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|
- Sun Oct 8 01:15:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
- -subjid 0050490 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/USM_2/0050490/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
- subjid 0050490
- 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-114 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: 264574092 251297724 13276368 1729880 0 245238352
- -/+ buffers/cache: 6059372 258514720
- 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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: 2017/10/07-23:15:11-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-114 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-6.0.0/0050490
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/USM_2/0050490/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/orig/001.mgz
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/USM_2/0050490/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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/USM_2/0050490/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-6.0.0/0050490/mri/orig/001.mgz...
- #--------------------------------------------
- #@# MotionCor Sun Oct 8 01:15:26 CEST 2017
- Found 1 runs
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/rawavg.mgz
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/orig.mgz --conform
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/mri/orig.mgz...
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Sun Oct 8 01:16:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-114 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 01:16:44 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.460
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.460/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.460/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.460/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sun Oct 8 01:16:54 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.460/nu0.mnc ./tmp.mri_nu_correct.mni.460/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.460/0/ -iterations 1000 -distance 50
- [ntraut@tars-114:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/] [2017-10-08 01:16:54] 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.460/0/ ./tmp.mri_nu_correct.mni.460/nu0.mnc ./tmp.mri_nu_correct.mni.460/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 37
- CV of field change: 0.000975682
-
-
-
- mri_convert ./tmp.mri_nu_correct.mni.460/nu1.mnc orig_nu.mgz --like orig.mgz --conform
- mri_convert.bin ./tmp.mri_nu_correct.mni.460/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.460/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 01:18:02 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 01:18:02 CEST 2017
- Ended at Sun Oct 8 01:19:56 CEST 2017
- talairach_avi done
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Sun Oct 8 01:19:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7061, pval=0.4932 >= threshold=0.0050)
- awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/transforms/talairach_avi.log
- tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/transforms/talairach_avi.log
- TalAviQA: 0.98353
- z-score: 1
- #--------------------------------------------
- #@# Nu Intensity Correction Sun Oct 8 01:19:58 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-6.0.0/0050490/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-114 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 01:19:58 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.1256
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1256/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1256/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.1256/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sun Oct 8 01:20:09 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.1256/nu0.mnc ./tmp.mri_nu_correct.mni.1256/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1256/0/
- [ntraut@tars-114:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/] [2017-10-08 01:20:09] 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.1256/0/ ./tmp.mri_nu_correct.mni.1256/nu0.mnc ./tmp.mri_nu_correct.mni.1256/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
- Number of iterations: 30
- CV of field change: 0.000983527
- Reading Volume: ...............................................................
- Reading Volume: ...............................................................
-
-
- --------------------------------------------------------
- Iteration 2 Sun Oct 8 01:21:25 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.1256/nu1.mnc ./tmp.mri_nu_correct.mni.1256/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.1256/1/
- [ntraut@tars-114:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/] [2017-10-08 01:21:25] 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.1256/1/ ./tmp.mri_nu_correct.mni.1256/nu1.mnc ./tmp.mri_nu_correct.mni.1256/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
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 18
- CV of field change: 0.000985363
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.1256/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1256/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-6.0.0/0050490/mri
- cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.1256/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1256/ones.mgz
- sysname Linux
- hostname tars-114
- machine x86_64
- user ntraut
- input ./tmp.mri_nu_correct.mni.1256/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.1256/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.1256/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1256/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1256/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.1256/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1256/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1256/input.mean.dat
- sysname Linux
- hostname tars-114
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.1256/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.1256/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1256/ones.mgz --i ./tmp.mri_nu_correct.mni.1256/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1256/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1256/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.1256/ones.mgz --i ./tmp.mri_nu_correct.mni.1256/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1256/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1256/output.mean.dat
- sysname Linux
- hostname tars-114
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.1256/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.1256/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.1256/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.1256/nu2.mnc ./tmp.mri_nu_correct.mni.1256/nu2.mnc mul 1.03906514931838336632
- Saving result to './tmp.mri_nu_correct.mni.1256/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.1256/nu2.mnc nu.mgz --like orig.mgz
- mri_convert.bin ./tmp.mri_nu_correct.mni.1256/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.1256/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 17 seconds.
- mapping ( 8, 113) to ( 3, 110)
-
-
- Sun Oct 8 01:24:07 CEST 2017
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Sun Oct 8 01:24:09 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- mri_normalize -g 1 -mprage nu.mgz T1.mgz
- using max gradient = 1.000
- assuming input volume is MGH (Van der Kouwe) MP-RAGE
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.05834 -0.05780 -0.04230 -9.37296;
- 0.04197 0.94733 0.30468 -38.87525;
- 0.00133 -0.23165 1.06828 6.75354;
- 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 = 15
- Starting OpenSpline(): npoints = 15
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 110
- white matter peak found at 109
- gm peak at 63 (63), valley at 35 (35)
- 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 63 (63), valley at 24 (24)
- 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 12 seconds.
- #--------------------------------------------
- #@# Skull Stripping Sun Oct 8 01:26:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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=7.0
- skull bounding box = (41, 24, 0) --> (207, 182, 223)
- using (96, 77, 112) as brain centroid...
- mean wm in atlas = 108, using box (76,58,84) --> (116, 96,139) to find MRI wm
- before smoothing, mri peak at 110
- robust fit to distribution - 109 +- 5.4
- after smoothing, mri peak at 109, scaling input intensities by 0.991
- scaling channel 0 by 0.990826
- initial log_p = -4.396
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.335263 @ (9.091, 9.091, -9.091)
- max log p = -4.156005 @ (-4.545, 4.545, 4.545)
- max log p = -4.091447 @ (-2.273, -2.273, 2.273)
- max log p = -4.083212 @ (-1.136, 1.136, 1.136)
- max log p = -4.078184 @ (-0.568, -1.705, 0.568)
- max log p = -4.078184 @ (0.000, 0.000, 0.000)
- Found translation: (0.6, 10.8, -0.6): log p = -4.078
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.788, old_max_log_p =-4.078 (thresh=-4.1)
- 1.05465 -0.03594 0.13412 -16.45666;
- 0.00000 1.11081 0.29764 -29.44774;
- -0.13885 -0.27296 1.01871 42.96675;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.782, old_max_log_p =-3.788 (thresh=-3.8)
- 1.06375 0.00000 0.00000 -6.37745;
- 0.00000 1.19413 0.31997 -42.31939;
- 0.00000 -0.25467 0.95044 31.53729;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.782, old_max_log_p =-3.782 (thresh=-3.8)
- 1.06375 0.00000 0.00000 -6.37745;
- 0.00000 1.19413 0.31997 -42.31939;
- 0.00000 -0.25467 0.95044 31.53729;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.687, old_max_log_p =-3.782 (thresh=-3.8)
- 1.04267 -0.00879 0.02780 -7.93726;
- 0.00241 1.17906 0.28077 -34.37264;
- -0.03795 -0.22207 0.97629 31.10920;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.684, old_max_log_p =-3.687 (thresh=-3.7)
- 1.04203 -0.04737 0.01860 -2.08969;
- 0.03652 1.17814 0.28153 -38.62361;
- -0.03795 -0.22207 0.97629 31.10920;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.662, old_max_log_p =-3.684 (thresh=-3.7)
- 1.04474 -0.01992 0.03319 -6.98353;
- 0.01113 1.17667 0.27160 -34.57709;
- -0.04587 -0.21170 0.97846 31.06960;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.656, old_max_log_p =-3.662 (thresh=-3.7)
- 1.04474 -0.01992 0.03319 -6.98353;
- 0.01074 1.17352 0.27927 -34.54782;
- -0.04591 -0.22106 0.97507 33.07893;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.655, old_max_log_p =-3.656 (thresh=-3.7)
- 1.04719 -0.01997 0.03327 -7.29258;
- 0.01074 1.17352 0.27927 -34.54782;
- -0.04591 -0.22106 0.97507 33.07893;
- 0.00000 0.00000 0.00000 1.00000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 3243 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.04719 -0.01997 0.03327 -7.29258;
- 0.01074 1.17352 0.27927 -34.54782;
- -0.04591 -0.22106 0.97507 33.07893;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3243
- Quasinewton: input matrix
- 1.04719 -0.01997 0.03327 -7.29258;
- 0.01074 1.17352 0.27927 -34.54782;
- -0.04591 -0.22106 0.97507 33.07893;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.04719 -0.01997 0.03327 -7.29258;
- 0.01074 1.17352 0.27927 -34.54782;
- -0.04591 -0.22106 0.97507 33.07893;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.655 (old=-4.396)
- transform before final EM align:
- 1.04719 -0.01997 0.03327 -7.29258;
- 0.01074 1.17352 0.27927 -34.54782;
- -0.04591 -0.22106 0.97507 33.07893;
- 0.00000 0.00000 0.00000 1.00000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 364799 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.04719 -0.01997 0.03327 -7.29258;
- 0.01074 1.17352 0.27927 -34.54782;
- -0.04591 -0.22106 0.97507 33.07893;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 364799
- Quasinewton: input matrix
- 1.04719 -0.01997 0.03327 -7.29258;
- 0.01074 1.17352 0.27927 -34.54782;
- -0.04591 -0.22106 0.97507 33.07893;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 012: -log(p) = 4.1 tol 0.000000
- final transform:
- 1.04719 -0.01997 0.03327 -7.29258;
- 0.01074 1.17352 0.27927 -34.54782;
- -0.04591 -0.22106 0.97507 33.07893;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach_with_skull.lta...
- mri_em_register utimesec 5814.068127
- mri_em_register stimesec 11.540245
- 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 157574
- 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 1789149
- mri_em_register ru_nivcsw 14984
- registration took 83 minutes and 39 seconds.
- mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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=125 y=98 z=108 r=73
- first estimation of the main basin volume: 1664660 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 18 found in the rest of the brain
- global maximum in x=109, y=82, z=74, Imax=255
- CSF=18, 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=9348481830 voxels, voxel volume =1.000
- = 9348481830 mmm3 = 9348482.048 cm3
- done.
- PostAnalyze...Basin Prior
- 12 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=125,y=105, z=104, r=10661 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=50 , nb = 45118
- RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=55 , nb = -1031211856
- LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=44 , nb = 1100087410
- RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=45 , nb = 1094517478
- LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=53 , nb = 1077211110
- OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1078909570
- Problem with the least square interpolation in GM_MIN calculation.
- Problem with the least square interpolation in GM_MIN calculation.
- (2) Problem with the least square interpolation in GM_MIN calculation.
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 50, 38, 31, 56
- after analyzing : 30, 38, 38, 42
- RIGHT_CER
- before analyzing : 55, 43, 37, 64
- after analyzing : 33, 43, 43, 48
- LEFT_CER
- before analyzing : 44, 40, 38, 59
- after analyzing : 29, 40, 40, 44
- RIGHT_BRAIN
- before analyzing : 45, 36, 31, 56
- after analyzing : 29, 36, 36, 41
- LEFT_BRAIN
- before analyzing : 53, 38, 31, 56
- after analyzing : 30, 38, 38, 42
- OTHER
- before analyzing : 3, 2, 0, 9
- after analyzing : 2, 17, 25, 19
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...60 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.010
- curvature mean = 72.019, std = 7.213
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 1.83, sigma = 2.91
- after rotation: sse = 1.83, sigma = 2.91
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 1.95, its var is 3.00
- before Erosion-Dilatation 0.27% of inacurate vertices
- after Erosion-Dilatation 0.00% of inacurate vertices
- Validation of the shape of the surface done.
- Scaling of atlas fields onto current surface fields
- ********FINAL ITERATIVE TEMPLATE DEFORMATION********
- Compute Local values csf/gray
- Fine Segmentation...41 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1763604 voxels, voxel volume = 1.000 mm3
- = 1763604 mmm3 = 1763.604 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- mri_watershed utimesec 62.087561
- mri_watershed stimesec 1.084835
- mri_watershed ru_maxrss 832900
- mri_watershed ru_ixrss 0
- mri_watershed ru_idrss 0
- mri_watershed ru_isrss 0
- mri_watershed ru_minflt 215559
- mri_watershed ru_majflt 0
- mri_watershed ru_nswap 0
- mri_watershed ru_inblock 0
- mri_watershed ru_oublock 2864
- mri_watershed ru_msgsnd 0
- mri_watershed ru_msgrcv 0
- mri_watershed ru_nsignals 0
- mri_watershed ru_nvcsw 5566
- mri_watershed ru_nivcsw 216
- mri_watershed done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Sun Oct 8 02:51:03 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta
- setting unknown_nbr_spacing = 3
- using MR volume brainmask.mgz to mask input volume...
