reduction 1 of 3 to 0.250...
- 003: dt: 0.5000, sse=884752.9, rms=3.578 (1.060%)
- 004: dt: 0.2500, sse=756702.8, rms=2.413 (32.562%)
- 005: dt: 0.2500, sse=709005.8, rms=2.175 (9.848%)
- 006: dt: 0.2500, sse=705124.2, rms=2.096 (3.620%)
- 007: dt: 0.2500, sse=694780.6, rms=2.043 (2.564%)
- rms = 2.01, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=692646.7, rms=2.012 (1.498%)
- 009: dt: 0.1250, sse=695707.4, rms=1.939 (3.632%)
- rms = 1.93, time step reduction 3 of 3 to 0.062...
- 010: dt: 0.1250, sse=684581.8, rms=1.926 (0.681%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- deleting segment 0 with 1 points - only 0.00% unknown
- deleting segment 1 with 41 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- deleting segment 3 with 112 points - only 0.00% unknown
- deleting segment 5 with 117 points - only 0.00% unknown
- deleting segment 6 with 108 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 4 points - only 0.00% unknown
- deleting segment 9 with 155 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 11 with 2 points - only 0.00% unknown
- deleting segment 12 with 84 points - only 0.00% unknown
- deleting segment 13 with 39 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- mean border=79.8, 153 (44) missing vertices, mean dist -0.2 [0.4 (%67.1)->0.2 (%32.9))]
- %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.27 (0.03-->6.48) (max @ vno 45001 --> 44976)
- face area 0.36 +- 0.19 (0.00-->5.40)
- mean absolute distance = 0.28 +- 0.46
- 3032 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=995905.4, rms=3.978
- 011: dt: 0.5000, sse=850508.9, rms=2.857 (28.173%)
- rms = 3.04, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.2500, sse=742900.4, rms=2.175 (23.893%)
- 013: dt: 0.2500, sse=722395.8, rms=1.790 (17.692%)
- 014: dt: 0.2500, sse=698424.2, rms=1.666 (6.944%)
- rms = 1.63, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=699930.3, rms=1.627 (2.327%)
- 016: dt: 0.1250, sse=688974.2, rms=1.562 (4.013%)
- rms = 1.55, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=702144.6, rms=1.549 (0.792%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- deleting segment 0 with 1 points - only 0.00% unknown
- deleting segment 1 with 33 points - only 0.00% unknown
- deleting segment 2 with 107 points - only 0.00% unknown
- deleting segment 4 with 137 points - only 0.00% unknown
- deleting segment 5 with 108 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 6 with 4 points - only 0.00% unknown
- deleting segment 7 with 145 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 8 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 points - only 0.00% unknown
- deleting segment 10 with 78 points - only 0.00% unknown
- deleting segment 11 with 40 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- mean border=81.4, 162 (29) missing vertices, mean dist -0.1 [0.3 (%62.2)->0.2 (%37.8))]
- %81 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 0.91 +- 0.27 (0.06-->6.51) (max @ vno 45001 --> 44976)
- face area 0.35 +- 0.18 (0.00-->5.32)
- mean absolute distance = 0.26 +- 0.39
- 3069 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=793921.4, rms=2.686
- 018: dt: 0.5000, sse=803041.9, rms=2.593 (3.483%)
- rms = 2.90, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=709633.7, rms=1.845 (28.824%)
- 020: dt: 0.2500, sse=677411.8, rms=1.560 (15.474%)
- 021: dt: 0.2500, sse=668925.4, rms=1.499 (3.924%)
- rms = 1.50, time step reduction 2 of 3 to 0.125...
- rms = 1.46, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=665414.1, rms=1.458 (2.719%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- deleting segment 0 with 1 points - only 0.00% unknown
- deleting segment 1 with 36 points - only 0.00% unknown
- deleting segment 2 with 112 points - only 0.00% unknown
- deleting segment 3 with 141 points - only 0.00% unknown
- deleting segment 4 with 109 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 5 with 3 points - only 0.00% unknown
- deleting segment 6 with 157 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 points - only 0.00% unknown
- deleting segment 9 with 78 points - only 0.00% unknown
- deleting segment 10 with 40 points - only 0.00% unknown
- mean border=82.1, 180 (21) missing vertices, mean dist -0.0 [0.3 (%53.0)->0.2 (%47.0))]
- %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-6.0.0/0050419/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=680193.8, rms=1.751
- rms = 1.99, time step reduction 1 of 3 to 0.250...
- 023: dt: 0.2500, sse=649265.1, rms=1.334 (23.856%)
- 024: dt: 0.2500, sse=638757.2, rms=1.148 (13.906%)
- rms = 1.17, time step reduction 2 of 3 to 0.125...
- rms = 1.13, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=635157.9, rms=1.127 (1.832%)
- positioning took 0.4 minutes
- generating cortex label...
- 10 non-cortical segments detected
- only using segment with 6549 vertices
- erasing segment 1 (vno[0] = 51399)
- erasing segment 2 (vno[0] = 82598)
- erasing segment 3 (vno[0] = 83759)
- erasing segment 4 (vno[0] = 85775)
- erasing segment 5 (vno[0] = 86579)
- erasing segment 6 (vno[0] = 87505)
- erasing segment 7 (vno[0] = 89177)
- erasing segment 8 (vno[0] = 89836)
- erasing segment 9 (vno[0] = 92564)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.area
- vertex spacing 0.91 +- 0.28 (0.03-->6.42) (max @ vno 44976 --> 45001)
- face area 0.35 +- 0.18 (0.00-->5.11)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 22 points - only 0.00% unknown
- deleting segment 1 with 33 points - only 0.00% unknown
- deleting segment 2 with 12 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=52.7, 155 (155) missing vertices, mean dist 1.5 [0.3 (%0.0)->2.8 (%100.0))]
- %10 local maxima, %41 large gradients and %45 min vals, 433 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=21345182.0, rms=30.020
- 001: dt: 0.0500, sse=18843466.0, rms=28.152 (6.223%)
- 002: dt: 0.0500, sse=17032700.0, rms=26.718 (5.093%)
- 003: dt: 0.0500, sse=15636521.0, rms=25.558 (4.343%)
- 004: dt: 0.0500, sse=14502217.0, rms=24.575 (3.847%)
- 005: dt: 0.0500, sse=13548160.0, rms=23.716 (3.494%)
- 006: dt: 0.0500, sse=12722069.0, rms=22.946 (3.245%)
- 007: dt: 0.0500, sse=11993256.0, rms=22.245 (3.055%)
- 008: dt: 0.0500, sse=11342199.0, rms=21.600 (2.902%)
- 009: dt: 0.0500, sse=10754317.0, rms=21.000 (2.778%)
- 010: dt: 0.0500, sse=10218041.0, rms=20.437 (2.680%)
- positioning took 0.8 minutes
- mean border=52.6, 163 (84) missing vertices, mean dist 1.3 [0.1 (%0.1)->2.3 (%99.9))]
- %11 local maxima, %41 large gradients and %44 min vals, 394 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=10889382.0, rms=21.138
- 011: dt: 0.0500, sse=10392600.0, rms=20.620 (2.446%)
- 012: dt: 0.0500, sse=9934282.0, rms=20.131 (2.371%)
- 013: dt: 0.0500, sse=9510461.0, rms=19.668 (2.300%)
- 014: dt: 0.0500, sse=9118092.0, rms=19.230 (2.231%)
- 015: dt: 0.0500, sse=8754194.0, rms=18.814 (2.164%)
- 016: dt: 0.0500, sse=8417119.0, rms=18.420 (2.094%)
- 017: dt: 0.0500, sse=8103557.5, rms=18.045 (2.032%)
- 018: dt: 0.0500, sse=7812604.0, rms=17.691 (1.964%)
- 019: dt: 0.0500, sse=7541889.0, rms=17.354 (1.902%)
- 020: dt: 0.0500, sse=7290439.5, rms=17.036 (1.836%)
- positioning took 0.8 minutes
- mean border=52.4, 201 (70) missing vertices, mean dist 1.1 [0.1 (%2.0)->2.0 (%98.0))]
- %11 local maxima, %41 large gradients and %43 min vals, 376 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=7396343.0, rms=17.176
- 021: dt: 0.0500, sse=7152739.0, rms=16.864 (1.816%)
- 022: dt: 0.0500, sse=6926473.5, rms=16.569 (1.749%)
- 023: dt: 0.0500, sse=6715051.0, rms=16.288 (1.693%)
- 024: dt: 0.0500, sse=6518868.5, rms=16.024 (1.626%)
- 025: dt: 0.0500, sse=6334735.5, rms=15.771 (1.577%)
- 026: dt: 0.0500, sse=6163739.0, rms=15.532 (1.512%)
- 027: dt: 0.0500, sse=6003479.0, rms=15.305 (1.461%)
- 028: dt: 0.0500, sse=5852159.5, rms=15.088 (1.421%)
- 029: dt: 0.0500, sse=5708597.0, rms=14.878 (1.388%)
- 030: dt: 0.0500, sse=5572252.0, rms=14.677 (1.356%)
- positioning took 0.8 minutes
- mean border=52.4, 239 (60) missing vertices, mean dist 0.9 [0.1 (%11.4)->1.9 (%88.6))]
- %11 local maxima, %42 large gradients and %43 min vals, 382 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=5661766.0, rms=14.807
- 031: dt: 0.5000, sse=4700159.0, rms=13.313 (10.085%)
- 032: dt: 0.5000, sse=4058720.5, rms=12.207 (8.311%)
- 033: dt: 0.5000, sse=3587216.2, rms=11.326 (7.216%)
- 034: dt: 0.5000, sse=3215667.2, rms=10.574 (6.638%)
- 035: dt: 0.5000, sse=2888702.2, rms=9.869 (6.665%)
- 036: dt: 0.5000, sse=2589104.0, rms=9.175 (7.041%)
- 037: dt: 0.5000, sse=2318204.5, rms=8.502 (7.331%)
- 038: dt: 0.5000, sse=2093042.6, rms=7.898 (7.103%)
- 039: dt: 0.5000, sse=1925816.8, rms=7.420 (6.052%)
- 040: dt: 0.5000, sse=1810688.8, rms=7.069 (4.726%)
- 041: dt: 0.5000, sse=1730716.9, rms=6.818 (3.558%)
- 042: dt: 0.5000, sse=1673375.5, rms=6.628 (2.784%)
- 043: dt: 0.5000, sse=1637380.1, rms=6.507 (1.828%)
- 044: dt: 0.5000, sse=1603178.8, rms=6.389 (1.816%)
- 045: dt: 0.5000, sse=1582254.9, rms=6.316 (1.137%)
- 046: dt: 0.5000, sse=1564638.4, rms=6.252 (1.017%)
- rms = 6.21, time step reduction 1 of 3 to 0.250...