- == Number of threads available to mri_em_register for OpenMP = 2 ==
- reading 1 input volumes...
- logging results to talairach.log
- reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
- average std = 7.3 using min determinant for regularization = 5.3
- 0 singular and 841 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- accounting for voxel sizes in initial transform
- bounding unknown intensity as < 6.3 or > 503.7
- total sample mean = 78.8 (1011 zeros)
- ************************************************
- spacing=8, using 2830 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 2830, passno 0, spacing 8
- resetting wm mean[0]: 98 --> 107
- resetting gm mean[0]: 61 --> 61
- input volume #1 is the most T1-like
- using real data threshold=21.9
- skull bounding box = (59, 43, 23) --> (193, 182, 200)
- using (104, 89, 112) as brain centroid...
- mean wm in atlas = 107, using box (88,72,90) --> (120, 106,133) to find MRI wm
- before smoothing, mri peak at 110
- robust fit to distribution - 109 +- 5.2
- after smoothing, mri peak at 109, scaling input intensities by 0.982
- scaling channel 0 by 0.981651
- initial log_p = -4.185
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.051234 @ (9.091, 9.091, -9.091)
- max log p = -3.745299 @ (-4.545, 4.545, 4.545)
- max log p = -3.626761 @ (-2.273, 2.273, 2.273)
- max log p = -3.623154 @ (-1.136, -1.136, 1.136)
- max log p = -3.612539 @ (0.568, -0.568, -1.705)
- max log p = -3.612539 @ (0.000, 0.000, 0.000)
- Found translation: (1.7, 14.2, -2.8): log p = -3.613
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.401, old_max_log_p =-3.613 (thresh=-3.6)
- 1.06580 -0.03087 0.11520 -15.75408;
- 0.00000 1.02750 0.27532 -18.49865;
- -0.14032 -0.23447 0.87506 60.37152;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.401, old_max_log_p =-3.401 (thresh=-3.4)
- 1.06580 -0.03087 0.11520 -15.75408;
- 0.00000 1.02750 0.27532 -18.49865;
- -0.14032 -0.23447 0.87506 60.37152;
- 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=-3.201, old_max_log_p =-3.401 (thresh=-3.4)
- 1.04896 0.01248 0.09083 -15.71046;
- -0.02894 1.07360 0.25300 -15.80520;
- -0.11395 -0.21304 0.93712 44.70525;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.201, old_max_log_p =-3.201 (thresh=-3.2)
- 1.04896 0.01248 0.09083 -15.71046;
- -0.02894 1.07360 0.25300 -15.80520;
- -0.11395 -0.21304 0.93712 44.70525;
- 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=-3.181, old_max_log_p =-3.201 (thresh=-3.2)
- 1.04809 -0.00502 0.08632 -13.30033;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86055;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.181, old_max_log_p =-3.181 (thresh=-3.2)
- 1.04809 -0.00502 0.08632 -13.30033;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86055;
- 0.00000 0.00000 0.00000 1.00000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 2830 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.04809 -0.00502 0.08632 -13.30033;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86055;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2830
- Quasinewton: input matrix
- 1.04809 -0.00502 0.08632 -13.30033;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86055;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.04809 -0.00502 0.08632 -13.30033;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86055;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.181 (old=-4.185)
- transform before final EM align:
- 1.04809 -0.00502 0.08632 -13.30033;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86055;
- 0.00000 0.00000 0.00000 1.00000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 315557 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.04809 -0.00502 0.08632 -13.30033;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86055;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 315557
- Quasinewton: input matrix
- 1.04809 -0.00502 0.08632 -13.30033;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86055;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 010: -log(p) = 3.7 tol 0.000000
- final transform:
- 1.04809 -0.00502 0.08632 -13.30033;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86055;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach.lta...
- mri_em_register utimesec 3479.343059
- mri_em_register stimesec 6.534006
- mri_em_register ru_maxrss 599052
- mri_em_register ru_ixrss 0
- mri_em_register ru_idrss 0
- mri_em_register ru_isrss 0
- mri_em_register ru_minflt 159485
- 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 875880
- mri_em_register ru_nivcsw 8606
- registration took 46 minutes and 9 seconds.
- #--------------------------------------
- #@# CA Normalize Sun Oct 8 03:37:12 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz
- writing control point volume to ctrl_pts.mgz
- using MR volume brainmask.mgz to mask input volume...
- reading 1 input volume
- reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
- reading transform from 'transforms/talairach.lta'...
- reading input volume from nu.mgz...
- resetting wm mean[0]: 98 --> 107
- resetting gm mean[0]: 61 --> 61
- input volume #1 is the most T1-like
- using real data threshold=22.9
- skull bounding box = (59, 43, 24) --> (193, 182, 200)
- using (104, 89, 112) as brain centroid...
- mean wm in atlas = 107, using box (88,72,90) --> (120, 106,133) to find MRI wm
- before smoothing, mri peak at 110
- robust fit to distribution - 109 +- 5.2
- after smoothing, mri peak at 109, scaling input intensities by 0.982
- scaling channel 0 by 0.981651
- using 246344 sample points...
- INFO: compute sample coordinates transform
- 1.04809 -0.00502 0.08632 -13.30033;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86055;
- 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, 45, 26) --> (189, 153, 196)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
- 0 of 589 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (64, 45, 22) --> (128, 149, 194)
- Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0
- 1 of 968 (0.1%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (128, 130, 56) --> (174, 168, 111)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 0 of 7 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (85, 130, 49) --> (128, 168, 108)
- Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 132.0
- 0 of 9 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (109, 116, 90) --> (142, 181, 122)
- Brain_Stem: limiting intensities to 97.0 --> 132.0
- 5 of 18 (27.8%) samples deleted
- using 1591 total control points for intensity normalization...
- bias field = 0.974 +- 0.041
- 4 of 1585 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (122, 45, 26) --> (189, 153, 196)
- Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
- 0 of 738 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (64, 45, 22) --> (128, 149, 194)
- Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
- 1 of 1411 (0.1%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (128, 130, 56) --> (174, 168, 111)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 15 of 74 (20.3%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (85, 130, 49) --> (128, 168, 108)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 8 of 60 (13.3%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (109, 116, 90) --> (142, 181, 122)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 18 of 72 (25.0%) samples deleted
- using 2355 total control points for intensity normalization...
- bias field = 1.012 +- 0.045
- 15 of 2297 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (122, 45, 26) --> (189, 153, 196)
- Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
- 2 of 755 (0.3%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (64, 45, 22) --> (128, 149, 194)
- Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
- 1 of 1465 (0.1%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (128, 130, 56) --> (174, 168, 111)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 50 of 94 (53.2%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (85, 130, 49) --> (128, 168, 108)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 23 of 60 (38.3%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (109, 116, 90) --> (142, 181, 122)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 106 of 189 (56.1%) samples deleted
- using 2563 total control points for intensity normalization...
- bias field = 1.013 +- 0.040
- 4 of 2343 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 29 seconds.
- #--------------------------------------
- #@# CA Reg Sun Oct 8 03:39:42 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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) = 1.12 (predicted orig area = 7.1)
- label assignment complete, 0 changed (0.00%)
- freeing gibbs priors...done.
- average std[0] = 5.0
- **************** pass 1 of 1 ************************
- enabling zero nodes
- setting smoothness coefficient to 0.039
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.771, neg=0, invalid=762
- 0001: dt=209.097143, rms=0.715 (7.172%), neg=0, invalid=762
- 0002: dt=140.545455, rms=0.702 (1.850%), neg=0, invalid=762
- 0003: dt=369.920000, rms=0.693 (1.310%), neg=0, invalid=762
- 0004: dt=110.976000, rms=0.688 (0.657%), neg=0, invalid=762
- 0005: dt=887.808000, rms=0.682 (0.926%), neg=0, invalid=762
- 0006: dt=129.472000, rms=0.680 (0.329%), neg=0, invalid=762
- 0007: dt=295.936000, rms=0.679 (0.159%), neg=0, invalid=762
- 0008: dt=295.936000, rms=0.679 (0.002%), neg=0, invalid=762
- 0009: dt=295.936000, rms=0.675 (0.511%), neg=0, invalid=762
- 0010: dt=295.936000, rms=0.672 (0.484%), neg=0, invalid=762
- 0011: dt=295.936000, rms=0.670 (0.237%), neg=0, invalid=762
- 0012: dt=295.936000, rms=0.667 (0.486%), neg=0, invalid=762
- 0013: dt=295.936000, rms=0.665 (0.388%), neg=0, invalid=762
- 0014: dt=295.936000, rms=0.664 (0.136%), neg=0, invalid=762
- 0015: dt=295.936000, rms=0.662 (0.234%), neg=0, invalid=762
- 0016: dt=295.936000, rms=0.660 (0.290%), neg=0, invalid=762
- 0017: dt=295.936000, rms=0.659 (0.233%), neg=0, invalid=762
- 0018: dt=295.936000, rms=0.658 (0.179%), neg=0, invalid=762
- 0019: dt=295.936000, rms=0.657 (0.151%), neg=0, invalid=762
- 0020: dt=295.936000, rms=0.655 (0.302%), neg=0, invalid=762
- 0021: dt=295.936000, rms=0.653 (0.160%), neg=0, invalid=762