- 047: dt: 0.5000, sse=1551781.1, rms=6.207 (0.709%)
- 048: dt: 0.2500, sse=1473321.2, rms=5.889 (5.133%)
- 049: dt: 0.2500, sse=1447589.1, rms=5.792 (1.638%)
- rms = 5.80, time step reduction 2 of 3 to 0.125...
- rms = 5.75, time step reduction 3 of 3 to 0.062...
- 050: dt: 0.1250, sse=1437029.8, rms=5.750 (0.729%)
- positioning took 2.4 minutes
- mean border=51.5, 2367 (23) missing vertices, mean dist 0.2 [0.2 (%49.0)->0.8 (%51.0))]
- %19 local maxima, %35 large gradients and %40 min vals, 189 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=1644775.0, rms=5.811
- 051: dt: 0.5000, sse=1563434.2, rms=5.510 (5.173%)
- 052: dt: 0.5000, sse=1505789.9, rms=5.300 (3.814%)
- rms = 5.36, time step reduction 1 of 3 to 0.250...
- 053: dt: 0.2500, sse=1415130.8, rms=4.876 (7.995%)
- 054: dt: 0.2500, sse=1393190.5, rms=4.765 (2.280%)
- rms = 4.79, time step reduction 2 of 3 to 0.125...
- 055: dt: 0.1250, sse=1380093.2, rms=4.701 (1.353%)
- 056: dt: 0.1250, sse=1366189.6, rms=4.630 (1.496%)
- rms = 4.58, time step reduction 3 of 3 to 0.062...
- 057: dt: 0.1250, sse=1356549.9, rms=4.585 (0.987%)
- positioning took 1.1 minutes
- mean border=50.8, 2584 (18) missing vertices, mean dist 0.1 [0.2 (%50.3)->0.6 (%49.7))]
- %27 local maxima, %27 large gradients and %39 min vals, 234 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=1398213.2, rms=4.746
- rms = 5.09, time step reduction 1 of 3 to 0.250...
- 058: dt: 0.2500, sse=1370177.5, rms=4.612 (2.815%)
- rms = 4.59, time step reduction 2 of 3 to 0.125...
- 059: dt: 0.2500, sse=1362897.1, rms=4.587 (0.561%)
- 060: dt: 0.1250, sse=1349253.2, rms=4.517 (1.515%)
- 061: dt: 0.1250, sse=1337339.4, rms=4.463 (1.200%)
- rms = 4.44, time step reduction 3 of 3 to 0.062...
- 062: dt: 0.1250, sse=1332830.6, rms=4.444 (0.421%)
- positioning took 0.8 minutes
- mean border=50.3, 4899 (16) missing vertices, mean dist 0.1 [0.2 (%49.4)->0.5 (%50.6))]
- %31 local maxima, %22 large gradients and %38 min vals, 228 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-6.0.0/0050419/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=1356995.8, rms=4.532
- rms = 4.78, time step reduction 1 of 3 to 0.250...
- 063: dt: 0.2500, sse=1335206.6, rms=4.427 (2.323%)
- 064: dt: 0.2500, sse=1316609.6, rms=4.353 (1.667%)
- rms = 4.37, time step reduction 2 of 3 to 0.125...
- rms = 4.31, time step reduction 3 of 3 to 0.062...
- 065: dt: 0.1250, sse=1309262.2, rms=4.314 (0.900%)
- positioning took 0.6 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.area.pial
- vertex spacing 1.05 +- 0.49 (0.07-->8.34) (max @ vno 50436 --> 50435)
- face area 0.44 +- 0.37 (0.00-->7.41)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 120570 vertices processed
- 25000 of 120570 vertices processed
- 50000 of 120570 vertices processed
- 75000 of 120570 vertices processed
- 100000 of 120570 vertices processed
- 0 of 120570 vertices processed
- 25000 of 120570 vertices processed
- 50000 of 120570 vertices processed
- 75000 of 120570 vertices processed
- 100000 of 120570 vertices processed
- thickness calculation complete, 255:811 truncations.
- 24468 vertices at 0 distance
- 79664 vertices at 1 distance
- 75359 vertices at 2 distance
- 33678 vertices at 3 distance
- 11058 vertices at 4 distance
- 3649 vertices at 5 distance
- 1367 vertices at 6 distance
- 564 vertices at 7 distance
- 242 vertices at 8 distance
- 140 vertices at 9 distance
- 102 vertices at 10 distance
- 63 vertices at 11 distance
- 40 vertices at 12 distance
- 29 vertices at 13 distance
- 24 vertices at 14 distance
- 19 vertices at 15 distance
- 15 vertices at 16 distance
- 17 vertices at 17 distance
- 10 vertices at 18 distance
- 6 vertices at 19 distance
- 16 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.thickness
- positioning took 13.5 minutes
- PIDs (29217 29220) completed and logs appended.
- #--------------------------------------------
- #@# Surf Volume lh Sun Oct 8 11:45:03 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0050419 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/lh.cortex.label
- Total face volume 219271
- Total vertex volume 217269 (mask=0)
- #@# 0050419 lh 217269
-
- vertexvol Done
- #--------------------------------------------
- #@# Surf Volume rh Sun Oct 8 11:45:06 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0050419 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/rh.cortex.label
- Total face volume 222558
- Total vertex volume 219604 (mask=0)
- #@# 0050419 rh 219604
-
- vertexvol Done
- #--------------------------------------------
- #@# Cortical ribbon mask Sun Oct 8 11:45:09 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0050419
- 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 = 593
- writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/ribbon.mgz
- mris_volmask took 8.65 minutes
- writing ribbon files
- #-----------------------------------------
- #@# Parcellation Stats lh Sun Oct 8 11:53:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0050419 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 0050419 lh pial
- #-----------------------------------------
- #@# Parcellation Stats rh Sun Oct 8 11:53:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0050419 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 0050419 rh pial
- Waiting for PID 30092 of (30092 30095 30098 30101) to complete...
- Waiting for PID 30095 of (30092 30095 30098 30101) to complete...
- Waiting for PID 30098 of (30092 30095 30098 30101) to complete...
- Waiting for PID 30101 of (30092 30095 30098 30101) 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 0050419 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 219271
- Total vertex volume 217269 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 910 615 1971 2.807 0.601 0.123 0.026 10 1.0 bankssts
- 737 460 1228 2.439 0.565 0.114 0.022 11 0.6 caudalanteriorcingulate
- 1985 1352 4141 2.729 0.610 0.132 0.034 20 2.9 caudalmiddlefrontal
- 2007 1474 3081 1.940 0.544 0.168 0.050 41 4.4 cuneus
- 389 288 884 2.501 1.236 0.122 0.039 4 0.6 entorhinal
- 3689 2718 7235 2.198 0.762 0.155 0.054 64 8.5 fusiform
- 4795 3482 10278 2.466 0.690 0.141 0.037 74 7.8 inferiorparietal
- 5221 3600 10174 2.432 0.698 0.136 0.040 78 9.3 inferiortemporal
- 1582 1068 2880 2.476 0.943 0.130 0.038 23 2.3 isthmuscingulate
- 7475 5337 12802 1.968 0.687 0.165 0.058 158 18.4 lateraloccipital
- 3228 2223 5714 2.311 0.654 0.153 0.058 59 8.4 lateralorbitofrontal
- 3179 2398 6028 2.190 0.578 0.160 0.047 62 6.4 lingual
- 2533 1779 4542 2.313 0.690 0.150 0.054 49 5.4 medialorbitofrontal
- 4177 2883 10693 2.935 0.700 0.140 0.061 129 14.3 middletemporal
- 766 524 1627 2.511 0.810 0.136 0.050 13 1.6 parahippocampal
- 2128 1432 3312 2.338 0.575 0.131 0.045 25 4.0 paracentral
- 2430 1677 4840 2.458 0.723 0.123 0.028 25 2.8 parsopercularis
- 889 655 2340 2.684 0.841 0.172 0.055 20 2.0 parsorbitalis
- 1783 1759 4984 2.610 0.897 0.201 0.060 37 4.9 parstriangularis
- 1328 932 1787 1.914 0.508 0.127 0.039 13 1.9 pericalcarine
- 5647 3851 9191 2.153 0.620 0.125 0.033 64 7.5 postcentral
- 1564 1092 2990 2.362 0.768 0.140 0.042 28 2.5 posteriorcingulate
- 5670 3983 12312 2.612 0.702 0.123 0.030 62 7.0 precentral
- 5172 3620 9641 2.302 0.584 0.148 0.047 89 10.6 precuneus
- 1256 830 2291 2.476 0.658 0.149 0.049 29 2.8 rostralanteriorcingulate
- 7222 5204 16386 2.526 0.705 0.157 0.047 122 15.1 rostralmiddlefrontal
- 8764 6170 20980 2.806 0.672 0.138 0.039 125 13.9 superiorfrontal
- 8179 5631 14054 2.107 0.642 0.137 0.042 123 14.3 superiorparietal
- 4818 3415 9429 2.600 0.645 0.129 0.032 50 6.8 superiortemporal
- 4559 3138 9335 2.515 0.677 0.133 0.034 64 6.1 supramarginal
- 423 258 902 2.291 0.816 0.177 0.090 12 1.7 frontalpole
- 552 451 1452 2.727 0.894 0.167 0.063 9 1.3 temporalpole
- 600 399 1035 2.279 0.511 0.137 0.031 8 0.6 transversetemporal
- 3148 1953 6709 2.862 1.269 0.117 0.043 39 5.2 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 0050419 lh pial
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 219271
- Total vertex volume 217269 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 910 760 1971 2.807 0.601 0.141 0.033 15 1.3 bankssts
- 737 566 1228 2.439 0.565 0.158 0.050 21 1.6 caudalanteriorcingulate
- 1985 1614 4141 2.729 0.610 0.147 0.037 39 3.4 caudalmiddlefrontal
- 2007 1901 3081 1.940 0.544 0.180 0.049 28 4.7 cuneus
- 389 555 884 2.501 1.236 0.241 0.041 5 0.9 entorhinal
- 3689 3881 7235 2.198 0.762 0.208 0.062 88 11.0 fusiform
- 4795 4778 10278 2.466 0.690 0.180 0.046 94 10.3 inferiorparietal
- 5221 4785 10174 2.432 0.698 0.179 0.048 82 12.3 inferiortemporal
- 1582 1277 2880 2.476 0.943 0.163 0.045 30 3.2 isthmuscingulate
- 7475 7486 12802 1.968 0.687 0.199 0.060 208 19.3 lateraloccipital
- 3228 2781 5714 2.311 0.654 0.183 0.055 63 8.3 lateralorbitofrontal
- 3179 3237 6028 2.190 0.578 0.193 0.049 59 7.4 lingual
- 2533 2226 4542 2.313 0.690 0.180 0.051 59 6.1 medialorbitofrontal
- 4177 4204 10693 2.935 0.700 0.169 0.040 55 8.3 middletemporal
- 766 790 1627 2.511 0.810 0.214 0.084 29 2.9 parahippocampal
- 2128 1477 3312 2.338 0.575 0.127 0.034 27 3.1 paracentral
- 2430 2164 4840 2.458 0.723 0.182 0.590 2723 109.3 parsopercularis
- 889 1105 2340 2.684 0.841 0.245 0.059 15 2.7 parsorbitalis
- 1783 2295 4984 2.610 0.897 0.204 0.049 31 3.8 parstriangularis
- 1328 956 1787 1.914 0.508 0.158 0.045 39 2.6 pericalcarine
- 5647 4600 9191 2.153 0.620 0.135 0.031 73 7.7 postcentral
- 1564 1385 2990 2.362 0.768 0.176 0.050 33 3.3 posteriorcingulate
- 5670 5216 12312 2.612 0.702 0.148 0.034 67 8.4 precentral
- 5172 4650 9641 2.302 0.584 0.171 0.047 86 11.2 precuneus
- 1256 1130 2291 2.476 0.658 0.189 0.061 27 3.5 rostralanteriorcingulate
- 7222 7528 16386 2.526 0.705 0.205 0.056 166 20.8 rostralmiddlefrontal
- 8764 8559 20980 2.806 0.672 0.178 0.045 177 18.5 superiorfrontal
- 8179 7459 14054 2.107 0.642 0.160 0.036 127 14.3 superiorparietal
- 4818 3765 9429 2.600 0.645 0.138 0.038 66 8.1 superiortemporal
- 4559 4054 9335 2.515 0.677 0.153 0.037 56 8.2 supramarginal
- 423 427 902 2.291 0.816 0.204 0.060 10 1.4 frontalpole
- 552 659 1452 2.727 0.894 0.185 0.055 8 1.1 temporalpole
- 600 510 1035 2.279 0.511 0.151 0.040 8 1.0 transversetemporal
- 3148 2263 6709 2.862 1.269 0.185 0.078 102 11.2 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 0050419 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 222558
- Total vertex volume 219604 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 1078 754 1741 2.352 0.463 0.098 0.017 6 0.8 bankssts
- 1104 757 2244 2.549 0.745 0.145 0.037 19 1.9 caudalanteriorcingulate
- 3027 2170 6529 2.624 0.638 0.130 0.029 36 3.7 caudalmiddlefrontal
- 2413 1626 3340 1.865 0.532 0.162 0.049 43 5.0 cuneus
- 498 332 1019 2.243 1.233 0.106 0.034 4 0.7 entorhinal
- 4461 3009 7640 2.203 0.592 0.136 0.043 71 7.6 fusiform
- 6624 4566 13399 2.551 0.585 0.133 0.034 88 8.5 inferiorparietal
- 3615 2494 6642 2.345 0.688 0.132 0.037 56 5.6 inferiortemporal
- 1422 959 2785 2.529 0.830 0.123 0.032 18 1.8 isthmuscingulate
- 7790 5224 12727 2.046 0.601 0.150 0.051 132 15.6 lateraloccipital
- 3073 2129 6029 2.472 0.763 0.142 0.050 47 6.2 lateralorbitofrontal
- 4209 2834 6416 2.027 0.532 0.150 0.047 67 8.2 lingual
- 2693 1800 4542 2.249 0.709 0.130 0.040 40 4.2 medialorbitofrontal
- 3868 2702 9279 2.760 0.712 0.131 0.034 58 5.2 middletemporal
- 899 582 1610 2.327 0.907 0.127 0.045 12 1.5 parahippocampal
- 2190 1421 3453 2.320 0.482 0.134 0.039 24 3.4 paracentral
- 2018 1429 3938 2.560 0.586 0.127 0.033 22 3.0 parsopercularis
- 940 668 2098 2.480 0.637 0.172 0.068 18 2.6 parsorbitalis
- 2370 1726 5021 2.462 0.679 0.143 0.038 34 3.9 parstriangularis
- 2008 1414 2305 1.835 0.498 0.130 0.038 21 2.9 pericalcarine
- 5039 3363 7856 2.029 0.660 0.119 0.031 53 6.3 postcentral
- 1750 1190 3431 2.544 0.774 0.144 0.040 26 2.9 posteriorcingulate
- 6215 4192 12459 2.553 0.650 0.122 0.033 67 8.2 precentral
- 4298 2958 8689 2.535 0.622 0.129 0.031 46 5.5 precuneus
- 853 588 1732 2.505 0.609 0.136 0.035 11 1.3 rostralanteriorcingulate
- 8193 5824 17424 2.504 0.674 0.153 0.046 152 15.5 rostralmiddlefrontal
- 11020 7713 25043 2.826 0.639 0.137 0.042 150 17.9 superiorfrontal
- 6108 4168 11156 2.311 0.618 0.129 0.030 72 7.9 superiorparietal
- 5008 3551 11243 2.692 0.680 0.123 0.034 56 7.1 superiortemporal
- 4243 2880 7820 2.372 0.587 0.126 0.039 52 6.8 supramarginal
- 433 286 1169 2.639 0.559 0.186 0.080 14 1.5 frontalpole
- 463 341 1689 3.293 1.011 0.144 0.036 9 0.7 temporalpole
- 581 404 1015 2.331 0.581 0.150 0.032 9 0.6 transversetemporal
- 2988 2111 6106 2.912 0.754 0.138 0.043 41 5.3 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 0050419 rh pial
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 222558
- Total vertex volume 219604 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 1078 729 1741 2.352 0.463 0.126 0.035 12 1.7 bankssts
- 1104 990 2244 2.549 0.745 0.180 0.045 23 2.3 caudalanteriorcingulate
- 3027 2755 6529 2.624 0.638 0.155 0.037 52 4.7 caudalmiddlefrontal
- 2413 2071 3340 1.865 0.532 0.167 0.043 33 4.8 cuneus
- 498 603 1019 2.243 1.233 0.194 0.046 5 1.2 entorhinal
- 4461 3840 7640 2.203 0.592 0.165 0.044 70 9.1 fusiform
- 6624 5838 13399 2.551 0.585 0.158 0.039 134 12.2 inferiorparietal
- 3615 3151 6642 2.345 0.688 0.165 0.047 52 8.1 inferiortemporal
- 1422 1181 2785 2.529 0.830 0.153 0.041 25 2.4 isthmuscingulate
- 7790 7039 12727 2.046 0.601 0.176 0.045 133 17.0 lateraloccipital
- 3073 2687 6029 2.472 0.763 0.188 0.058 68 7.7 lateralorbitofrontal
- 4209 3546 6416 2.027 0.532 0.165 0.047 100 9.2 lingual
- 2693 2320 4542 2.249 0.709 0.174 0.052 48 6.2 medialorbitofrontal
- 3868 4034 9279 2.760 0.712 0.176 0.042 67 7.5 middletemporal
- 899 760 1610 2.327 0.907 0.175 0.053 15 2.0 parahippocampal
- 2190 1521 3453 2.320 0.482 0.130 0.041 31 3.8 paracentral
- 2018 1718 3938 2.560 0.586 0.155 0.044 33 3.8 parsopercularis
- 940 1018 2098 2.480 0.637 0.224 0.063 17 2.9 parsorbitalis
- 2370 2441 5021 2.462 0.679 0.176 0.038 27 4.2 parstriangularis
- 2008 1263 2305 1.835 0.498 0.124 0.034 26 3.1 pericalcarine
- 5039 4395 7856 2.029 0.660 0.147 0.032 116 7.8 postcentral
- 1750 1458 3431 2.544 0.774 0.165 0.043 33 3.5 posteriorcingulate
- 6215 5221 12459 2.553 0.650 0.133 0.030 101 8.9 precentral
- 4298 3810 8689 2.535 0.622 0.165 0.041 70 8.1 precuneus
- 853 823 1732 2.505 0.609 0.180 0.048 10 2.0 rostralanteriorcingulate
- 8193 8155 17424 2.504 0.674 0.189 0.047 177 19.1 rostralmiddlefrontal
- 11020 9714 25043 2.826 0.639 0.155 0.041 182 20.3 superiorfrontal
- 6108 5318 11156 2.311 0.618 0.151 0.035 89 10.1 superiorparietal
- 5008 4701 11243 2.692 0.680 0.154 0.036 58 8.7 superiortemporal
- 4243 3519 7820 2.372 0.587 0.150 0.037 51 7.2 supramarginal
- 433 614 1169 2.639 0.559 0.247 0.068 7 1.6 frontalpole
- 463 680 1689 3.293 1.011 0.209 0.036 5 0.9 temporalpole
- 581 483 1015 2.331 0.581 0.151 0.039 12 0.9 transversetemporal
- 2988 1974 6106 2.912 0.754 0.154 0.045 92 5.7 insula
- PIDs (30092 30095 30098 30101) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 2 lh Sun Oct 8 11:54:53 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot
- #-----------------------------------------
- #@# Cortical Parc 2 rh Sun Oct 8 11:54:54 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 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 30184 of (30184 30187) to complete...
- Waiting for PID 30187 of (30184 30187) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 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...
- 91 labels changed using aseg
- relabeling using gibbs priors...
- 000: 7804 changed, 115741 examined...
- 001: 1813 changed, 30690 examined...
- 002: 558 changed, 9658 examined...
- 003: 231 changed, 3221 examined...
- 004: 80 changed, 1345 examined...
- 005: 42 changed, 488 examined...
- 006: 23 changed, 222 examined...
- 007: 17 changed, 142 examined...
- 008: 8 changed, 78 examined...
- 009: 7 changed, 49 examined...
- 010: 4 changed, 37 examined...
- 011: 2 changed, 25 examined...
- 012: 0 changed, 6 examined...
- 14 labels changed using aseg
- 000: 290 total segments, 207 labels (2069 vertices) changed
- 001: 92 total segments, 11 labels (43 vertices) changed
- 002: 81 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 18 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1304 vertices marked for relabeling...
- 1304 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 0 minutes and 16 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 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...
- 16 labels changed using aseg
- relabeling using gibbs priors...
- 000: 7912 changed, 120570 examined...
- 001: 1784 changed, 31236 examined...
- 002: 455 changed, 9415 examined...
- 003: 176 changed, 2617 examined...
- 004: 79 changed, 1016 examined...