- 0022: dt=295.936000, rms=0.653 (0.024%), neg=0, invalid=762
- 0023: dt=295.936000, rms=0.651 (0.297%), neg=0, invalid=762
- 0024: dt=295.936000, rms=0.651 (0.126%), neg=0, invalid=762
- 0025: dt=295.936000, rms=0.650 (0.032%), neg=0, invalid=762
- 0026: dt=295.936000, rms=0.649 (0.214%), neg=0, invalid=762
- 0027: dt=295.936000, rms=0.648 (0.103%), neg=0, invalid=762
- 0028: dt=295.936000, rms=0.648 (0.048%), neg=0, invalid=762
- 0029: dt=129.472000, rms=0.647 (0.082%), neg=0, invalid=762
- 0030: dt=73.984000, rms=0.647 (-0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.648, neg=0, invalid=762
- 0031: dt=295.936000, rms=0.647 (0.163%), neg=0, invalid=762
- 0032: dt=295.936000, rms=0.647 (0.045%), neg=0, invalid=762
- 0033: dt=295.936000, rms=0.647 (-0.023%), neg=0, invalid=762
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.653, neg=0, invalid=762
- 0034: dt=197.680473, rms=0.646 (1.025%), neg=0, invalid=762
- 0035: dt=108.547842, rms=0.640 (0.980%), neg=0, invalid=762
- 0036: dt=64.709534, rms=0.637 (0.401%), neg=0, invalid=762
- 0037: dt=414.720000, rms=0.630 (1.066%), neg=0, invalid=762
- 0038: dt=64.831169, rms=0.626 (0.651%), neg=0, invalid=762
- 0039: dt=145.152000, rms=0.624 (0.374%), neg=0, invalid=762
- 0040: dt=36.288000, rms=0.623 (0.145%), neg=0, invalid=762
- 0041: dt=36.288000, rms=0.623 (0.080%), neg=0, invalid=762
- 0042: dt=36.288000, rms=0.622 (0.124%), neg=0, invalid=762
- 0043: dt=36.288000, rms=0.621 (0.186%), neg=0, invalid=762
- 0044: dt=36.288000, rms=0.619 (0.255%), neg=0, invalid=762
- 0045: dt=36.288000, rms=0.617 (0.283%), neg=0, invalid=762
- 0046: dt=36.288000, rms=0.616 (0.283%), neg=0, invalid=762
- 0047: dt=36.288000, rms=0.614 (0.291%), neg=0, invalid=762
- 0048: dt=36.288000, rms=0.612 (0.286%), neg=0, invalid=762
- 0049: dt=36.288000, rms=0.610 (0.277%), neg=0, invalid=762
- 0050: dt=36.288000, rms=0.609 (0.277%), neg=0, invalid=762
- 0051: dt=36.288000, rms=0.607 (0.274%), neg=0, invalid=762
- 0052: dt=36.288000, rms=0.605 (0.256%), neg=0, invalid=762
- 0053: dt=36.288000, rms=0.604 (0.224%), neg=0, invalid=762
- 0054: dt=36.288000, rms=0.603 (0.210%), neg=0, invalid=762
- 0055: dt=36.288000, rms=0.602 (0.190%), neg=0, invalid=762
- 0056: dt=36.288000, rms=0.601 (0.177%), neg=0, invalid=762
- 0057: dt=36.288000, rms=0.600 (0.168%), neg=0, invalid=762
- 0058: dt=36.288000, rms=0.599 (0.152%), neg=0, invalid=762
- 0059: dt=36.288000, rms=0.598 (0.137%), neg=0, invalid=762
- 0060: dt=36.288000, rms=0.597 (0.120%), neg=0, invalid=762
- 0061: dt=36.288000, rms=0.596 (0.102%), neg=0, invalid=762
- 0062: dt=145.152000, rms=0.596 (0.013%), neg=0, invalid=762
- 0063: dt=145.152000, rms=0.596 (0.020%), neg=0, invalid=762
- 0064: dt=145.152000, rms=0.596 (0.032%), neg=0, invalid=762
- 0065: dt=145.152000, rms=0.596 (0.047%), neg=0, invalid=762
- 0066: dt=145.152000, rms=0.595 (0.059%), neg=0, invalid=762
- 0067: dt=145.152000, rms=0.595 (0.064%), neg=0, invalid=762
- 0068: dt=145.152000, rms=0.594 (0.113%), neg=0, invalid=762
- 0069: dt=145.152000, rms=0.594 (0.095%), neg=0, invalid=762
- 0070: dt=145.152000, rms=0.593 (0.122%), neg=0, invalid=762
- 0071: dt=145.152000, rms=0.592 (0.180%), neg=0, invalid=762
- 0072: dt=145.152000, rms=0.591 (0.133%), neg=0, invalid=762
- 0073: dt=145.152000, rms=0.590 (0.231%), neg=0, invalid=762
- 0074: dt=145.152000, rms=0.589 (0.147%), neg=0, invalid=762
- 0075: dt=145.152000, rms=0.588 (0.146%), neg=0, invalid=762
- 0076: dt=145.152000, rms=0.587 (0.179%), neg=0, invalid=762
- 0077: dt=145.152000, rms=0.587 (0.106%), neg=0, invalid=762
- 0078: dt=145.152000, rms=0.586 (0.172%), neg=0, invalid=762
- 0079: dt=145.152000, rms=0.585 (0.056%), neg=0, invalid=762
- 0080: dt=145.152000, rms=0.585 (0.096%), neg=0, invalid=762
- 0081: dt=145.152000, rms=0.584 (0.123%), neg=0, invalid=762
- 0082: dt=145.152000, rms=0.584 (0.018%), neg=0, invalid=762
- 0083: dt=82.944000, rms=0.584 (0.041%), neg=0, invalid=762
- 0084: dt=0.006328, rms=0.584 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.584, neg=0, invalid=762
- 0085: dt=124.416000, rms=0.583 (0.285%), neg=0, invalid=762
- 0086: dt=62.208000, rms=0.582 (0.050%), neg=0, invalid=762
- 0087: dt=62.208000, rms=0.582 (0.021%), neg=0, invalid=762
- 0088: dt=62.208000, rms=0.582 (0.020%), neg=0, invalid=762
- 0089: dt=62.208000, rms=0.582 (0.015%), neg=0, invalid=762
- 0090: dt=248.832000, rms=0.582 (0.021%), neg=0, invalid=762
- 0091: dt=9.072000, rms=0.582 (-0.003%), neg=0, invalid=762
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.605, neg=0, invalid=762
- 0092: dt=0.000000, rms=0.605 (0.090%), neg=0, invalid=762
- 0093: dt=0.000000, rms=0.605 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.605, neg=0, invalid=762
- 0094: dt=0.000000, rms=0.605 (0.090%), neg=0, invalid=762
- 0095: dt=0.000000, rms=0.605 (0.000%), neg=0, invalid=762
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.674, neg=0, invalid=762
- 0096: dt=5.323810, rms=0.650 (3.449%), neg=0, invalid=762
- 0097: dt=2.637681, rms=0.650 (0.147%), neg=0, invalid=762
- 0098: dt=2.637681, rms=0.650 (-0.037%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.650, neg=0, invalid=762
- 0099: dt=0.000000, rms=0.650 (0.074%), neg=0, invalid=762
- 0100: dt=0.000000, rms=0.650 (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=0.706, neg=0, invalid=762
- 0101: dt=1.536000, rms=0.701 (0.736%), neg=0, invalid=762
- 0102: dt=2.170886, rms=0.694 (0.955%), neg=0, invalid=762
- 0103: dt=0.448000, rms=0.694 (0.053%), neg=0, invalid=762
- 0104: dt=0.448000, rms=0.693 (0.029%), neg=0, invalid=762
- 0105: dt=0.448000, rms=0.693 (0.028%), neg=0, invalid=762
- 0106: dt=0.448000, rms=0.693 (0.021%), neg=0, invalid=762
- 0107: dt=1.792000, rms=0.691 (0.274%), neg=0, invalid=762
- 0108: dt=0.000000, rms=0.691 (-0.000%), neg=0, invalid=762
- 0109: dt=0.100000, rms=0.691 (-0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.692, neg=0, invalid=762
- 0110: dt=0.448000, rms=0.691 (0.111%), neg=0, invalid=762
- 0111: dt=0.448000, rms=0.691 (0.015%), neg=0, invalid=762
- 0112: dt=0.448000, rms=0.691 (0.015%), neg=0, invalid=762
- 0113: dt=0.448000, rms=0.691 (0.009%), neg=0, invalid=762
- 0114: dt=0.448000, rms=0.691 (-0.008%), 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=0.663, neg=0, invalid=762
- 0115: dt=0.814962, rms=0.645 (2.597%), neg=0, invalid=762
- 0116: dt=0.080000, rms=0.645 (0.127%), neg=0, invalid=762
- 0117: dt=0.080000, rms=0.645 (-0.098%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.645, neg=0, invalid=762
- 0118: dt=0.028000, rms=0.645 (0.090%), neg=0, invalid=762
- 0119: dt=0.000000, rms=0.645 (-0.001%), neg=0, invalid=762
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.10027 (20)
- mri peak = 0.09359 (16)
- Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (1068 voxels, overlap=0.628)
- Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (1068 voxels, peak = 15), gca=14.9
- gca peak = 0.15565 (16)
- mri peak = 0.07212 (17)
- Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (775 voxels, overlap=0.818)
- Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (775 voxels, peak = 17), gca=16.6
- gca peak = 0.26829 (96)
- mri peak = 0.08229 (95)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1028 voxels, overlap=1.000)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1028 voxels, peak = 96), gca=96.5
- gca peak = 0.20183 (93)
- mri peak = 0.08190 (96)
- Left_Pallidum (13): linear fit = 1.01 x + 0.0 (846 voxels, overlap=1.002)
- Left_Pallidum (13): linear fit = 1.01 x + 0.0 (846 voxels, peak = 94), gca=94.4
- gca peak = 0.21683 (55)
- mri peak = 0.07240 (64)
- Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (707 voxels, overlap=0.716)
- Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (707 voxels, peak = 57), gca=57.5
- gca peak = 0.30730 (58)
- mri peak = 0.09161 (63)
- Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (848 voxels, overlap=0.997)
- Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (848 voxels, peak = 64), gca=63.5
- gca peak = 0.11430 (101)
- mri peak = 0.11192 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65922 voxels, overlap=0.549)
- Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65922 voxels, peak = 107), gca=106.6
- gca peak = 0.12076 (102)
- mri peak = 0.10490 (105)
- Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (65364 voxels, overlap=0.656)
- Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (65364 voxels, peak = 108), gca=107.6
- gca peak = 0.14995 (59)
- mri peak = 0.04769 (52)
- Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (27850 voxels, overlap=0.988)
- Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (27850 voxels, peak = 54), gca=54.0
- gca peak = 0.15082 (58)
- mri peak = 0.03747 (52)
- Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28840 voxels, overlap=0.997)
- Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28840 voxels, peak = 59), gca=59.4
- gca peak = 0.14161 (67)
- mri peak = 0.10177 (70)
- Right_Caudate (50): linear fit = 1.05 x + 0.0 (960 voxels, overlap=0.879)
- Right_Caudate (50): linear fit = 1.05 x + 0.0 (960 voxels, peak = 71), gca=70.7
- gca peak = 0.15243 (71)
- mri peak = 0.10115 (72)
- Left_Caudate (11): linear fit = 0.95 x + 0.0 (1125 voxels, overlap=0.905)
- Left_Caudate (11): linear fit = 0.95 x + 0.0 (1125 voxels, peak = 68), gca=67.8
- gca peak = 0.13336 (57)
- mri peak = 0.04316 (55)
- Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (27569 voxels, overlap=0.984)
- Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (27569 voxels, peak = 60), gca=59.6
- gca peak = 0.13252 (56)
- mri peak = 0.04617 (61)
- Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (29302 voxels, overlap=0.944)
- Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (29302 voxels, peak = 59), gca=58.5
- gca peak = 0.18181 (84)
- mri peak = 0.07413 (85)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (8773 voxels, overlap=0.784)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (8773 voxels, peak = 89), gca=88.6
- gca peak = 0.20573 (83)
- mri peak = 0.07956 (85)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8325 voxels, overlap=0.806)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8325 voxels, peak = 88), gca=87.6
- gca peak = 0.21969 (57)
- mri peak = 0.08469 (62)