- 005: 43 changed, 480 examined...
- 006: 10 changed, 242 examined...
- 007: 5 changed, 61 examined...
- 008: 4 changed, 33 examined...
- 009: 0 changed, 27 examined...
- 5 labels changed using aseg
- 000: 225 total segments, 139 labels (1773 vertices) changed
- 001: 88 total segments, 2 labels (34 vertices) changed
- 002: 86 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...
- 911 vertices marked for relabeling...
- 911 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 0 minutes and 17 seconds.
- PIDs (30184 30187) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Sun Oct 8 11:55:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0050419 lh white
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Sun Oct 8 11:55:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0050419 rh white
- Waiting for PID 30233 of (30233 30236) to complete...
- Waiting for PID 30236 of (30233 30236) 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 0050419 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 219271
- Total vertex volume 217269 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 1054 740 2221 2.565 0.695 0.154 0.045 19 1.9 G&S_frontomargin
- 1539 1258 3026 1.940 0.654 0.186 0.060 40 3.6 G&S_occipital_inf
- 1793 1186 3035 2.235 0.636 0.136 0.054 24 3.6 G&S_paracentral
- 1286 870 2851 2.670 0.639 0.131 0.029 15 1.5 G&S_subcentral
- 576 409 1551 2.536 0.733 0.193 0.081 17 2.2 G&S_transv_frontopol
- 2233 1508 4197 2.597 0.548 0.124 0.033 25 3.0 G&S_cingul-Ant
- 1095 762 2041 2.648 0.455 0.114 0.025 10 1.0 G&S_cingul-Mid-Ant
- 1323 940 2456 2.562 0.507 0.142 0.043 17 2.2 G&S_cingul-Mid-Post
- 668 460 1772 2.775 0.734 0.168 0.056 15 1.6 G_cingul-Post-dorsal
- 390 278 942 2.830 0.767 0.155 0.043 6 0.8 G_cingul-Post-ventral
- 1919 1478 3303 1.866 0.502 0.181 0.056 45 4.9 G_cuneus
- 1460 962 3631 2.672 0.728 0.127 0.030 18 1.8 G_front_inf-Opercular
- 469 377 1490 3.030 1.045 0.198 0.061 12 1.3 G_front_inf-Orbital
- 1278 1147 3264 2.478 0.817 0.186 0.057 25 3.3 G_front_inf-Triangul
- 3604 2619 9772 2.710 0.712 0.163 0.050 65 8.3 G_front_middle
- 6145 4308 16357 2.879 0.734 0.150 0.049 112 12.6 G_front_sup
- 624 366 1581 3.442 1.053 0.124 0.057 11 1.5 G_Ins_lg&S_cent_ins
- 623 415 2223 3.500 1.063 0.116 0.043 8 0.8 G_insular_short
- 2223 1527 4688 2.221 0.722 0.171 0.061 57 5.8 G_occipital_middle
- 1229 904 2279 2.051 0.537 0.145 0.041 19 1.8 G_occipital_sup
- 1779 1330 3865 2.156 0.799 0.180 0.067 43 5.3 G_oc-temp_lat-fusifor
- 2141 1639 4553 2.215 0.590 0.180 0.056 53 5.1 G_oc-temp_med-Lingual
- 964 671 2149 2.426 0.953 0.143 0.059 17 2.5 G_oc-temp_med-Parahip
- 2189 1501 5067 2.422 0.802 0.175 0.081 57 8.0 G_orbital
- 1960 1459 5646 2.841 0.760 0.178 0.049 43 4.4 G_pariet_inf-Angular
- 1974 1366 4665 2.677 0.720 0.142 0.039 34 2.8 G_pariet_inf-Supramar
- 3496 2385 7154 2.207 0.722 0.153 0.058 72 8.4 G_parietal_sup
- 2222 1505 3912 2.155 0.680 0.135 0.044 33 3.9 G_postcentral
- 1778 1329 5080 2.867 0.729 0.148 0.035 27 2.7 G_precentral
- 2726 1969 6110 2.303 0.668 0.167 0.060 64 7.3 G_precuneus
- 1126 784 2141 2.234 0.723 0.182 0.065 31 3.4 G_rectus
- 839 484 794 1.634 1.233 0.142 0.080 20 2.1 G_subcallosal
- 458 307 917 2.365 0.489 0.127 0.030 6 0.5 G_temp_sup-G_T_transv
- 1648 1165 4508 2.808 0.680 0.158 0.052 28 3.6 G_temp_sup-Lateral
- 334 277 977 3.185 0.843 0.135 0.045 4 0.5 G_temp_sup-Plan_polar
- 1254 831 2184 2.383 0.571 0.112 0.029 13 1.3 G_temp_sup-Plan_tempo
- 2981 2058 6642 2.458 0.741 0.146 0.049 54 6.7 G_temporal_inf
- 2197 1506 6448 3.105 0.707 0.156 0.091 110 12.2 G_temporal_middle
- 196 296 894 2.833 0.843 0.241 0.058 5 0.5 Lat_Fis-ant-Horizont
- 375 250 557 2.011 0.524 0.093 0.034 3 0.4 Lat_Fis-ant-Vertical
- 1063 697 1314 2.273 0.503 0.118 0.028 8 1.3 Lat_Fis-post
- 1957 1371 3724 2.088 0.773 0.162 0.061 40 4.8 Pole_occipital
- 1447 1078 3967 2.740 0.823 0.165 0.057 31 3.3 Pole_temporal
- 1932 1367 2544 2.075 0.641 0.124 0.034 18 3.0 S_calcarine
- 2684 1850 3780 2.179 0.544 0.111 0.021 19 2.5 S_central
- 1040 721 1531 2.369 0.508 0.104 0.019 6 0.8 S_cingul-Marginalis
- 629 423 766 2.178 0.566 0.115 0.024 4 0.7 S_circular_insula_ant
- 1263 882 2385 2.887 0.883 0.096 0.023 6 1.2 S_circular_insula_inf
- 1244 935 2154 2.699 0.761 0.144 0.034 13 2.0 S_circular_insula_sup
- 884 598 1380 2.561 0.868 0.104 0.018 6 0.8 S_collat_transv_ant
- 470 344 605 1.857 0.463 0.137 0.037 4 0.7 S_collat_transv_post
- 2032 1443 3223 2.182 0.653 0.133 0.037 24 3.3 S_front_inf
- 1022 742 2253 2.603 0.551 0.127 0.030 10 1.1 S_front_middle
- 1797 1266 2991 2.568 0.524 0.120 0.023 14 1.8 S_front_sup
- 245 182 407 2.416 0.639 0.095 0.010 1 0.1 S_interm_prim-Jensen
- 2634 1782 3625 2.122 0.483 0.121 0.027 28 3.1 S_intrapariet&P_trans
- 894 627 1215 2.040 0.499 0.132 0.029 9 1.1 S_oc_middle&Lunatus
- 1024 730 1392 2.160 0.532 0.115 0.021 7 0.9 S_oc_sup&transversal
- 751 501 738 1.625 0.848 0.173 0.099 19 3.8 S_occipital_ant
- 580 421 810 1.926 0.525 0.130 0.033 5 0.7 S_oc-temp_lat
- 1376 993 2380 2.249 0.626 0.119 0.034 11 1.6 S_oc-temp_med&Lingual
- 257 193 451 2.534 0.446 0.150 0.034 3 0.4 S_orbital_lateral
- 402 297 812 2.715 0.624 0.119 0.025 3 0.3 S_orbital_med-olfact
- 1007 696 1585 2.396 0.514 0.138 0.037 11 1.5 S_orbital-H_Shaped
- 2053 1353 2970 2.204 0.523 0.129 0.036 21 2.8 S_parieto_occipital
- 1173 709 1089 1.867 0.930 0.126 0.029 25 1.2 S_pericallosal
- 2692 1831 3400 1.926 0.536 0.102 0.020 19 2.2 S_postcentral
- 1849 1239 2989 2.365 0.605 0.117 0.029 20 2.5 S_precentral-inf-part
- 531 377 958 2.458 0.562 0.112 0.024 4 0.5 S_precentral-sup-part
- 742 518 1231 2.404 0.629 0.139 0.041 14 1.3 S_suborbital
- 669 467 1119 2.478 0.488 0.124 0.024 6 0.5 S_subparietal
- 1834 1282 2622 2.408 0.461 0.112 0.021 12 1.6 S_temporal_inf
- 4179 2912 7595 2.541 0.567 0.117 0.024 39 4.2 S_temporal_sup
- 262 187 325 2.260 0.485 0.164 0.025 3 0.3 S_temporal_transverse
- mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050419 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 222558
- Total vertex volume 219604 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 777 582 1677 2.272 0.592 0.163 0.042 14 1.4 G&S_frontomargin
- 1459 1017 3020 2.269 0.676 0.149 0.044 21 2.6 G&S_occipital_inf
- 1343 879 2364 2.241 0.600 0.144 0.054 18 3.0 G&S_paracentral
- 1348 840 2504 2.522 0.744 0.132 0.042 19 2.3 G&S_subcentral
- 1159 795 2767 2.687 0.630 0.154 0.051 24 2.2 G&S_transv_frontopol
- 2830 1959 5008 2.472 0.615 0.124 0.033 31 3.7 G&S_cingul-Ant
- 1282 936 2768 2.904 0.563 0.128 0.032 15 1.7 G&S_cingul-Mid-Ant
- 1494 1015 3048 2.749 0.620 0.135 0.038 16 2.4 G&S_cingul-Mid-Post
- 512 360 1387 2.795 0.699 0.164 0.044 10 1.0 G_cingul-Post-dorsal
- 431 280 1160 2.928 0.708 0.136 0.034 7 0.6 G_cingul-Post-ventral
- 2253 1539 3089 1.821 0.549 0.160 0.048 38 4.5 G_cuneus
- 1276 904 3257 2.649 0.687 0.136 0.038 19 2.1 G_front_inf-Opercular
- 366 253 905 2.825 0.445 0.180 0.053 10 0.9 G_front_inf-Orbital