- Left_Amygdala (18): linear fit = 1.04 x + 0.0 (456 voxels, overlap=0.991)
- Left_Amygdala (18): linear fit = 1.04 x + 0.0 (456 voxels, peak = 60), gca=59.6
- gca peak = 0.39313 (56)
- mri peak = 0.08413 (57)
- Right_Amygdala (54): linear fit = 1.04 x + 0.0 (527 voxels, overlap=0.996)
- Right_Amygdala (54): linear fit = 1.04 x + 0.0 (527 voxels, peak = 59), gca=58.5
- gca peak = 0.14181 (85)
- mri peak = 0.05492 (90)
- Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5866 voxels, overlap=0.911)
- Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5866 voxels, peak = 91), gca=90.5
- gca peak = 0.11978 (83)
- mri peak = 0.06106 (87)
- Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4831 voxels, overlap=0.929)
- Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4831 voxels, peak = 87), gca=86.7
- gca peak = 0.13399 (79)
- mri peak = 0.07592 (79)
- Left_Putamen (12): linear fit = 1.01 x + 0.0 (2675 voxels, overlap=0.995)
- Left_Putamen (12): linear fit = 1.01 x + 0.0 (2675 voxels, peak = 80), gca=80.2
- gca peak = 0.14159 (79)
- mri peak = 0.08762 (80)
- Right_Putamen (51): linear fit = 1.02 x + 0.0 (2695 voxels, overlap=0.973)
- Right_Putamen (51): linear fit = 1.02 x + 0.0 (2695 voxels, peak = 81), gca=81.0
- gca peak = 0.10025 (80)
- mri peak = 0.08399 (83)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (11973 voxels, overlap=0.402)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (11973 voxels, peak = 88), gca=87.6
- gca peak = 0.13281 (86)
- mri peak = 0.07352 (92)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1356 voxels, overlap=0.651)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1356 voxels, peak = 93), gca=93.3
- gca peak = 0.12801 (89)
- mri peak = 0.06529 (92)
- Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1516 voxels, overlap=0.670)
- Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1516 voxels, peak = 97), gca=96.6
- gca peak = 0.20494 (23)
- mri peak = 0.07026 (23)
- gca peak = 0.15061 (21)
- mri peak = 0.07500 (15)
- Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (436 voxels, overlap=0.605)
- Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (436 voxels, peak = 17), gca=17.1
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.18056 (32)
- gca peak Left_Thalamus = 0.64095 (94)
- gca peak Third_Ventricle = 0.20494 (23)
- gca peak CSF = 0.20999 (34)
- gca peak Left_Accumbens_area = 0.39030 (62)
- gca peak Left_undetermined = 0.95280 (25)
- gca peak Left_vessel = 0.67734 (53)
- gca peak Left_choroid_plexus = 0.09433 (44)
- gca peak Right_Inf_Lat_Vent = 0.23544 (26)
- gca peak Right_Accumbens_area = 0.30312 (64)
- gca peak Right_vessel = 0.46315 (51)
- gca peak Right_choroid_plexus = 0.14086 (44)
- gca peak Fifth_Ventricle = 0.51669 (36)
- gca peak WM_hypointensities = 0.09722 (76)
- gca peak non_WM_hypointensities = 0.11899 (47)
- gca peak Optic_Chiasm = 0.39033 (72)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.03 x + 0.0
- estimating mean wm scale to be 1.05 x + 0.0
- estimating mean csf scale to be 0.87 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=0.675, neg=0, invalid=762
- 0120: dt=151.327103, rms=0.670 (0.856%), neg=0, invalid=762
- 0121: dt=129.472000, rms=0.668 (0.278%), neg=0, invalid=762
- 0122: dt=295.936000, rms=0.666 (0.249%), neg=0, invalid=762
- 0123: dt=110.976000, rms=0.665 (0.178%), neg=0, invalid=762
- 0124: dt=221.952000, rms=0.664 (0.141%), neg=0, invalid=762
- 0125: dt=110.976000, rms=0.663 (0.094%), neg=0, invalid=762
- 0126: dt=369.920000, rms=0.662 (0.127%), neg=0, invalid=762
- 0127: dt=92.480000, rms=0.662 (0.111%), neg=0, invalid=762
- 0128: dt=517.888000, rms=0.661 (0.175%), neg=0, invalid=762
- 0129: dt=110.976000, rms=0.660 (0.066%), neg=0, invalid=762
- 0130: dt=295.936000, rms=0.660 (0.070%), neg=0, invalid=762
- 0131: dt=110.976000, rms=0.659 (0.062%), neg=0, invalid=762
- 0132: dt=295.936000, rms=0.659 (0.062%), neg=0, invalid=762
- 0133: dt=110.976000, rms=0.659 (0.054%), neg=0, invalid=762
- 0134: dt=295.936000, rms=0.658 (0.056%), neg=0, invalid=762
- 0135: dt=110.976000, rms=0.658 (0.044%), neg=0, invalid=762
- 0136: dt=110.976000, rms=0.658 (0.031%), neg=0, invalid=762
- 0137: dt=110.976000, rms=0.657 (0.042%), neg=0, invalid=762
- 0138: dt=110.976000, rms=0.657 (0.066%), neg=0, invalid=762
- 0139: dt=110.976000, rms=0.656 (0.071%), neg=0, invalid=762
- 0140: dt=110.976000, rms=0.656 (0.078%), neg=0, invalid=762
- 0141: dt=110.976000, rms=0.655 (0.077%), neg=0, invalid=762
- 0142: dt=110.976000, rms=0.655 (0.074%), neg=0, invalid=762
- 0143: dt=110.976000, rms=0.654 (0.074%), neg=0, invalid=762
- 0144: dt=110.976000, rms=0.654 (0.069%), neg=0, invalid=762
- 0145: dt=110.976000, rms=0.654 (0.058%), neg=0, invalid=762
- 0146: dt=110.976000, rms=0.653 (0.055%), neg=0, invalid=762
- 0147: dt=110.976000, rms=0.653 (0.054%), neg=0, invalid=762
- 0148: dt=110.976000, rms=0.653 (0.056%), neg=0, invalid=762
- 0149: dt=110.976000, rms=0.652 (0.053%), neg=0, invalid=762
- 0150: dt=110.976000, rms=0.652 (0.053%), neg=0, invalid=762
- 0151: dt=110.976000, rms=0.652 (0.048%), neg=0, invalid=762
- 0152: dt=110.976000, rms=0.651 (0.048%), neg=0, invalid=762
- 0153: dt=110.976000, rms=0.651 (0.049%), neg=0, invalid=762
- 0154: dt=110.976000, rms=0.651 (0.046%), neg=0, invalid=762
- 0155: dt=110.976000, rms=0.650 (0.043%), neg=0, invalid=762
- 0156: dt=110.976000, rms=0.650 (0.042%), neg=0, invalid=762
- 0157: dt=110.976000, rms=0.650 (0.043%), neg=0, invalid=762
- 0158: dt=110.976000, rms=0.650 (0.041%), neg=0, invalid=762
- 0159: dt=110.976000, rms=0.649 (0.038%), neg=0, invalid=762
- 0160: dt=110.976000, rms=0.649 (0.038%), neg=0, invalid=762
- 0161: dt=110.976000, rms=0.649 (0.039%), neg=0, invalid=762
- 0162: dt=110.976000, rms=0.649 (0.040%), neg=0, invalid=762
- 0163: dt=110.976000, rms=0.648 (0.041%), neg=0, invalid=762
- 0164: dt=110.976000, rms=0.648 (0.040%), neg=0, invalid=762
- 0165: dt=110.976000, rms=0.648 (0.038%), neg=0, invalid=762
- 0166: dt=110.976000, rms=0.648 (0.037%), neg=0, invalid=762
- 0167: dt=110.976000, rms=0.647 (0.037%), neg=0, invalid=762
- 0168: dt=110.976000, rms=0.647 (0.035%), neg=0, invalid=762
- 0169: dt=110.976000, rms=0.647 (0.033%), neg=0, invalid=762
- 0170: dt=110.976000, rms=0.647 (0.033%), neg=0, invalid=762
- 0171: dt=110.976000, rms=0.646 (0.032%), neg=0, invalid=762
- 0172: dt=110.976000, rms=0.646 (0.032%), neg=0, invalid=762
- 0173: dt=110.976000, rms=0.646 (0.031%), neg=0, invalid=762
- 0174: dt=110.976000, rms=0.646 (0.030%), neg=0, invalid=762
- 0175: dt=110.976000, rms=0.646 (0.028%), neg=0, invalid=762
- 0176: dt=110.976000, rms=0.645 (0.028%), neg=0, invalid=762
- 0177: dt=110.976000, rms=0.645 (0.027%), neg=0, invalid=762
- 0178: dt=110.976000, rms=0.645 (0.026%), neg=0, invalid=762
- 0179: dt=110.976000, rms=0.645 (0.028%), neg=0, invalid=762
- 0180: dt=110.976000, rms=0.645 (0.027%), neg=0, invalid=762
- 0181: dt=110.976000, rms=0.645 (0.025%), neg=0, invalid=762
- 0182: dt=110.976000, rms=0.644 (0.025%), neg=0, invalid=762
- 0183: dt=110.976000, rms=0.644 (0.025%), neg=0, invalid=762
- 0184: dt=110.976000, rms=0.644 (0.025%), neg=0, invalid=762
- 0185: dt=110.976000, rms=0.644 (0.024%), neg=0, invalid=762
- 0186: dt=2071.552000, rms=0.644 (0.014%), neg=0, invalid=762
- 0187: dt=2071.552000, rms=0.644 (-4.863%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.645, neg=0, invalid=762
- 0188: dt=129.472000, rms=0.643 (0.186%), neg=0, invalid=762
- 0189: dt=443.904000, rms=0.643 (0.082%), neg=0, invalid=762
- 0190: dt=92.480000, rms=0.643 (0.027%), neg=0, invalid=762
- 0191: dt=92.480000, rms=0.643 (0.010%), neg=0, invalid=762
- 0192: dt=92.480000, rms=0.642 (0.014%), neg=0, invalid=762
- 0193: dt=92.480000, rms=0.642 (0.018%), neg=0, invalid=762
- 0194: dt=92.480000, rms=0.642 (0.023%), neg=0, invalid=762
- 0195: dt=92.480000, rms=0.642 (0.028%), neg=0, invalid=762
- 0196: dt=92.480000, rms=0.642 (0.028%), neg=0, invalid=762
- 0197: dt=92.480000, rms=0.642 (0.024%), neg=0, invalid=762
- 0198: dt=92.480000, rms=0.642 (0.023%), neg=0, invalid=762
- 0199: dt=517.888000, rms=0.641 (0.009%), neg=0, invalid=762
- 0200: dt=517.888000, rms=0.641 (0.029%), neg=0, invalid=762
- 0201: dt=517.888000, rms=0.641 (-0.117%), neg=0, invalid=762
- 0202: dt=55.488000, rms=0.641 (0.004%), neg=0, invalid=762
- 0203: dt=55.488000, rms=0.641 (-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=0.643, neg=0, invalid=762
- 0204: dt=199.804878, rms=0.636 (1.022%), neg=0, invalid=762
- 0205: dt=103.680000, rms=0.630 (0.922%), neg=0, invalid=762
- 0206: dt=62.208000, rms=0.627 (0.460%), neg=0, invalid=762
- 0207: dt=145.152000, rms=0.624 (0.574%), neg=0, invalid=762
- 0208: dt=62.208000, rms=0.622 (0.353%), neg=0, invalid=762
- 0209: dt=145.152000, rms=0.619 (0.399%), neg=0, invalid=762
- 0210: dt=36.288000, rms=0.617 (0.269%), neg=0, invalid=762
- 0211: dt=497.664000, rms=0.612 (0.811%), neg=0, invalid=762
- 0212: dt=36.288000, rms=0.609 (0.514%), neg=0, invalid=762
- 0213: dt=76.952381, rms=0.608 (0.242%), neg=0, invalid=762
- 0214: dt=82.944000, rms=0.607 (0.146%), neg=0, invalid=762
- 0215: dt=103.680000, rms=0.606 (0.169%), neg=0, invalid=762
- 0216: dt=36.288000, rms=0.605 (0.105%), neg=0, invalid=762
- 0217: dt=580.608000, rms=0.602 (0.611%), neg=0, invalid=762
- 0218: dt=36.288000, rms=0.600 (0.253%), neg=0, invalid=762
- 0219: dt=145.152000, rms=0.599 (0.158%), neg=0, invalid=762
- 0220: dt=36.288000, rms=0.599 (0.092%), neg=0, invalid=762
- 0221: dt=414.720000, rms=0.597 (0.222%), neg=0, invalid=762
- 0222: dt=36.288000, rms=0.596 (0.217%), neg=0, invalid=762
- 0223: dt=145.152000, rms=0.595 (0.144%), neg=0, invalid=762
- 0224: dt=36.288000, rms=0.595 (0.066%), neg=0, invalid=762
- 0225: dt=331.776000, rms=0.594 (0.156%), neg=0, invalid=762
- 0226: dt=36.288000, rms=0.593 (0.145%), neg=0, invalid=762
- 0227: dt=145.152000, rms=0.592 (0.137%), neg=0, invalid=762
- 0228: dt=36.288000, rms=0.592 (0.043%), neg=0, invalid=762
- 0229: dt=36.288000, rms=0.592 (0.029%), neg=0, invalid=762
- 0230: dt=36.288000, rms=0.591 (0.049%), neg=0, invalid=762
- 0231: dt=36.288000, rms=0.591 (0.077%), neg=0, invalid=762
- 0232: dt=36.288000, rms=0.590 (0.104%), neg=0, invalid=762
- 0233: dt=36.288000, rms=0.590 (0.123%), neg=0, invalid=762
- 0234: dt=36.288000, rms=0.589 (0.134%), neg=0, invalid=762
- 0235: dt=36.288000, rms=0.588 (0.138%), neg=0, invalid=762
- 0236: dt=36.288000, rms=0.587 (0.145%), neg=0, invalid=762
- 0237: dt=36.288000, rms=0.586 (0.148%), neg=0, invalid=762
- 0238: dt=36.288000, rms=0.585 (0.155%), neg=0, invalid=762
- 0239: dt=36.288000, rms=0.584 (0.157%), neg=0, invalid=762
- 0240: dt=36.288000, rms=0.583 (0.154%), neg=0, invalid=762
- 0241: dt=36.288000, rms=0.583 (0.155%), neg=0, invalid=762
- 0242: dt=36.288000, rms=0.582 (0.149%), neg=0, invalid=762
- 0243: dt=36.288000, rms=0.581 (0.140%), neg=0, invalid=762
- 0244: dt=36.288000, rms=0.581 (0.014%), neg=0, invalid=762
- 0245: dt=36.288000, rms=0.581 (0.025%), neg=0, invalid=762
- 0246: dt=36.288000, rms=0.580 (0.037%), neg=0, invalid=762
- 0247: dt=36.288000, rms=0.580 (0.049%), neg=0, invalid=762
- 0248: dt=36.288000, rms=0.580 (0.059%), neg=0, invalid=762
- 0249: dt=36.288000, rms=0.579 (0.068%), neg=0, invalid=762
- 0250: dt=36.288000, rms=0.579 (0.071%), neg=0, invalid=762
- 0251: dt=36.288000, rms=0.579 (0.074%), neg=0, invalid=762
- 0252: dt=36.288000, rms=0.578 (0.078%), neg=0, invalid=762
- 0253: dt=36.288000, rms=0.578 (0.082%), neg=0, invalid=762
- 0254: dt=36.288000, rms=0.577 (0.087%), neg=0, invalid=762
- 0255: dt=36.288000, rms=0.577 (0.011%), neg=0, invalid=762
- 0256: dt=36.288000, rms=0.577 (0.022%), neg=0, invalid=762
- 0257: dt=36.288000, rms=0.577 (0.030%), neg=0, invalid=762
- 0258: dt=36.288000, rms=0.577 (0.010%), neg=0, invalid=762
- 0259: dt=36.288000, rms=0.577 (0.010%), neg=0, invalid=762
- 0260: dt=9.072000, rms=0.577 (0.003%), neg=0, invalid=762
- 0261: dt=2.268000, rms=0.577 (0.001%), neg=0, invalid=762
- 0262: dt=2.268000, rms=0.577 (0.001%), neg=0, invalid=762
- 0263: dt=0.141750, rms=0.577 (0.000%), neg=0, invalid=762
- 0264: dt=0.070875, rms=0.577 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.577, neg=0, invalid=762
- 0265: dt=145.152000, rms=0.574 (0.527%), neg=0, invalid=762
- 0266: dt=82.944000, rms=0.574 (0.113%), neg=0, invalid=762
- 0267: dt=124.416000, rms=0.573 (0.107%), neg=0, invalid=762
- 0268: dt=36.288000, rms=0.573 (0.060%), neg=0, invalid=762
- 0269: dt=331.776000, rms=0.572 (0.138%), neg=0, invalid=762
- 0270: dt=36.288000, rms=0.571 (0.091%), neg=0, invalid=762
- 0271: dt=145.152000, rms=0.571 (0.056%), neg=0, invalid=762
- 0272: dt=62.208000, rms=0.571 (0.033%), neg=0, invalid=762
- 0273: dt=62.208000, rms=0.571 (0.031%), neg=0, invalid=762
- 0274: dt=62.208000, rms=0.571 (0.045%), neg=0, invalid=762
- 0275: dt=62.208000, rms=0.570 (0.063%), neg=0, invalid=762
- 0276: dt=62.208000, rms=0.570 (0.072%), neg=0, invalid=762
- 0277: dt=62.208000, rms=0.570 (0.023%), neg=0, invalid=762
- 0278: dt=31.104000, rms=0.570 (0.009%), neg=0, invalid=762
- 0279: dt=25.920000, rms=0.569 (0.009%), neg=0, invalid=762
- 0280: dt=1.620000, rms=0.569 (0.001%), neg=0, invalid=762
- 0281: dt=0.101250, rms=0.569 (0.000%), neg=0, invalid=762
- 0282: dt=0.050625, rms=0.569 (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=0.577, neg=0, invalid=762
- 0283: dt=79.520958, rms=0.570 (1.375%), neg=0, invalid=762
- 0284: dt=55.334917, rms=0.561 (1.575%), neg=0, invalid=762
- 0285: dt=22.456140, rms=0.557 (0.683%), neg=0, invalid=762
- 0286: dt=225.676538, rms=0.547 (1.770%), neg=0, invalid=762
- 0287: dt=23.746479, rms=0.541 (1.082%), neg=0, invalid=762
- 0288: dt=44.800000, rms=0.539 (0.362%), neg=0, invalid=762
- 0289: dt=32.000000, rms=0.538 (0.125%), neg=0, invalid=762
- 0290: dt=44.800000, rms=0.537 (0.183%), neg=0, invalid=762
- 0291: dt=25.600000, rms=0.537 (0.148%), neg=0, invalid=762
- 0292: dt=38.400000, rms=0.536 (0.120%), neg=0, invalid=762
- 0293: dt=32.000000, rms=0.535 (0.150%), neg=0, invalid=762
- 0294: dt=25.600000, rms=0.535 (0.104%), neg=0, invalid=762
- 0295: dt=44.800000, rms=0.534 (0.137%), neg=0, invalid=762
- 0296: dt=2.800000, rms=0.534 (0.016%), neg=0, invalid=762
- 0297: dt=0.087500, rms=0.534 (0.004%), neg=0, invalid=762
- 0298: dt=0.010937, rms=0.534 (0.000%), neg=0, invalid=762
- 0299: dt=0.005469, rms=0.534 (0.000%), neg=0, invalid=762
- 0300: dt=0.002734, rms=0.534 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.534, neg=0, invalid=762
- 0301: dt=32.000000, rms=0.532 (0.437%), neg=0, invalid=762
- 0302: dt=32.000000, rms=0.531 (0.235%), neg=0, invalid=762
- 0303: dt=25.600000, rms=0.530 (0.113%), neg=0, invalid=762
- 0304: dt=32.000000, rms=0.529 (0.134%), neg=0, invalid=762
- 0305: dt=25.600000, rms=0.529 (0.072%), neg=0, invalid=762
- 0306: dt=32.000000, rms=0.528 (0.105%), neg=0, invalid=762
- 0307: dt=19.200000, rms=0.528 (0.058%), neg=0, invalid=762
- 0308: dt=44.800000, rms=0.527 (0.121%), neg=0, invalid=762
- 0309: dt=25.600000, rms=0.527 (0.044%), neg=0, invalid=762
- 0310: dt=25.600000, rms=0.527 (0.085%), neg=0, invalid=762
- 0311: dt=25.600000, rms=0.526 (0.111%), neg=0, invalid=762
- 0312: dt=25.600000, rms=0.525 (0.139%), neg=0, invalid=762
- 0313: dt=25.600000, rms=0.525 (0.077%), neg=0, invalid=762
- 0314: dt=25.600000, rms=0.524 (0.098%), neg=0, invalid=762
- 0315: dt=25.600000, rms=0.524 (0.121%), neg=0, invalid=762
- 0316: dt=25.600000, rms=0.523 (0.187%), neg=0, invalid=762
- 0317: dt=25.600000, rms=0.522 (0.191%), neg=0, invalid=762
- 0318: dt=25.600000, rms=0.521 (0.201%), neg=0, invalid=762
- 0319: dt=25.600000, rms=0.520 (0.191%), neg=0, invalid=762
- 0320: dt=25.600000, rms=0.519 (0.228%), neg=0, invalid=762
- 0321: dt=25.600000, rms=0.519 (0.026%), neg=0, invalid=762
- 0322: dt=25.600000, rms=0.518 (0.053%), neg=0, invalid=762
- 0323: dt=25.600000, rms=0.518 (0.071%), neg=0, invalid=762
- 0324: dt=25.600000, rms=0.517 (0.087%), neg=0, invalid=762
- 0325: dt=25.600000, rms=0.517 (0.094%), neg=0, invalid=762
- 0326: dt=25.600000, rms=0.516 (0.107%), neg=0, invalid=762
- 0327: dt=25.600000, rms=0.516 (0.111%), neg=0, invalid=762
- 0328: dt=25.600000, rms=0.515 (0.117%), neg=0, invalid=762
- 0329: dt=25.600000, rms=0.515 (0.128%), neg=0, invalid=762
- 0330: dt=25.600000, rms=0.514 (0.012%), neg=0, invalid=762
- 0331: dt=25.600000, rms=0.514 (0.035%), neg=0, invalid=762
- 0332: dt=25.600000, rms=0.514 (0.020%), neg=0, invalid=762
- 0333: dt=3.200000, rms=0.514 (-0.002%), neg=0, invalid=762
- 0334: dt=2.800000, rms=0.514 (0.002%), neg=0, invalid=762
- 0335: dt=2.000000, rms=0.514 (0.001%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.534, neg=0, invalid=762
- 0336: dt=0.000000, rms=0.534 (0.127%), neg=0, invalid=762
- 0337: dt=0.000000, rms=0.534 (0.000%), neg=0, invalid=762
- 0338: dt=0.150000, rms=0.534 (-0.017%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.534, neg=0, invalid=762
- 0339: dt=0.000000, rms=0.534 (0.127%), neg=0, invalid=762
- 0340: dt=0.000000, rms=0.534 (0.000%), neg=0, invalid=762
- 0341: dt=0.150000, rms=0.534 (-0.018%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.573, neg=0, invalid=762
- 0342: dt=1.024000, rms=0.571 (0.458%), neg=0, invalid=762
- 0343: dt=0.256000, rms=0.571 (0.013%), neg=0, invalid=762
- 0344: dt=0.256000, rms=0.571 (-0.008%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.571, neg=0, invalid=762
- 0345: dt=0.448000, rms=0.570 (0.161%), neg=0, invalid=762
- 0346: dt=0.112000, rms=0.570 (0.005%), neg=0, invalid=762
- 0347: dt=0.112000, rms=0.570 (0.001%), neg=0, invalid=762
- 0348: dt=0.112000, rms=0.570 (-0.006%), 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=0.522, neg=0, invalid=762
- 0349: dt=0.448000, rms=0.508 (2.724%), neg=0, invalid=762
- 0350: dt=0.448000, rms=0.505 (0.619%), neg=0, invalid=762
- 0351: dt=0.448000, rms=0.503 (0.352%), neg=0, invalid=762
- 0352: dt=0.448000, rms=0.502 (0.216%), neg=0, invalid=762
- 0353: dt=0.466667, rms=0.501 (0.163%), neg=0, invalid=762
- 0354: dt=0.448000, rms=0.500 (0.112%), neg=0, invalid=762
- 0355: dt=0.448000, rms=0.500 (0.092%), neg=0, invalid=762
- 0356: dt=0.448000, rms=0.500 (0.068%), neg=0, invalid=762
- 0357: dt=0.448000, rms=0.499 (0.062%), neg=0, invalid=762
- 0358: dt=0.448000, rms=0.499 (0.047%), neg=0, invalid=762
- 0359: dt=0.448000, rms=0.499 (0.042%), neg=0, invalid=762
- 0360: dt=0.448000, rms=0.498 (0.070%), neg=0, invalid=762
- 0361: dt=0.448000, rms=0.498 (0.085%), neg=0, invalid=762
- 0362: dt=0.448000, rms=0.498 (0.087%), neg=0, invalid=762
- 0363: dt=0.448000, rms=0.497 (0.077%), neg=0, invalid=762
- 0364: dt=0.448000, rms=0.497 (0.057%), neg=0, invalid=762
- 0365: dt=0.448000, rms=0.497 (0.037%), neg=0, invalid=762
- 0366: dt=0.448000, rms=0.497 (-0.009%), neg=0, invalid=762
- 0367: dt=0.000000, rms=0.497 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.498, neg=0, invalid=762
- 0368: dt=0.448000, rms=0.493 (0.964%), neg=0, invalid=762
- 0369: dt=0.448000, rms=0.492 (0.054%), neg=0, invalid=762
- 0370: dt=0.448000, rms=0.492 (0.014%), neg=0, invalid=762
- 0371: dt=0.448000, rms=0.492 (-0.013%), 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=0.491, neg=0, invalid=762
- 0372: dt=0.000000, rms=0.490 (0.158%), neg=0, invalid=762
- 0373: dt=0.000000, rms=0.490 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.491, neg=0, invalid=762
- 0374: dt=295.936000, rms=0.490 (0.194%), neg=0, invalid=762
- 0375: dt=73.984000, rms=0.490 (0.010%), neg=0, invalid=762
- 0376: dt=73.984000, rms=0.490 (0.008%), neg=0, invalid=762
- 0377: dt=73.984000, rms=0.490 (0.007%), neg=0, invalid=762
- 0378: dt=73.984000, rms=0.490 (0.010%), neg=0, invalid=762
- 0379: dt=73.984000, rms=0.490 (0.013%), neg=0, invalid=762
- 0380: dt=73.984000, rms=0.489 (0.014%), neg=0, invalid=762
- 0381: dt=73.984000, rms=0.489 (0.012%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.490, neg=0, invalid=762
- 0382: dt=36.288000, rms=0.489 (0.200%), neg=0, invalid=762
- 0383: dt=36.288000, rms=0.489 (0.022%), neg=0, invalid=762
- 0384: dt=36.288000, rms=0.489 (0.014%), neg=0, invalid=762
- 0385: dt=36.288000, rms=0.489 (-0.003%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.490, neg=0, invalid=762
- 0386: dt=124.416000, rms=0.488 (0.457%), neg=0, invalid=762
- 0387: dt=36.288000, rms=0.487 (0.103%), neg=0, invalid=762
- 0388: dt=36.288000, rms=0.487 (0.045%), neg=0, invalid=762
- 0389: dt=36.288000, rms=0.487 (0.063%), neg=0, invalid=762
- 0390: dt=36.288000, rms=0.486 (0.079%), neg=0, invalid=762