- 1265 910 3013 2.534 0.703 0.162 0.050 23 2.9 G_front_inf-Triangul
- 4470 3137 11976 2.718 0.752 0.171 0.055 107 10.9 G_front_middle
- 7301 5076 18241 2.776 0.739 0.151 0.055 138 15.7 G_front_sup
- 668 484 1500 2.907 0.908 0.158 0.067 12 1.9 G_Ins_lg&S_cent_ins
- 618 422 1677 2.994 0.898 0.164 0.059 16 1.4 G_insular_short
- 2397 1559 5099 2.394 0.712 0.163 0.056 57 4.8 G_occipital_middle
- 1669 1153 2972 2.030 0.577 0.151 0.044 29 3.4 G_occipital_sup
- 2180 1451 4372 2.381 0.617 0.142 0.050 44 4.0 G_oc-temp_lat-fusifor
- 2554 1718 4294 2.055 0.567 0.162 0.054 48 5.9 G_oc-temp_med-Lingual
- 1186 752 2394 2.292 1.128 0.138 0.059 24 3.0 G_oc-temp_med-Parahip
- 2062 1487 5101 2.464 0.768 0.175 0.078 50 6.8 G_orbital
- 2692 1830 6580 2.708 0.601 0.149 0.045 48 4.5 G_pariet_inf-Angular
- 2381 1556 4826 2.390 0.632 0.131 0.046 36 4.6 G_pariet_inf-Supramar
- 1604 1122 4226 2.617 0.748 0.131 0.029 21 1.9 G_parietal_sup
- 1690 1181 3332 2.079 0.669 0.141 0.041 25 2.9 G_postcentral
- 2277 1568 6318 2.790 0.684 0.127 0.037 28 3.1 G_precentral
- 1615 1173 4223 2.707 0.696 0.144 0.036 22 2.5 G_precuneus
- 741 507 1661 2.446 0.737 0.164 0.056 15 1.6 G_rectus
- 351 201 600 2.618 0.766 0.088 0.041 5 0.5 G_subcallosal
- 415 299 794 2.191 0.568 0.143 0.033 7 0.5 G_temp_sup-G_T_transv
- 1810 1294 5450 2.957 0.758 0.165 0.057 34 4.5 G_temp_sup-Lateral
- 502 413 1306 2.591 0.815 0.087 0.021 2 0.3 G_temp_sup-Plan_polar
- 793 543 1669 2.787 0.583 0.104 0.033 6 0.8 G_temp_sup-Plan_tempo
- 1841 1291 3905 2.337 0.659 0.148 0.045 39 3.4 G_temporal_inf
- 2444 1665 6772 2.968 0.690 0.150 0.045 50 4.4 G_temporal_middle
- 294 236 478 2.126 0.545 0.103 0.015 2 0.1 Lat_Fis-ant-Horizont
- 320 243 418 2.014 0.476 0.093 0.015 1 0.2 Lat_Fis-ant-Vertical
- 1208 805 1571 2.430 0.632 0.112 0.023 10 1.1 Lat_Fis-post
- 3492 2352 5481 1.962 0.557 0.165 0.066 72 8.8 Pole_occipital
- 1495 982 3391 2.460 0.884 0.127 0.035 25 2.0 Pole_temporal
- 2200 1545 2541 1.922 0.444 0.123 0.034 21 3.0 S_calcarine
- 2450 1652 2618 1.809 0.454 0.107 0.021 16 2.2 S_central
- 1207 778 1651 2.382 0.514 0.122 0.026 9 1.4 S_cingul-Marginalis
- 575 380 903 2.763 0.561 0.100 0.024 2 0.5 S_circular_insula_ant
- 1060 784 1853 2.835 0.694 0.099 0.022 5 1.0 S_circular_insula_inf
- 1280 858 2110 2.769 0.459 0.109 0.022 7 1.2 S_circular_insula_sup
- 971 670 1502 2.334 0.813 0.110 0.020 5 0.9 S_collat_transv_ant
- 349 244 425 2.078 0.613 0.143 0.035 3 0.6 S_collat_transv_post
- 1809 1373 3154 2.348 0.656 0.130 0.028 21 1.9 S_front_inf
- 2323 1639 3837 2.429 0.487 0.127 0.032 22 2.6 S_front_middle
- 2455 1753 4542 2.700 0.490 0.119 0.027 19 2.7 S_front_sup
- 390 275 551 2.249 0.440 0.111 0.019 2 0.3 S_interm_prim-Jensen
- 2285 1525 3516 2.361 0.430 0.110 0.023 19 2.0 S_intrapariet&P_trans
- 915 629 1054 1.873 0.492 0.112 0.026 5 1.0 S_oc_middle&Lunatus
- 1645 1117 2237 2.242 0.513 0.119 0.026 12 1.8 S_oc_sup&transversal
- 470 326 648 2.503 0.473 0.132 0.034 5 0.6 S_occipital_ant
- 777 549 1140 2.177 0.589 0.138 0.041 10 1.4 S_oc-temp_lat
- 1824 1260 2373 2.013 0.425 0.118 0.026 14 1.7 S_oc-temp_med&Lingual
- 283 195 387 2.297 0.371 0.135 0.033 3 0.4 S_orbital_lateral
- 579 420 1090 2.726 0.674 0.120 0.024 5 0.4 S_orbital_med-olfact
- 1115 742 1715 2.244 0.716 0.123 0.034 11 1.5 S_orbital-H_Shaped
- 1968 1321 2869 2.268 0.517 0.121 0.025 17 2.0 S_parieto_occipital
- 1566 996 1592 1.914 0.698 0.112 0.022 20 1.2 S_pericallosal
- 1893 1262 2442 2.213 0.502 0.104 0.020 11 1.5 S_postcentral
- 1663 1111 2476 2.536 0.529 0.112 0.023 12 1.7 S_precentral-inf-part
- 1302 885 1997 2.646 0.366 0.121 0.023 10 1.2 S_precentral-sup-part
- 328 220 413 2.124 0.549 0.103 0.017 2 0.2 S_suborbital
- 934 624 1797 2.582 0.589 0.123 0.031 9 1.1 S_subparietal
- 988 688 1456 2.219 0.556 0.097 0.016 5 0.7 S_temporal_inf
- 4667 3329 7701 2.380 0.505 0.109 0.022 32 4.2 S_temporal_sup
- 350 246 417 2.336 0.444 0.138 0.020 4 0.3 S_temporal_transverse
- PIDs (30233 30236) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 3 lh Sun Oct 8 11:55:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot
- #-----------------------------------------
- #@# Cortical Parc 3 rh Sun Oct 8 11:55:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 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 30298 of (30298 30301) to complete...
- Waiting for PID 30301 of (30298 30301) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 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...
- 1557 labels changed using aseg
- relabeling using gibbs priors...
- 000: 1799 changed, 115741 examined...
- 001: 433 changed, 8473 examined...
- 002: 122 changed, 2353 examined...
- 003: 52 changed, 725 examined...
- 004: 21 changed, 293 examined...
- 005: 5 changed, 116 examined...
- 006: 3 changed, 39 examined...
- 007: 1 changed, 13 examined...
- 008: 2 changed, 7 examined...
- 009: 0 changed, 8 examined...
- 116 labels changed using aseg
- 000: 55 total segments, 22 labels (312 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 7 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 948 vertices marked for relabeling...
- 948 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas.annot...
- classification took 0 minutes and 13 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050419 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...
- 1242 labels changed using aseg
- relabeling using gibbs priors...
- 000: 1790 changed, 120570 examined...
- 001: 372 changed, 8355 examined...
- 002: 96 changed, 2139 examined...
- 003: 37 changed, 598 examined...
- 004: 13 changed, 211 examined...
- 005: 13 changed, 94 examined...
- 006: 10 changed, 68 examined...
- 007: 8 changed, 46 examined...
- 008: 6 changed, 48 examined...
- 009: 6 changed, 36 examined...
- 010: 3 changed, 23 examined...
- 011: 5 changed, 17 examined...
- 012: 4 changed, 19 examined...
- 013: 3 changed, 18 examined...
- 014: 2 changed, 14 examined...
- 015: 2 changed, 14 examined...
- 016: 3 changed, 12 examined...
- 017: 2 changed, 17 examined...
- 018: 3 changed, 13 examined...
- 019: 1 changed, 12 examined...
- 020: 2 changed, 7 examined...
- 021: 3 changed, 11 examined...
- 022: 4 changed, 16 examined...
- 023: 5 changed, 19 examined...
- 024: 1 changed, 24 examined...
- 025: 0 changed, 7 examined...
- 162 labels changed using aseg
- 000: 56 total segments, 23 labels (209 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 6 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 774 vertices marked for relabeling...
- 774 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas.annot...
- classification took 0 minutes and 13 seconds.
- PIDs (30298 30301) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Sun Oct 8 11:55:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0050419 lh white
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Sun Oct 8 11:55:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0050419 rh white
- Waiting for PID 30348 of (30348 30351) to complete...