- 0391: dt=36.288000, rms=0.486 (0.096%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0392: dt=36.288000, rms=0.485 (0.106%), neg=0, invalid=762
- 0393: dt=36.288000, rms=0.485 (0.096%), neg=0, invalid=762
- 0394: dt=36.288000, rms=0.484 (0.086%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0395: dt=124.416000, rms=0.484 (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=0.485, neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 2 iterations, nbhd size=0, neg = 0
- 0396: dt=44.800000, rms=0.482 (0.665%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 10 iterations, nbhd size=1, neg = 0
- 0397: dt=38.400000, rms=0.480 (0.379%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0398: dt=25.474510, rms=0.479 (0.267%), neg=0, invalid=762
- 0399: dt=23.200000, rms=0.478 (0.147%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0400: dt=23.200000, rms=0.477 (0.163%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 3 iterations, nbhd size=0, neg = 0
- 0401: dt=23.200000, rms=0.476 (0.224%), neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 2 iterations, nbhd size=0, neg = 0
- 0402: dt=23.200000, rms=0.475 (0.186%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 9 iterations, nbhd size=1, neg = 0
- 0403: dt=23.200000, rms=0.474 (0.261%), neg=0, invalid=762
- iter 0, gcam->neg = 17
- after 11 iterations, nbhd size=1, neg = 0
- 0404: dt=23.200000, rms=0.473 (0.205%), neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 10 iterations, nbhd size=1, neg = 0
- 0405: dt=23.200000, rms=0.472 (0.200%), neg=0, invalid=762
- iter 0, gcam->neg = 13
- after 14 iterations, nbhd size=1, neg = 0
- 0406: dt=23.200000, rms=0.472 (0.119%), neg=0, invalid=762
- iter 0, gcam->neg = 8
- after 4 iterations, nbhd size=0, neg = 0
- 0407: dt=23.200000, rms=0.471 (0.192%), neg=0, invalid=762
- iter 0, gcam->neg = 8
- after 3 iterations, nbhd size=0, neg = 0
- 0408: dt=23.200000, rms=0.470 (0.191%), neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 8 iterations, nbhd size=1, neg = 0
- 0409: dt=23.200000, rms=0.469 (0.180%), neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 8 iterations, nbhd size=1, neg = 0
- 0410: dt=23.200000, rms=0.469 (0.114%), neg=0, invalid=762
- iter 0, gcam->neg = 6
- after 1 iterations, nbhd size=0, neg = 0
- 0411: dt=23.200000, rms=0.468 (0.155%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 1 iterations, nbhd size=0, neg = 0
- 0412: dt=23.200000, rms=0.467 (0.154%), neg=0, invalid=762
- iter 0, gcam->neg = 10
- after 10 iterations, nbhd size=1, neg = 0
- 0413: dt=23.200000, rms=0.467 (0.121%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0414: dt=23.200000, rms=0.466 (0.066%), neg=0, invalid=762
- 0415: dt=11.200000, rms=0.466 (0.074%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 2 iterations, nbhd size=0, neg = 0
- 0416: dt=76.800000, rms=0.466 (0.063%), neg=0, invalid=762
- 0417: dt=76.800000, rms=0.466 (-0.341%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.467, neg=0, invalid=762
- 0418: dt=38.400000, rms=0.463 (0.709%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0419: dt=25.600000, rms=0.462 (0.185%), neg=0, invalid=762
- 0420: dt=25.600000, rms=0.462 (0.147%), neg=0, invalid=762
- 0421: dt=25.600000, rms=0.461 (0.181%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0422: dt=25.600000, rms=0.460 (0.096%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 4 iterations, nbhd size=0, neg = 0
- 0423: dt=25.600000, rms=0.460 (0.157%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 2 iterations, nbhd size=0, neg = 0
- 0424: dt=25.600000, rms=0.459 (0.043%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 7 iterations, nbhd size=1, neg = 0
- 0425: dt=25.600000, rms=0.459 (0.034%), neg=0, invalid=762
- 0426: dt=11.200000, rms=0.459 (0.052%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0427: dt=44.800000, rms=0.459 (0.066%), neg=0, invalid=762
- 0428: dt=11.200000, rms=0.459 (0.016%), neg=0, invalid=762
- 0429: dt=11.200000, rms=0.459 (0.010%), neg=0, invalid=762
- 0430: dt=11.200000, rms=0.459 (0.015%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0431: dt=11.200000, rms=0.458 (0.023%), neg=0, invalid=762
- 0432: dt=11.200000, rms=0.458 (0.025%), neg=0, invalid=762
- 0433: dt=11.200000, rms=0.458 (0.021%), neg=0, invalid=762
- 0434: dt=11.200000, rms=0.458 (0.025%), neg=0, invalid=762
- 0435: dt=11.200000, rms=0.458 (0.022%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.465, neg=0, invalid=762
- 0436: dt=0.000000, rms=0.464 (0.173%), neg=0, invalid=762
- 0437: 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=0.465, neg=0, invalid=762
- 0438: dt=2.304000, rms=0.464 (0.187%), neg=0, invalid=762
- 0439: dt=1.008000, rms=0.464 (0.005%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0440: dt=1.008000, rms=0.464 (-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=0.475, neg=0, invalid=762
- 0441: dt=1.280000, rms=0.474 (0.352%), neg=0, invalid=762
- 0442: dt=0.112000, rms=0.474 (0.002%), neg=0, invalid=762
- 0443: dt=0.112000, rms=0.474 (0.004%), neg=0, invalid=762
- 0444: dt=0.112000, rms=0.474 (-0.006%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.474, neg=0, invalid=762
- 0445: dt=1.536000, rms=0.473 (0.336%), neg=0, invalid=762
- 0446: dt=0.448000, rms=0.473 (0.014%), neg=0, invalid=762
- 0447: dt=0.448000, rms=0.473 (0.005%), neg=0, invalid=762
- 0448: dt=0.448000, rms=0.473 (-0.014%), 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=0.465, neg=0, invalid=762
- iter 0, gcam->neg = 709
- after 16 iterations, nbhd size=1, neg = 0
- 0449: dt=2.292771, rms=0.434 (6.731%), neg=0, invalid=762
- 0450: dt=0.096000, rms=0.434 (0.075%), neg=0, invalid=762
- 0451: dt=0.096000, rms=0.434 (-0.063%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.434, neg=0, invalid=762
- 0452: dt=0.080000, rms=0.433 (0.254%), neg=0, invalid=762
- 0453: dt=0.000000, rms=0.433 (0.001%), neg=0, invalid=762
- 0454: dt=0.050000, rms=0.433 (-0.017%), 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=0.418, neg=0, invalid=762
- 0455: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.418, neg=0, invalid=762
- 0456: dt=55.488000, rms=0.418 (0.005%), neg=0, invalid=762
- 0457: dt=92.480000, rms=0.418 (0.002%), neg=0, invalid=762
- 0458: dt=92.480000, rms=0.418 (0.001%), neg=0, invalid=762
- 0459: dt=92.480000, rms=0.418 (0.001%), neg=0, invalid=762
- 0460: dt=92.480000, rms=0.418 (0.001%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.418, neg=0, invalid=762
- 0461: dt=-0.001465, rms=0.418 (0.000%), neg=0, invalid=762
- 0462: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.418, neg=0, invalid=762
- 0463: dt=145.152000, rms=0.418 (0.080%), neg=0, invalid=762
- 0464: dt=145.152000, rms=0.418 (0.050%), neg=0, invalid=762
- 0465: dt=145.152000, rms=0.418 (-0.013%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.419, neg=0, invalid=762
- 0466: dt=11.200000, rms=0.418 (0.097%), neg=0, invalid=762
- 0467: dt=11.200000, rms=0.418 (0.039%), neg=0, invalid=762
- 0468: dt=11.200000, rms=0.418 (0.015%), neg=0, invalid=762
- 0469: dt=11.200000, rms=0.418 (-0.028%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.418, neg=0, invalid=762
- 0470: dt=60.595745, rms=0.416 (0.512%), neg=0, invalid=762
- 0471: dt=25.600000, rms=0.415 (0.255%), neg=0, invalid=762
- 0472: dt=44.800000, rms=0.414 (0.138%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 9 iterations, nbhd size=1, neg = 0
- 0473: dt=44.800000, rms=0.414 (0.036%), neg=0, invalid=762
- 0474: dt=44.800000, rms=0.413 (0.321%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0475: dt=44.800000, rms=0.412 (0.144%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 9 iterations, nbhd size=1, neg = 0
- 0476: dt=44.800000, rms=0.411 (0.248%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 1 iterations, nbhd size=0, neg = 0
- 0477: dt=44.800000, rms=0.410 (0.221%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0478: dt=44.800000, rms=0.410 (0.137%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 10 iterations, nbhd size=1, neg = 0
- 0479: dt=44.800000, rms=0.409 (0.201%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 11 iterations, nbhd size=1, neg = 0
- 0480: dt=44.800000, rms=0.408 (0.085%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0481: dt=44.800000, rms=0.408 (0.121%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 3 iterations, nbhd size=0, neg = 0
- 0482: dt=44.800000, rms=0.408 (0.119%), neg=0, invalid=762
- 0483: dt=25.600000, rms=0.407 (0.014%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 6 iterations, nbhd size=0, neg = 0
- 0484: dt=25.600000, rms=0.407 (0.006%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 3 iterations, nbhd size=0, neg = 0
- 0485: dt=25.600000, rms=0.407 (0.009%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0486: dt=25.600000, rms=0.407 (0.010%), neg=0, invalid=762
- 0487: dt=25.600000, rms=0.407 (0.004%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0488: dt=25.600000, rms=0.407 (0.002%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.412, neg=0, invalid=762
- 0489: dt=0.000246, rms=0.412 (0.000%), neg=0, invalid=762
- 0490: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.412, neg=0, invalid=762
- 0491: dt=1.500000, rms=0.412 (0.005%), neg=0, invalid=762
- 0492: dt=0.750000, rms=0.412 (0.001%), neg=0, invalid=762
- 0493: dt=0.750000, rms=0.412 (-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=0.421, neg=0, invalid=762
- 0494: dt=0.000000, rms=0.421 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.421, neg=0, invalid=762
- 0495: dt=0.000000, rms=0.421 (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=0.406, neg=0, invalid=762
- iter 0, gcam->neg = 638
- after 20 iterations, nbhd size=1, neg = 0
- 0496: dt=1.280000, rms=0.397 (2.251%), neg=0, invalid=762
- 0497: dt=0.000013, rms=0.397 (0.000%), neg=0, invalid=762
- 0498: dt=0.000013, rms=0.397 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.397, neg=0, invalid=762
- 0499: dt=0.096000, rms=0.396 (0.045%), neg=0, invalid=762
- 0500: dt=0.028000, rms=0.396 (0.005%), neg=0, invalid=762
- 0501: dt=0.028000, rms=0.396 (0.003%), neg=0, invalid=762
- 0502: dt=0.028000, rms=0.396 (-0.005%), neg=0, invalid=762
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- mri_ca_register took 2 hours, 53 minutes and 53 seconds.
- mri_ca_register utimesec 11318.304356
- mri_ca_register stimesec 11.715219
- mri_ca_register ru_maxrss 1343100
- mri_ca_register ru_ixrss 0
- mri_ca_register ru_idrss 0
- mri_ca_register ru_isrss 0
- mri_ca_register ru_minflt 4785063
- mri_ca_register ru_majflt 0
- mri_ca_register ru_nswap 0
- mri_ca_register ru_inblock 0
- mri_ca_register ru_oublock 63592
- mri_ca_register ru_msgsnd 0
- mri_ca_register ru_msgrcv 0
- mri_ca_register ru_nsignals 0
- mri_ca_register ru_nvcsw 10632
- mri_ca_register ru_nivcsw 36667
- FSRUNTIME@ mri_ca_register 2.8981 hours 2 threads
- #--------------------------------------
- #@# SubCort Seg Sun Oct 8 06:33:35 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-114
- 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-6.0.0/0050490/mri
- mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz
- == Number of threads available to mri_ca_label for OpenMP = 2 ==
- relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
- using Gibbs prior factor = 0.500
- renormalizing sequences with structure alignment, equivalent to:
- -renormalize
- -renormalize_mean 0.500
- -regularize 0.500
- reading 1 input volumes
- reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
- reading input volume from norm.mgz
- average std[0] = 7.3
- reading transform from transforms/talairach.m3z
- setting orig areas to linear transform determinant scaled 7.14
- 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 = 0.09531 (16)
- Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (1326 voxels, overlap=0.741)
- Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (1326 voxels, peak = 15), gca=15.3
- gca peak = 0.17677 (13)
- mri peak = 0.09173 (18)
- Right_Lateral_Ventricle (43): linear fit = 1.20 x + 0.0 (1316 voxels, overlap=0.866)
- Right_Lateral_Ventricle (43): linear fit = 1.20 x + 0.0 (1316 voxels, peak = 16), gca=15.5
- gca peak = 0.28129 (95)
- mri peak = 0.09444 (91)
- Right_Pallidum (52): linear fit = 0.96 x + 0.0 (715 voxels, overlap=1.015)
- Right_Pallidum (52): linear fit = 0.96 x + 0.0 (715 voxels, peak = 92), gca=91.7
- gca peak = 0.16930 (96)
- mri peak = 0.10200 (95)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (798 voxels, overlap=1.011)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (798 voxels, peak = 96), gca=95.5
- gca peak = 0.24553 (55)
- mri peak = 0.09026 (60)
- Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (981 voxels, overlap=1.009)
- Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (981 voxels, peak = 59), gca=59.1
- gca peak = 0.30264 (59)
- mri peak = 0.09751 (63)
- Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (968 voxels, overlap=1.009)
- Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (968 voxels, peak = 62), gca=61.7
- gca peak = 0.07580 (103)
- mri peak = 0.12302 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (44092 voxels, overlap=0.597)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (44092 voxels, peak = 105), gca=104.5
- gca peak = 0.07714 (104)
- mri peak = 0.10848 (105)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46449 voxels, overlap=0.612)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46449 voxels, peak = 107), gca=106.6
- gca peak = 0.09712 (58)
- mri peak = 0.04938 (52)
- Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (38278 voxels, overlap=0.978)
- Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (38278 voxels, peak = 56), gca=56.0
- gca peak = 0.11620 (58)
- mri peak = 0.04476 (52)
- Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (37424 voxels, overlap=0.984)
- Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (37424 voxels, peak = 56), gca=56.0
- gca peak = 0.30970 (66)
- mri peak = 0.09771 (74)
- Right_Caudate (50): linear fit = 1.07 x + 0.0 (1269 voxels, overlap=1.008)
- Right_Caudate (50): linear fit = 1.07 x + 0.0 (1269 voxels, peak = 70), gca=70.3
- gca peak = 0.15280 (69)
- mri peak = 0.10579 (72)
- Left_Caudate (11): linear fit = 0.96 x + 0.0 (1190 voxels, overlap=0.937)
- Left_Caudate (11): linear fit = 0.96 x + 0.0 (1190 voxels, peak = 67), gca=66.6
- gca peak = 0.13902 (56)
- mri peak = 0.04663 (59)
- Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (26156 voxels, overlap=0.984)
- Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (26156 voxels, peak = 59), gca=58.5
- gca peak = 0.14777 (55)
- mri peak = 0.05413 (59)
- Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (30314 voxels, overlap=0.987)
- Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (30314 voxels, peak = 59), gca=58.6
- gca peak = 0.16765 (84)
- mri peak = 0.09096 (85)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6077 voxels, overlap=0.865)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6077 voxels, peak = 89), gca=88.6
- gca peak = 0.18739 (84)
- mri peak = 0.09687 (85)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6138 voxels, overlap=0.862)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6138 voxels, peak = 87), gca=86.9
- gca peak = 0.29869 (57)
- mri peak = 0.08256 (59)
- Left_Amygdala (18): linear fit = 1.04 x + 0.0 (591 voxels, overlap=1.031)
- Left_Amygdala (18): linear fit = 1.04 x + 0.0 (591 voxels, peak = 60), gca=59.6
- gca peak = 0.33601 (57)
- mri peak = 0.11715 (62)
- Right_Amygdala (54): linear fit = 1.04 x + 0.0 (468 voxels, overlap=0.999)
- Right_Amygdala (54): linear fit = 1.04 x + 0.0 (468 voxels, peak = 60), gca=59.6
- gca peak = 0.11131 (90)
- mri peak = 0.06079 (90)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5210 voxels, overlap=0.953)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5210 voxels, peak = 91), gca=91.3
- gca peak = 0.11793 (83)
- mri peak = 0.06680 (90)
- Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4970 voxels, overlap=0.979)
- Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4970 voxels, peak = 87), gca=86.7
- gca peak = 0.08324 (81)
- mri peak = 0.07906 (81)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2754 voxels, overlap=0.905)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2754 voxels, peak = 81), gca=81.0
- gca peak = 0.10360 (77)
- mri peak = 0.07630 (80)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (2824 voxels, overlap=0.984)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (2824 voxels, peak = 76), gca=75.8
- gca peak = 0.08424 (78)
- mri peak = 0.08097 (87)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (12302 voxels, overlap=0.476)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (12302 voxels, peak = 85), gca=85.4
- gca peak = 0.12631 (89)
- mri peak = 0.07186 (92)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1436 voxels, overlap=0.786)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1436 voxels, peak = 97), gca=96.6
- gca peak = 0.14500 (87)
- mri peak = 0.06384 (93)
- Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1557 voxels, overlap=0.844)
- Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1557 voxels, peak = 94), gca=93.5
- gca peak = 0.14975 (24)
- mri peak = 0.12633 (18)
- gca peak = 0.19357 (14)
- mri peak = 0.12961 (18)
- Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (279 voxels, overlap=0.815)
- Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (279 voxels, peak = 14), gca=14.5
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.16825 (27)
- gca peak Left_Thalamus = 1.00000 (94)
- gca peak Third_Ventricle = 0.14975 (24)
- gca peak CSF = 0.23379 (36)
- gca peak Left_Accumbens_area = 0.70037 (62)
- gca peak Left_undetermined = 1.00000 (26)
- gca peak Left_vessel = 0.75997 (52)
- gca peak Left_choroid_plexus = 0.12089 (35)
- gca peak Right_Inf_Lat_Vent = 0.24655 (23)
- gca peak Right_Accumbens_area = 0.45042 (65)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14516 (37)
- gca peak Fifth_Ventricle = 0.65475 (32)
- gca peak WM_hypointensities = 0.07854 (76)
- gca peak non_WM_hypointensities = 0.08491 (43)
- gca peak Optic_Chiasm = 0.71127 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.02 x + 0.0
- estimating mean wm scale to be 1.02 x + 0.0
- estimating mean csf scale to be 1.00 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.18464 (14)
- mri peak = 0.09531 (16)
- Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (1326 voxels, overlap=0.958)
- Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (1326 voxels, peak = 14), gca=14.5
- gca peak = 0.16350 (15)
- mri peak = 0.09173 (18)
- Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (1316 voxels, overlap=0.710)
- Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (1316 voxels, peak = 16), gca=15.5
- gca peak = 0.26422 (90)
- mri peak = 0.09444 (91)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (715 voxels, overlap=1.011)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (715 voxels, peak = 90), gca=89.6
- gca peak = 0.18432 (96)
- mri peak = 0.10200 (95)
- Left_Pallidum (13): linear fit = 1.01 x + 0.0 (798 voxels, overlap=1.009)
- Left_Pallidum (13): linear fit = 1.01 x + 0.0 (798 voxels, peak = 97), gca=97.4
- gca peak = 0.27675 (60)
- mri peak = 0.09026 (60)
- Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (981 voxels, overlap=1.005)
- Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (981 voxels, peak = 59), gca=59.1
- gca peak = 0.31447 (59)
- mri peak = 0.09751 (63)
- Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (968 voxels, overlap=1.007)
- Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (968 voxels, peak = 60), gca=59.9
- gca peak = 0.07772 (104)
- mri peak = 0.12302 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (44092 voxels, overlap=0.666)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (44092 voxels, peak = 104), gca=104.0
- gca peak = 0.07686 (107)
- mri peak = 0.10848 (105)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46449 voxels, overlap=0.722)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46449 voxels, peak = 106), gca=106.5
- gca peak = 0.10057 (56)
- mri peak = 0.04938 (52)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (38278 voxels, overlap=0.989)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (38278 voxels, peak = 57), gca=57.4
- gca peak = 0.11969 (56)
- mri peak = 0.04476 (52)
- Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (37424 voxels, overlap=0.973)
- Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (37424 voxels, peak = 59), gca=58.5
- gca peak = 0.26195 (71)
- mri peak = 0.09771 (74)
- Right_Caudate (50): linear fit = 1.03 x + 0.0 (1269 voxels, overlap=1.008)
- Right_Caudate (50): linear fit = 1.03 x + 0.0 (1269 voxels, peak = 73), gca=73.5
- gca peak = 0.14125 (66)
- mri peak = 0.10579 (72)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (1190 voxels, overlap=1.000)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (1190 voxels, peak = 66), gca=66.0
- gca peak = 0.13225 (57)
- mri peak = 0.04663 (59)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (26156 voxels, overlap=0.999)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (26156 voxels, peak = 58), gca=58.4
- gca peak = 0.13860 (58)
- mri peak = 0.05413 (59)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (30314 voxels, overlap=0.998)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (30314 voxels, peak = 59), gca=59.4
- gca peak = 0.16050 (89)
- mri peak = 0.09096 (85)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6077 voxels, overlap=0.979)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6077 voxels, peak = 89), gca=88.6
- gca peak = 0.18302 (87)
- mri peak = 0.09687 (85)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6138 voxels, overlap=0.963)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6138 voxels, peak = 87), gca=86.6
- gca peak = 0.26844 (61)
- mri peak = 0.08256 (59)
- Left_Amygdala (18): linear fit = 1.02 x + 0.0 (591 voxels, overlap=1.020)
- Left_Amygdala (18): linear fit = 1.02 x + 0.0 (591 voxels, peak = 63), gca=62.5
- gca peak = 0.31426 (60)
- mri peak = 0.11715 (62)
- Right_Amygdala (54): linear fit = 1.02 x + 0.0 (468 voxels, overlap=1.024)
- Right_Amygdala (54): linear fit = 1.02 x + 0.0 (468 voxels, peak = 62), gca=61.5
- gca peak = 0.11210 (90)
- mri peak = 0.06079 (90)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5210 voxels, overlap=0.973)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5210 voxels, peak = 90), gca=89.6
- gca peak = 0.09869 (90)
- mri peak = 0.06680 (90)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4970 voxels, overlap=0.996)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4970 voxels, peak = 92), gca=92.2
- gca peak = 0.08313 (81)
- mri peak = 0.07906 (81)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2754 voxels, overlap=0.905)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2754 voxels, peak = 81), gca=81.0
- gca peak = 0.09873 (76)
- mri peak = 0.07630 (80)
- Right_Putamen (51): linear fit = 1.02 x + 0.0 (2824 voxels, overlap=0.938)
- Right_Putamen (51): linear fit = 1.02 x + 0.0 (2824 voxels, peak = 78), gca=77.9
- gca peak = 0.07843 (86)
- mri peak = 0.08097 (87)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (12302 voxels, overlap=0.767)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (12302 voxels, peak = 86), gca=86.4
- gca peak = 0.10980 (96)
- mri peak = 0.07186 (92)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1436 voxels, overlap=0.879)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1436 voxels, peak = 96), gca=95.5
- gca peak = 0.17061 (92)
- mri peak = 0.06384 (93)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1557 voxels, overlap=0.934)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1557 voxels, peak = 92), gca=91.5
- gca peak = 0.16923 (26)
- mri peak = 0.12633 (18)
- gca peak = 0.18343 (17)
- mri peak = 0.12961 (18)
- Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (279 voxels, overlap=0.796)
- Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (279 voxels, peak = 17), gca=17.4
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.16507 (28)
- gca peak Left_Thalamus = 1.00000 (96)
- gca peak Third_Ventricle = 0.16923 (26)
- gca peak CSF = 0.23651 (36)
- gca peak Left_Accumbens_area = 0.81130 (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 = 0.24205 (25)
- gca peak Right_Accumbens_area = 0.29950 (69)
- 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 = 0.07134 (78)
- gca peak non_WM_hypointensities = 0.08683 (44)
- gca peak Optic_Chiasm = 0.70610 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.02 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 1.03 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
- 63163 voxels changed in iteration 0 of unlikely voxel relabeling
- 198 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
- 35010 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels)
- 368 hippocampal voxels changed.
- 0 amygdala voxels changed.
- pass 1: 71539 changed. image ll: -2.124, PF=0.500
- pass 2: 20395 changed. image ll: -2.124, PF=0.500
- pass 3: 6675 changed.
- pass 4: 2379 changed.