- Waiting for PID 30351 of (30348 30351) 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 0050419 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 219271
- Total vertex volume 217269 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 1584 1058 3012 2.567 0.609 0.127 0.036 38 2.4 caudalanteriorcingulate
- 2127 1447 4554 2.748 0.619 0.133 0.034 22 3.1 caudalmiddlefrontal
- 2744 1996 4237 1.971 0.552 0.163 0.048 50 5.7 cuneus
- 325 251 729 2.305 1.115 0.115 0.034 3 0.5 entorhinal
- 3485 2565 6456 2.140 0.757 0.156 0.053 59 8.0 fusiform
- 4782 3475 10420 2.520 0.694 0.144 0.037 71 7.8 inferiorparietal
- 5059 3527 10462 2.447 0.730 0.140 0.043 80 9.9 inferiortemporal
- 1587 1070 2922 2.488 0.926 0.133 0.040 24 2.5 isthmuscingulate
- 7497 5353 12933 1.972 0.693 0.166 0.059 162 18.9 lateraloccipital
- 3416 2299 6379 2.395 0.707 0.156 0.063 72 9.3 lateralorbitofrontal
- 3263 2446 6132 2.175 0.580 0.160 0.046 63 6.5 lingual
- 2629 1778 4194 2.058 0.926 0.159 0.063 64 6.7 medialorbitofrontal
- 5297 3655 12581 2.835 0.708 0.137 0.055 143 15.7 middletemporal
- 797 540 1674 2.493 0.832 0.131 0.049 13 1.6 parahippocampal
- 2375 1616 4014 2.391 0.594 0.132 0.045 29 4.3 paracentral
- 2318 1580 4498 2.444 0.744 0.127 0.032 29 3.1 parsopercularis
- 947 824 2390 2.469 0.827 0.170 0.040 17 1.5 parsorbitalis
- 2268 2018 5797 2.571 0.846 0.178 0.052 41 5.4 parstriangularis
- 1299 919 1762 1.912 0.513 0.126 0.039 12 1.9 pericalcarine
- 6429 4386 10166 2.108 0.620 0.126 0.034 72 8.8 postcentral
- 1730 1205 3306 2.388 0.762 0.143 0.044 31 2.8 posteriorcingulate
- 5650 3969 12115 2.618 0.682 0.123 0.028 57 6.6 precentral
- 5096 3604 9746 2.306 0.584 0.148 0.046 90 10.1 precuneus
- 1810 1209 3511 2.578 0.645 0.133 0.038 27 2.8 rostralanteriorcingulate
- 5481 3933 12879 2.546 0.721 0.162 0.050 99 12.6 rostralmiddlefrontal
- 8872 6233 20780 2.754 0.689 0.140 0.039 116 14.8 superiorfrontal
- 6607 4501 11517 2.142 0.651 0.134 0.042 100 11.4 superiorparietal
- 6095 4314 12502 2.640 0.671 0.130 0.035 69 8.9 superiortemporal
- 4283 2926 8459 2.482 0.651 0.131 0.034 59 5.7 supramarginal
- 595 401 1036 2.270 0.511 0.141 0.032 8 0.6 transversetemporal
- 2339 1538 6105 3.241 1.030 0.108 0.033 19 2.9 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 0050419 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 222558
- Total vertex volume 219604 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 1160 804 2358 2.564 0.736 0.147 0.036 20 1.9 caudalanteriorcingulate
- 3154 2269 6892 2.635 0.639 0.131 0.029 38 3.8 caudalmiddlefrontal
- 2943 1990 4199 1.914 0.562 0.153 0.046 47 5.6 cuneus
- 424 284 976 2.360 1.293 0.100 0.030 3 0.5 entorhinal
- 4116 2810 7124 2.223 0.581 0.139 0.043 67 7.2 fusiform
- 6625 4575 13404 2.552 0.578 0.134 0.034 89 8.6 inferiorparietal
- 3951 2669 7111 2.310 0.694 0.128 0.036 57 6.1 inferiortemporal
- 1412 953 2780 2.542 0.825 0.124 0.032 18 1.8 isthmuscingulate
- 7801 5247 12680 2.043 0.600 0.152 0.052 134 15.7 lateraloccipital
- 3341 2328 6596 2.381 0.770 0.148 0.053 59 7.3 lateralorbitofrontal
- 4112 2782 6336 2.027 0.536 0.149 0.047 65 8.0 lingual
- 1880 1257 3567 2.394 0.703 0.135 0.041 30 2.9 medialorbitofrontal
- 4632 3241 10633 2.702 0.696 0.128 0.033 67 5.9 middletemporal
- 1014 653 1739 2.280 0.891 0.124 0.042 14 1.6 parahippocampal
- 2325 1511 3816 2.336 0.514 0.139 0.049 39 5.3 paracentral
- 2272 1599 4409 2.532 0.627 0.128 0.034 26 3.3 parsopercularis
- 913 660 1994 2.623 0.670 0.166 0.065 16 2.5 parsorbitalis
- 2358 1723 4947 2.442 0.657 0.146 0.039 38 3.9 parstriangularis
- 1934 1360 2186 1.837 0.500 0.129 0.038 20 2.8 pericalcarine
- 5456 3649 8461 2.037 0.654 0.121 0.031 57 6.8 postcentral
- 1834 1247 3548 2.545 0.765 0.143 0.040 27 3.0 posteriorcingulate
- 5991 4036 12090 2.563 0.649 0.120 0.031 58 7.5 precentral
- 4434 3045 9046 2.510 0.625 0.127 0.030 47 5.5 precuneus
- 1149 773 2068 2.458 0.618 0.122 0.032 14 1.6 rostralanteriorcingulate
- 5692 4038 12362 2.546 0.680 0.159 0.050 110 12.3 rostralmiddlefrontal
- 13887 9695 30608 2.727 0.670 0.137 0.042 189 21.4 superiorfrontal
- 4983 3392 9300 2.348 0.621 0.130 0.030 61 6.5 superiorparietal
- 6224 4460 14154 2.687 0.721 0.124 0.033 72 8.5 superiortemporal
- 4077 2743 7381 2.367 0.599 0.125 0.040 50 6.6 supramarginal
- 582 401 1021 2.310 0.577 0.151 0.032 10 0.7 transversetemporal
- 2810 1968 5818 2.953 0.718 0.135 0.041 36 4.7 insula
- PIDs (30348 30351) completed and logs appended.
- #-----------------------------------------
- #@# WM/GM Contrast lh Sun Oct 8 11:56:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- pctsurfcon --s 0050419 --lh-only
- #-----------------------------------------
- #@# WM/GM Contrast rh Sun Oct 8 11:56:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts
- pctsurfcon --s 0050419 --rh-only
- Waiting for PID 30404 of (30404 30414) to complete...
- Waiting for PID 30414 of (30404 30414) to complete...
- pctsurfcon --s 0050419 --lh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts/pctsurfcon.log
- Sun Oct 8 11:56:32 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-6.0.0/0050419/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-586 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-6.0.0/0050419/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30404/lh.wm.mgh --regheader 0050419 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00000;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 = 54898
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30404/lh.wm.mgh
- Dim: 115741 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30404/lh.gm.mgh --projfrac 0.3 --regheader 0050419 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00000;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 = 66701
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30404/lh.gm.mgh
- Dim: 115741 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30404/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30404/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/surf/lh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.w-g.pct.mgh --annot 0050419 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/surf/lh.w-g.pct.mgh --annot 0050419 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-586
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/surf/lh.w-g.pct.mgh
- Vertex Area is 0.701995 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 0050419 --rh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/scripts/pctsurfcon.log
- Sun Oct 8 11:56:32 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-6.0.0/0050419/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-586 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-6.0.0/0050419/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30414/rh.wm.mgh --regheader 0050419 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00000;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 = 57385
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30414/rh.wm.mgh
- Dim: 120570 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30414/rh.gm.mgh --projfrac 0.3 --regheader 0050419 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00000;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 = 69647
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30414/rh.gm.mgh
- Dim: 120570 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30414/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/tmp.pctsurfcon.30414/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/surf/rh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.w-g.pct.mgh --annot 0050419 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/surf/rh.w-g.pct.mgh --annot 0050419 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-586
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/surf/rh.w-g.pct.mgh
- Vertex Area is 0.687342 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 (30404 30414) completed and logs appended.
- #-----------------------------------------
- #@# Relabel Hypointensities Sun Oct 8 11:56:37 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri
- mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
- reading input surface ../surf/lh.white...
- relabeling lh hypointensities...
- 2183 voxels changed to hypointensity...
- reading input surface ../surf/rh.white...
- relabeling rh hypointensities...
- 1866 voxels changed to hypointensity...
- 4395 hypointense voxels neighboring cortex changed
- #-----------------------------------------
- #@# AParc-to-ASeg aparc Sun Oct 8 11:56:56 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419
- mri_aparc2aseg --s 0050419 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
- #-----------------------------------------
- #@# AParc-to-ASeg a2009s Sun Oct 8 11:56:56 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419
- mri_aparc2aseg --s 0050419 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s
- #-----------------------------------------
- #@# AParc-to-ASeg DKTatlas Sun Oct 8 11:56:56 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419
- mri_aparc2aseg --s 0050419 --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 30584 of (30584 30587 30590) to complete...
- Waiting for PID 30587 of (30584 30587 30590) to complete...
- Waiting for PID 30590 of (30584 30587 30590) to complete...
- mri_aparc2aseg --s 0050419 --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 0050419
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/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-6.0.0/0050419/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 6.01
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 105
- rescaling Left_Cerebral_Cortex from 61 --> 60
- rescaling Left_Lateral_Ventricle from 13 --> 15
- rescaling Left_Inf_Lat_Vent from 34 --> 28
- rescaling Left_Cerebellum_White_Matter from 86 --> 88
- rescaling Left_Cerebellum_Cortex from 60 --> 54
- rescaling Left_Thalamus from 94 --> 101
- rescaling Left_Thalamus_Proper from 84 --> 85
- rescaling Left_Caudate from 75 --> 66
- rescaling Left_Putamen from 80 --> 74
- rescaling Left_Pallidum from 98 --> 92
- rescaling Third_Ventricle from 25 --> 25
- rescaling Fourth_Ventricle from 22 --> 15
- rescaling Brain_Stem from 81 --> 81
- rescaling Left_Hippocampus from 57 --> 59
- rescaling Left_Amygdala from 56 --> 61
- rescaling CSF from 32 --> 36
- rescaling Left_Accumbens_area from 62 --> 59
- rescaling Left_VentralDC from 87 --> 83
- rescaling Right_Cerebral_White_Matter from 105 --> 107
- rescaling Right_Cerebral_Cortex from 58 --> 60
- rescaling Right_Lateral_Ventricle from 13 --> 14
- rescaling Right_Inf_Lat_Vent from 25 --> 26
- rescaling Right_Cerebellum_White_Matter from 87 --> 91
- rescaling Right_Cerebellum_Cortex from 59 --> 58
- rescaling Right_Thalamus_Proper from 85 --> 82
- rescaling Right_Caudate from 62 --> 69
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 62
- rescaling Right_Amygdala from 55 --> 63
- rescaling Right_Accumbens_area from 65 --> 67
- rescaling Right_VentralDC from 86 --> 88
- rescaling Fifth_Ventricle from 40 --> 32
- rescaling WM_hypointensities from 78 --> 78
- rescaling non_WM_hypointensities from 40 --> 44
- 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
- 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
- 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
- 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
- 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
- 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
- 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
- 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
- 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
- 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
- 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
- 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
- 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 432068
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 156 changed.
- pass 2: 8 changed.
- pass 3: 2 changed.
- pass 4: 1 changed.
- pass 5: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/aparc+aseg.mgz
- mri_aparc2aseg --s 0050419 --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 0050419
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/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-6.0.0/0050419/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 6.01
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 105
- rescaling Left_Cerebral_Cortex from 61 --> 60
- rescaling Left_Lateral_Ventricle from 13 --> 15
- rescaling Left_Inf_Lat_Vent from 34 --> 28
- rescaling Left_Cerebellum_White_Matter from 86 --> 88
- rescaling Left_Cerebellum_Cortex from 60 --> 54
- rescaling Left_Thalamus from 94 --> 101
- rescaling Left_Thalamus_Proper from 84 --> 85
- rescaling Left_Caudate from 75 --> 66
- rescaling Left_Putamen from 80 --> 74
- rescaling Left_Pallidum from 98 --> 92
- rescaling Third_Ventricle from 25 --> 25
- rescaling Fourth_Ventricle from 22 --> 15
- rescaling Brain_Stem from 81 --> 81
- rescaling Left_Hippocampus from 57 --> 59
- rescaling Left_Amygdala from 56 --> 61
- rescaling CSF from 32 --> 36
- rescaling Left_Accumbens_area from 62 --> 59
- rescaling Left_VentralDC from 87 --> 83
- rescaling Right_Cerebral_White_Matter from 105 --> 107
- rescaling Right_Cerebral_Cortex from 58 --> 60
- rescaling Right_Lateral_Ventricle from 13 --> 14
- rescaling Right_Inf_Lat_Vent from 25 --> 26
- rescaling Right_Cerebellum_White_Matter from 87 --> 91
- rescaling Right_Cerebellum_Cortex from 59 --> 58
- rescaling Right_Thalamus_Proper from 85 --> 82
- rescaling Right_Caudate from 62 --> 69
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 62
- rescaling Right_Amygdala from 55 --> 63
- rescaling Right_Accumbens_area from 65 --> 67
- rescaling Right_VentralDC from 86 --> 88
- rescaling Fifth_Ventricle from 40 --> 32
- rescaling WM_hypointensities from 78 --> 78
- rescaling non_WM_hypointensities from 40 --> 44
- 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
- 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
- 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
- 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
- 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
- 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
- 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
- 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
- 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
- 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
- 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
- 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
- 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 431970
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 156 changed.
- pass 2: 8 changed.
- pass 3: 2 changed.
- pass 4: 1 changed.
- pass 5: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/aparc.a2009s+aseg.mgz
- mri_aparc2aseg --s 0050419 --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 0050419
- outvol mri/aparc.DKTatlas+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/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-6.0.0/0050419/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 6.01
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 105
- rescaling Left_Cerebral_Cortex from 61 --> 60
- rescaling Left_Lateral_Ventricle from 13 --> 15
- rescaling Left_Inf_Lat_Vent from 34 --> 28
- rescaling Left_Cerebellum_White_Matter from 86 --> 88
- rescaling Left_Cerebellum_Cortex from 60 --> 54
- rescaling Left_Thalamus from 94 --> 101
- rescaling Left_Thalamus_Proper from 84 --> 85
- rescaling Left_Caudate from 75 --> 66
- rescaling Left_Putamen from 80 --> 74
- rescaling Left_Pallidum from 98 --> 92
- rescaling Third_Ventricle from 25 --> 25
- rescaling Fourth_Ventricle from 22 --> 15
- rescaling Brain_Stem from 81 --> 81
- rescaling Left_Hippocampus from 57 --> 59
- rescaling Left_Amygdala from 56 --> 61
- rescaling CSF from 32 --> 36
- rescaling Left_Accumbens_area from 62 --> 59
- rescaling Left_VentralDC from 87 --> 83
- rescaling Right_Cerebral_White_Matter from 105 --> 107
- rescaling Right_Cerebral_Cortex from 58 --> 60
- rescaling Right_Lateral_Ventricle from 13 --> 14
- rescaling Right_Inf_Lat_Vent from 25 --> 26
- rescaling Right_Cerebellum_White_Matter from 87 --> 91
- rescaling Right_Cerebellum_Cortex from 59 --> 58
- rescaling Right_Thalamus_Proper from 85 --> 82
- rescaling Right_Caudate from 62 --> 69
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 62
- rescaling Right_Amygdala from 55 --> 63
- rescaling Right_Accumbens_area from 65 --> 67
- rescaling Right_VentralDC from 86 --> 88
- rescaling Fifth_Ventricle from 40 --> 32
- rescaling WM_hypointensities from 78 --> 78
- rescaling non_WM_hypointensities from 40 --> 44
- 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
- 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
- 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
- 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
- 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
- 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
- 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
- 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
- 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
- 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
- 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
- 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
- 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 431970
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 156 changed.
- pass 2: 8 changed.
- pass 3: 2 changed.
- pass 4: 1 changed.
- pass 5: 0 changed.
- nchanged = 0
- Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
- PIDs (30584 30587 30590) completed and logs appended.
- #-----------------------------------------
- #@# APas-to-ASeg Sun Oct 8 12:04:56 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri
- apas2aseg --i aparc+aseg.mgz --o aseg.mgz
- Sun Oct 8 12:04:57 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-6.0.0/0050419/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-586 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-6.0.0/0050419/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-586
- 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 12:04:57 CEST 2017
- Ended at Sun Oct 8 12:05:02 CEST 2017
- Apas2aseg-Run-Time-Sec 5
-
- apas2aseg Done
- #--------------------------------------------
- #@# ASeg Stats Sun Oct 8 12:05:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419
- 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 0050419
- $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 0050419
- sysname Linux
- hostname tars-586
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1377752 mm^3 (det: 1.413974 )
- Computing euler number
- orig.nofix lheno = -274, rheno = -192
- orig.nofix lhholes = 138, rhholes = 97
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 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 12:06:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419
- mri_aparc2aseg --s 0050419 --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 0050419
- 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-6.0.0/0050419/mri/aparc+aseg.mgz
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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-6.0.0/0050419/mri/ribbon.mgz
- Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/ribbon.mgz
- Ripping vertices labeled as unkown
- Ripped 6936 vertices from left hemi
- Ripped 7078 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-6.0.0/0050419/mri/aseg.mgz
- Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 = 836064
- Used brute-force search on 98 voxels
- Fixing Parahip LH WM
- Found 5 clusters
- 0 k 1.000000
- 1 k 1.000000
- 2 k 1.000000
- 3 k 1002.000000
- 4 k 1.000000
- Fixing Parahip RH WM
- Found 7 clusters
- 0 k 2.000000
- 1 k 1.000000
- 2 k 1.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 1224.000000
- 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 0050419 --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 0050419 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname tars-586
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1377752 mm^3 (det: 1.413974 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 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-6.0.0/0050419/label
- #--------------------------------------------
- #@# BA_exvivo Labels lh Sun Oct 8 12:14:45 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 0050419 --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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 31513 of (31513 31519 31525 31531 31536) to complete...
- Waiting for PID 31519 of (31513 31519 31525 31531 31536) to complete...
- Waiting for PID 31525 of (31513 31519 31525 31531 31536) to complete...
- Waiting for PID 31531 of (31513 31519 31525 31531 31536) to complete...
- Waiting for PID 31536 of (31513 31519 31525 31531 31536) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 298
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.label 4427
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 530
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.label 8439
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 127
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.label 4204
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 308
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.label 6291
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 248
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.label 6032
- mri_label2label: Done
- PIDs (31513 31519 31525 31531 31536) 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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 31582 of (31582 31588 31594 31599) to complete...
- Waiting for PID 31588 of (31582 31588 31594 31599) to complete...
- Waiting for PID 31594 of (31582 31588 31594 31599) to complete...
- Waiting for PID 31599 of (31582 31588 31594 31599) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 79
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.label 4149
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 572
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.label 14161
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 585
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.label 4766
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 960
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.label 4382
- mri_label2label: Done
- PIDs (31582 31588 31594 31599) 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 0050419 --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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 31644 of (31644 31650 31656 31662 31668) to complete...
- Waiting for PID 31650 of (31644 31650 31656 31662 31668) to complete...
- Waiting for PID 31656 of (31644 31650 31656 31662 31668) to complete...
- Waiting for PID 31662 of (31644 31650 31656 31662 31668) to complete...
- Waiting for PID 31668 of (31644 31650 31656 31662 31668) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 867
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.label 5508
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 2034
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.label 10148
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 694
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.label 2712
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 91
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.label 1381
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 79
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.label 1278
- mri_label2label: Done
- PIDs (31644 31650 31656 31662 31668) 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 0050419 --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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 31726 of (31726 31732 31738 31744 31747) to complete...
- Waiting for PID 31732 of (31726 31732 31738 31744 31747) to complete...
- Waiting for PID 31738 of (31726 31732 31738 31744 31747) to complete...
- Waiting for PID 31744 of (31726 31732 31738 31744 31747) to complete...
- Waiting for PID 31747 of (31726 31732 31738 31744 31747) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 86
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.thresh.label 1100
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 247
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.thresh.label 2339
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 43
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.thresh.label 1547
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 101
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.thresh.label 2097
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 102
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.thresh.label 2421
- mri_label2label: Done
- PIDs (31726 31732 31738 31744 31747) 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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 31798 of (31798 31804 31810 31816) to complete...
- Waiting for PID 31804 of (31798 31804 31810 31816) to complete...
- Waiting for PID 31810 of (31798 31804 31810 31816) to complete...
- Waiting for PID 31816 of (31798 31804 31810 31816) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 34
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.thresh.label 1583
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 183
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.thresh.label 7218
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 286
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.thresh.label 2198
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 487
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.thresh.label 1638
- mri_label2label: Done
- PIDs (31798 31804 31810 31816) 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 0050419 --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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 31861 of (31861 31867 31873 31879 31884) to complete...
- Waiting for PID 31867 of (31861 31867 31873 31879 31884) to complete...
- Waiting for PID 31873 of (31861 31867 31873 31879 31884) to complete...
- Waiting for PID 31879 of (31861 31867 31873 31879 31884) to complete...
- Waiting for PID 31884 of (31861 31867 31873 31879 31884) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 491
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.thresh.label 3896
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 985
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.thresh.label 4319
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 207
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.thresh.label 720
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 6
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.thresh.label 476
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 115741
- Number of reverse mapping hits = 45
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.thresh.label 495
- mri_label2label: Done
- PIDs (31861 31867 31873 31879 31884) completed and logs appended.
- mris_label2annot --s 0050419 --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-6.0.0/0050419/label
- cmdline mris_label2annot --s 0050419 --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-586
- machine x86_64
- user ntraut
- subject 0050419
- 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-6.0.0/0050419/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 81130 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/lh.BA_exvivo.annot
- mris_label2annot --s 0050419 --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-6.0.0/0050419/label
- cmdline mris_label2annot --s 0050419 --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-586
- machine x86_64
- user ntraut
- subject 0050419
- 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-6.0.0/0050419/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 95556 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0050419 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 219271
- Total vertex volume 217269 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 1004 653 1597 2.054 0.636 0.134 0.048 15 1.7 BA1_exvivo
- 3590 2460 5338 1.988 0.593 0.116 0.028 36 4.3 BA2_exvivo
- 980 650 1285 2.140 0.529 0.108 0.023 6 0.8 BA3a_exvivo
- 1955 1362 3416 2.231 0.652 0.126 0.034 24 2.5 BA3b_exvivo
- 1286 888 2505 2.494 0.676 0.147 0.054 19 3.1 BA4a_exvivo
- 959 647 1492 2.400 0.517 0.114 0.026 7 1.1 BA4p_exvivo
- 6566 4737 16770 2.752 0.725 0.138 0.036 84 9.3 BA6_exvivo
- 2514 1643 4998 2.513 0.681 0.117 0.028 29 3.2 BA44_exvivo
- 2992 2419 7100 2.469 0.811 0.160 0.049 47 6.4 BA45_exvivo
- 2609 1873 4459 2.050 0.626 0.148 0.054 48 5.5 V1_exvivo
- 6983 5101 11819 2.023 0.606 0.163 0.050 131 14.6 V2_exvivo
- 2171 1575 3445 1.889 0.841 0.172 0.069 50 7.2 MT_exvivo
- 440 311 769 2.190 0.968 0.126 0.049 6 1.0 perirhinal_exvivo
- 562 388 1329 2.788 1.018 0.152 0.066 11 1.8 entorhinal_exvivo
- mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050419 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 219271
- Total vertex volume 217269 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 647 439 1067 2.025 0.791 0.133 0.048 9 1.2 BA1_exvivo
- 1622 1124 2546 2.041 0.587 0.128 0.033 18 2.3 BA2_exvivo
- 766 506 1024 2.123 0.517 0.100 0.022 5 0.6 BA3a_exvivo
- 1268 923 1959 2.114 0.598 0.126 0.030 13 1.6 BA3b_exvivo
- 1120 780 2260 2.570 0.661 0.139 0.051 16 2.4 BA4a_exvivo
- 845 573 1263 2.301 0.525 0.115 0.032 6 1.2 BA4p_exvivo
- 3326 2451 8102 2.708 0.695 0.140 0.035 43 4.9 BA6_exvivo
- 1597 1040 3054 2.470 0.629 0.113 0.024 16 1.6 BA44_exvivo
- 1468 1074 3398 2.502 0.718 0.154 0.050 22 3.2 BA45_exvivo
- 2760 1993 4936 2.085 0.669 0.148 0.054 53 6.1 V1_exvivo
- 3622 2657 6102 1.985 0.599 0.168 0.055 71 8.4 V2_exvivo
- 644 518 1004 1.947 0.712 0.164 0.065 13 1.4 MT_exvivo
- 200 154 374 1.861 0.963 0.082 0.028 1 0.2 perirhinal_exvivo
- 300 201 610 2.475 1.084 0.146 0.083 8 1.2 entorhinal_exvivo
- #--------------------------------------------
- #@# BA_exvivo Labels rh Sun Oct 8 12:17:32 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 0050419 --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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 31997 of (31997 32003 32009 32014 32021) to complete...
- Waiting for PID 32003 of (31997 32003 32009 32014 32021) to complete...
- Waiting for PID 32009 of (31997 32003 32009 32014 32021) to complete...
- Waiting for PID 32014 of (31997 32003 32009 32014 32021) to complete...
- Waiting for PID 32021 of (31997 32003 32009 32014 32021) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 227
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.label 4189
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 194
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.label 6881
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 58
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.label 4038
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 129
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.label 4651
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 331
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.label 6078
- mri_label2label: Done
- PIDs (31997 32003 32009 32014 32021) 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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 32077 of (32077 32083 32089 32093) to complete...
- Waiting for PID 32083 of (32077 32083 32089 32093) to complete...
- Waiting for PID 32089 of (32077 32083 32089 32093) to complete...
- Waiting for PID 32093 of (32077 32083 32089 32093) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 130
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.label 4603
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 1048
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.label 13304
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 801
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.label 7713
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 921
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.label 6276
- mri_label2label: Done
- PIDs (32077 32083 32089 32093) 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 0050419 --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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 32142 of (32142 32148 32154 32160 32164) to complete...
- Waiting for PID 32148 of (32142 32148 32154 32160 32164) to complete...
- Waiting for PID 32154 of (32142 32148 32154 32160 32164) to complete...
- Waiting for PID 32160 of (32142 32148 32154 32160 32164) to complete...
- Waiting for PID 32164 of (32142 32148 32154 32160 32164) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 1448
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.label 6175
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 2740
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.label 10756
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 391
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.label 2323
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 215
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.label 1253
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 165
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.label 917
- mri_label2label: Done
- PIDs (32142 32148 32154 32160 32164) 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 0050419 --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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 32210 of (32210 32216 32222 32227 32232) to complete...
- Waiting for PID 32216 of (32210 32216 32222 32227 32232) to complete...
- Waiting for PID 32222 of (32210 32216 32222 32227 32232) to complete...
- Waiting for PID 32227 of (32210 32216 32222 32227 32232) to complete...
- Waiting for PID 32232 of (32210 32216 32222 32227 32232) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 110
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.thresh.label 986
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 19
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.thresh.label 2707
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 23
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.thresh.label 1721
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 21
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.thresh.label 2204
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 131
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.thresh.label 1519
- mri_label2label: Done
- PIDs (32210 32216 32222 32227 32232) 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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 32290 of (32290 32296 32302 32307) to complete...
- Waiting for PID 32296 of (32290 32296 32302 32307) to complete...
- Waiting for PID 32302 of (32290 32296 32302 32307) to complete...
- Waiting for PID 32307 of (32290 32296 32302 32307) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 17
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.thresh.label 1506
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 485
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.thresh.label 7444
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 153
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.thresh.label 1165
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 264
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.thresh.label 1442
- mri_label2label: Done
- PIDs (32290 32296 32302 32307) 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 0050419 --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 0050419 --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 0050419 --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 0050419 --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 0050419 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 32351 of (32351 32357 32363 32368 32374) to complete...
- Waiting for PID 32357 of (32351 32357 32363 32368 32374) to complete...
- Waiting for PID 32363 of (32351 32357 32363 32368 32374) to complete...
- Waiting for PID 32368 of (32351 32357 32363 32368 32374) to complete...
- Waiting for PID 32374 of (32351 32357 32363 32368 32374) 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 900
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.thresh.label 4132
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 1266
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.thresh.label 4703
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 27
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.thresh.label 295
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 151
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.thresh.label 845
- 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 0050419 --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 = 0050419
- 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-6.0.0/0050419/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 120570
- Number of reverse mapping hits = 72
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.thresh.label 363
- mri_label2label: Done
- PIDs (32351 32357 32363 32368 32374) completed and logs appended.
- mris_label2annot --s 0050419 --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-6.0.0/0050419/label
- cmdline mris_label2annot --s 0050419 --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-586
- machine x86_64
- user ntraut
- subject 0050419
- 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-6.0.0/0050419/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 82590 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/label/rh.BA_exvivo.annot
- mris_label2annot --s 0050419 --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-6.0.0/0050419/label
- cmdline mris_label2annot --s 0050419 --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-586
- machine x86_64
- user ntraut
- subject 0050419
- 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-6.0.0/0050419/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 99451 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/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 0050419 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 222558
- Total vertex volume 219604 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 847 548 1672 2.154 0.627 0.174 0.064 18 2.3 BA1_exvivo
- 2258 1555 3524 2.162 0.562 0.108 0.022 16 2.0 BA2_exvivo
- 942 618 791 1.732 0.433 0.149 0.037 13 1.6 BA3a_exvivo
- 1693 1131 2248 1.713 0.543 0.105 0.025 14 1.7 BA3b_exvivo
- 1400 881 2481 2.277 0.559 0.117 0.045 15 2.5 BA4a_exvivo
- 1003 697 1440 2.119 0.457 0.105 0.031 6 1.2 BA4p_exvivo
- 7722 5414 18425 2.824 0.658 0.133 0.041 109 12.7 BA6_exvivo
- 3441 2374 6950 2.655 0.569 0.124 0.030 37 4.5 BA44_exvivo
- 4097 3024 8823 2.439 0.709 0.151 0.043 67 7.2 BA45_exvivo
- 3674 2527 4884 1.837 0.526 0.144 0.051 54 7.6 V1_exvivo
- 7936 5374 11812 1.973 0.557 0.158 0.052 140 16.6 V2_exvivo
- 1892 1296 3361 2.369 0.581 0.143 0.044 26 3.1 MT_exvivo
- 657 412 1138 2.183 1.092 0.119 0.049 9 1.2 perirhinal_exvivo
- 418 257 669 2.015 0.981 0.157 0.063 9 1.1 entorhinal_exvivo
- mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050419 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050419/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 222558
- Total vertex volume 219604 (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) = 1377752 mm^3 (det: 1.413974 )
- lhCtxGM: 215314.692 215465.000 diff= -150.3 pctdiff=-0.070
- rhCtxGM: 218299.905 217436.000 diff= 863.9 pctdiff= 0.396
- lhCtxWM: 200620.154 200871.500 diff= -251.3 pctdiff=-0.125
- rhCtxWM: 204756.754 205915.500 diff=-1158.7 pctdiff=-0.566
- SubCortGMVol 53302.000
- SupraTentVol 900844.505 (898812.000) diff=2032.505 pctdiff=0.226
- SupraTentVolNotVent 895037.505 (893005.000) diff=2032.505 pctdiff=0.227
- BrainSegVol 1023743.000 (1021851.000) diff=1892.000 pctdiff=0.185
- BrainSegVolNotVent 1015328.000 (1014465.505) diff=862.495 pctdiff=0.085
- BrainSegVolNotVent 1015328.000
- CerebellumVol 122157.000
- VentChorVol 5807.000
- 3rd4th5thCSF 2608.000
- CSFVol 716.000, OptChiasmVol 166.000
- MaskVol 1339372.000
- 579 359 1147 2.167 0.659 0.175 0.063 12 1.7 BA1_exvivo
- 1284 901 2322 2.201 0.581 0.097 0.021 7 1.0 BA2_exvivo
- 804 533 651 1.753 0.386 0.149 0.033 9 1.1 BA3a_exvivo
- 1255 888 1415 1.539 0.316 0.088 0.012 6 0.6 BA3b_exvivo
- 970 613 1524 2.126 0.526 0.147 0.065 15 2.5 BA4a_exvivo
- 802 564 1093 2.051 0.437 0.095 0.022 4 0.7 BA4p_exvivo
- 4723 3283 10805 2.765 0.633 0.132 0.044 74 8.2 BA6_exvivo
- 903 669 2034 2.493 0.650 0.139 0.039 11 1.8 BA44_exvivo
- 1233 880 2689 2.363 0.738 0.140 0.038 17 1.9 BA45_exvivo
- 3488 2398 4540 1.834 0.522 0.141 0.051 50 7.0 V1_exvivo
- 4165 2823 6193 1.918 0.548 0.166 0.059 81 9.8 V2_exvivo
- 222 158 363 2.338 0.491 0.135 0.041 2 0.3 MT_exvivo
- 410 257 693 2.014 1.033 0.105 0.042 5 0.6 perirhinal_exvivo
- 281 186 449 1.809 0.822 0.124 0.044 4 0.5 entorhinal_exvivo
- Started at Sun Oct 8 00:35:26 CEST 2017
- Ended at Sun Oct 8 12:20:20 CEST 2017
- #@#%# recon-all-run-time-hours 11.748
- recon-all -s 0050419 finished without error at Sun Oct 8 12:20:21 CEST 2017
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