- 37445 voxels changed in iteration 0 of unlikely voxel relabeling
- 192 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
- 6548 voxels changed in iteration 0 of unlikely voxel relabeling
- 77 voxels changed in iteration 1 of unlikely voxel relabeling
- 2 voxels changed in iteration 2 of unlikely voxel relabeling
- 1 voxels changed in iteration 3 of unlikely voxel relabeling
- 0 voxels changed in iteration 4 of unlikely voxel relabeling
- 5766 voxels changed in iteration 0 of unlikely voxel relabeling
- 47 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
- 4782 voxels changed in iteration 0 of unlikely voxel relabeling
- 24 voxels changed in iteration 1 of unlikely voxel relabeling
- 0 voxels changed in iteration 2 of unlikely voxel relabeling
- MRItoUCHAR: min=0, max=85
- MRItoUCHAR: converting to UCHAR
- writing labeled volume to aseg.auto_noCCseg.mgz
- mri_ca_label utimesec 4547.695645
- mri_ca_label stimesec 5.390180
- mri_ca_label ru_maxrss 2100388
- mri_ca_label ru_ixrss 0
- mri_ca_label ru_idrss 0
- mri_ca_label ru_isrss 0
- mri_ca_label ru_minflt 829856
- mri_ca_label ru_majflt 0
- mri_ca_label ru_nswap 0
- mri_ca_label ru_inblock 0
- mri_ca_label ru_oublock 512
- mri_ca_label ru_msgsnd 0
- mri_ca_label ru_msgrcv 0
- mri_ca_label ru_nsignals 0
- mri_ca_label ru_nvcsw 381
- mri_ca_label ru_nivcsw 15328
- auto-labeling took 75 minutes and 6 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/transforms/cc_up.lta 0050490
- 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-6.0.0/0050490/mri/transforms/cc_up.lta
- reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aseg.auto_noCCseg.mgz
- reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/norm.mgz
- 53197 voxels in left wm, 58180 in right wm, xrange [119, 130]
- searching rotation angles z=[-7 7], y=[-4 10]
-
searching scale 1 Z rot -6.8
searching scale 1 Z rot -6.6
searching scale 1 Z rot -6.3
searching scale 1 Z rot -6.1
searching scale 1 Z rot -5.8
searching scale 1 Z rot -5.6
searching scale 1 Z rot -5.3
searching scale 1 Z rot -5.1
searching scale 1 Z rot -4.8
searching scale 1 Z rot -4.6
searching scale 1 Z rot -4.3
searching scale 1 Z rot -4.1
searching scale 1 Z rot -3.8
searching scale 1 Z rot -3.6
searching scale 1 Z rot -3.3
searching scale 1 Z rot -3.1
searching scale 1 Z rot -2.8
searching scale 1 Z rot -2.6
searching scale 1 Z rot -2.3
searching scale 1 Z rot -2.1
searching scale 1 Z rot -1.8
searching scale 1 Z rot -1.6
searching scale 1 Z rot -1.3
searching scale 1 Z rot -1.1
searching scale 1 Z rot -0.8
searching scale 1 Z rot -0.6
searching scale 1 Z rot -0.3
searching scale 1 Z rot -0.1
searching scale 1 Z rot 0.2
searching scale 1 Z rot 0.4
searching scale 1 Z rot 0.7
searching scale 1 Z rot 0.9
searching scale 1 Z rot 1.2
searching scale 1 Z rot 1.4
searching scale 1 Z rot 1.7
searching scale 1 Z rot 1.9
searching scale 1 Z rot 2.2
searching scale 1 Z rot 2.4
searching scale 1 Z rot 2.7
searching scale 1 Z rot 2.9
searching scale 1 Z rot 3.2
searching scale 1 Z rot 3.4
searching scale 1 Z rot 3.7
searching scale 1 Z rot 3.9
searching scale 1 Z rot 4.2
searching scale 1 Z rot 4.4
searching scale 1 Z rot 4.7
searching scale 1 Z rot 4.9
searching scale 1 Z rot 5.2
searching scale 1 Z rot 5.4
searching scale 1 Z rot 5.7
searching scale 1 Z rot 5.9
searching scale 1 Z rot 6.2
searching scale 1 Z rot 6.4
searching scale 1 Z rot 6.7
searching scale 1 Z rot 6.9
searching scale 1 Z rot 7.2 global minimum found at slice 125.0, rotations (3.04, 0.41)
- final transformation (x=125.0, yr=3.037, zr=0.410):
- 0.99857 -0.00716 0.05298 -1.43615;
- 0.00715 0.99997 0.00038 39.07113;
- -0.05298 -0.00000 0.99860 35.76150;
- 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 88 99
- eigenvectors:
- 0.00004 -0.00129 1.00000;
- -0.08572 -0.99632 -0.00128;
- 0.99632 -0.08572 -0.00015;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aseg.auto.mgz...
- corpus callosum segmentation took 1.3 minutes
- #--------------------------------------
- #@# Merge ASeg Sun Oct 8 07:49:58 CEST 2017
- cp aseg.auto.mgz aseg.presurf.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Sun Oct 8 07:49:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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...
- 1473 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 110
- white matter peak found at 109
- gm peak at 58 (58), valley at 0 (-1)
- csf peak at 29, setting threshold to 48
- 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 58 (58), valley at 0 (-1)
- csf peak at 29, setting threshold to 48
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 4 minutes and 23 seconds.
- #--------------------------------------------
- #@# Mask BFS Sun Oct 8 07:54:24 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1746576 voxels in mask (pct= 10.41)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Sun Oct 8 07:54:28 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 (105.0): 105.5 +- 4.8 [79.0 --> 125.0]
- GM (70.0) : 68.5 +- 9.1 [30.0 --> 95.0]
- setting bottom of white matter range to 77.6
- setting top of gray matter range to 86.7
- 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...
- 5980 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 5134 filled
- 496 bright non-wm voxels segmented.
- 3154 diagonally connected voxels added...
- white matter segmentation took 1.6 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 0.82 minutes
- reading wm segmentation from wm.seg.mgz...
- 307 voxels added to wm to prevent paths from MTL structures to cortex
- 3105 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 50593 voxels turned on, 47427 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+): 11 found - 11 modified | TOTAL: 11
- pass 2 (xy+): 0 found - 11 modified | TOTAL: 11
- pass 1 (xy-): 17 found - 17 modified | TOTAL: 28
- pass 2 (xy-): 0 found - 17 modified | TOTAL: 28
- pass 1 (yz+): 9 found - 9 modified | TOTAL: 37
- pass 2 (yz+): 0 found - 9 modified | TOTAL: 37
- pass 1 (yz-): 18 found - 18 modified | TOTAL: 55
- pass 2 (yz-): 0 found - 18 modified | TOTAL: 55
- pass 1 (xz+): 7 found - 7 modified | TOTAL: 62
- pass 2 (xz+): 0 found - 7 modified | TOTAL: 62
- pass 1 (xz-): 10 found - 10 modified | TOTAL: 72
- pass 2 (xz-): 0 found - 10 modified | TOTAL: 72
- Iteration Number : 1
- pass 1 (+++): 7 found - 7 modified | TOTAL: 7
- pass 2 (+++): 0 found - 7 modified | TOTAL: 7
- pass 1 (+++): 13 found - 13 modified | TOTAL: 20
- pass 2 (+++): 0 found - 13 modified | TOTAL: 20
- pass 1 (+++): 6 found - 6 modified | TOTAL: 26
- pass 2 (+++): 0 found - 6 modified | TOTAL: 26
- pass 1 (+++): 20 found - 20 modified | TOTAL: 46
- pass 2 (+++): 0 found - 20 modified | TOTAL: 46
- Iteration Number : 1
- pass 1 (++): 98 found - 98 modified | TOTAL: 98
- pass 2 (++): 0 found - 98 modified | TOTAL: 98
- pass 1 (+-): 57 found - 57 modified | TOTAL: 155
- pass 2 (+-): 0 found - 57 modified | TOTAL: 155
- pass 1 (--): 99 found - 99 modified | TOTAL: 254
- pass 2 (--): 0 found - 99 modified | TOTAL: 254
- pass 1 (-+): 61 found - 61 modified | TOTAL: 315
- pass 2 (-+): 0 found - 61 modified | TOTAL: 315
- Iteration Number : 2
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 3 found - 3 modified | TOTAL: 6
- pass 2 (xy-): 0 found - 3 modified | TOTAL: 6
- pass 1 (yz+): 5 found - 5 modified | TOTAL: 11
- pass 2 (yz+): 0 found - 5 modified | TOTAL: 11
- pass 1 (yz-): 3 found - 3 modified | TOTAL: 14
- pass 2 (yz-): 0 found - 3 modified | TOTAL: 14
- pass 1 (xz+): 6 found - 6 modified | TOTAL: 20
- pass 2 (xz+): 0 found - 6 modified | TOTAL: 20
- pass 1 (xz-): 2 found - 2 modified | TOTAL: 22
- pass 2 (xz-): 0 found - 2 modified | TOTAL: 22
- 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 (+-): 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 (-+): 0 found - 0 modified | TOTAL: 7
- Iteration Number : 3
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 2
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 2
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 464 (out of 598344: 0.077547)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Sun Oct 8 07:57:01 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
- logging cutting plane coordinates to ../scripts/ponscc.cut.log...
- INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
- using segmentation aseg.auto_noCCseg.mgz...
- reading input volume...done.
- searching for cutting planes...voxel to talairach voxel transform
- 1.04809 -0.00502 0.08632 -13.30034;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86054;
- 0.00000 0.00000 0.00000 1.00000;
- voxel to talairach voxel transform
- 1.04809 -0.00502 0.08632 -13.30034;
- -0.01272 1.07313 0.26244 -19.71896;
- -0.11331 -0.22127 0.93285 46.86054;
- 0.00000 0.00000 0.00000 1.00000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1143 (min = 350, max = 1400), aspect = 0.60 (min = 0.10, max = 0.75)
- no need to search
- using seed (126, 114, 89), TAL = (2.0, -39.0, 14.0)
- talairach voxel to voxel transform
- 0.94490 -0.01286 -0.08382 16.24174;
- -0.01594 0.88098 -0.24637 28.70499;
- 0.11099 0.20741 1.00337 -41.45222;
- 0.00000 0.00000 0.00000 1.00000;
- segmentation indicates cc at (126, 114, 89) --> (2.0, -39.0, 14.0)
- done.
- writing output to filled.mgz...
- filling took 1.3 minutes
- talairach cc position changed to (2.00, -39.00, 14.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, -39.00, 14.00) SRC: (109.36, 105.49, 83.48)
- search lh wm seed point around talairach space (-16.00, -39.00, 14.00), SRC: (143.38, 104.91, 87.47)
- 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 07:58:21 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 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 (xz+): 1 found - 1 modified | TOTAL: 2
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 2
- pass 1 (xz-): 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 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 2 (out of 286167: 0.000699)
- 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 30: 665 vertices, 768 faces
- slice 40: 6929 vertices, 7200 faces
- slice 50: 16085 vertices, 16430 faces
- slice 60: 27421 vertices, 27815 faces
- slice 70: 39321 vertices, 39729 faces
- slice 80: 50975 vertices, 51374 faces
- slice 90: 62652 vertices, 63078 faces
- slice 100: 74560 vertices, 74975 faces
- slice 110: 85825 vertices, 86215 faces
- slice 120: 96753 vertices, 97160 faces
- slice 130: 107890 vertices, 108278 faces
- slice 140: 118518 vertices, 118897 faces
- slice 150: 127631 vertices, 128009 faces
- slice 160: 136136 vertices, 136453 faces
- slice 170: 143334 vertices, 143627 faces
- slice 180: 149033 vertices, 149264 faces
- slice 190: 153234 vertices, 153416 faces
- slice 200: 154422 vertices, 154490 faces
- slice 210: 154422 vertices, 154490 faces
- slice 220: 154422 vertices, 154490 faces
- slice 230: 154422 vertices, 154490 faces
- slice 240: 154422 vertices, 154490 faces
- slice 250: 154422 vertices, 154490 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...
- 154422 voxel in cpt #1: X=-68 [v=154422,e=463470,f=308980] located at (-24.351089, -24.472206, 28.391066)
- For the whole surface: X=-68 [v=154422,e=463470,f=308980]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Tessellate rh Sun Oct 8 07:58:34 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy-): 0 found - 3 modified | TOTAL: 3
- pass 1 (yz+): 4 found - 4 modified | TOTAL: 7
- pass 2 (yz+): 0 found - 4 modified | TOTAL: 7
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 8
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 8
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 9
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 9
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 9
- 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 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- 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 (-+): 1 found - 1 modified | TOTAL: 3
- pass 2 (-+): 0 found - 1 modified | TOTAL: 3
- 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 = 14 (out of 291514: 0.004803)
- 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 30: 647 vertices, 730 faces
- slice 40: 6085 vertices, 6363 faces
- slice 50: 15423 vertices, 15783 faces
- slice 60: 26866 vertices, 27277 faces
- slice 70: 40135 vertices, 40592 faces
- slice 80: 53374 vertices, 53834 faces
- slice 90: 66440 vertices, 66867 faces
- slice 100: 78690 vertices, 79126 faces
- slice 110: 90296 vertices, 90725 faces
- slice 120: 101042 vertices, 101444 faces
- slice 130: 111975 vertices, 112376 faces
- slice 140: 122269 vertices, 122624 faces
- slice 150: 130691 vertices, 131042 faces
- slice 160: 138861 vertices, 139196 faces
- slice 170: 145901 vertices, 146180 faces
- slice 180: 151170 vertices, 151410 faces
- slice 190: 155064 vertices, 155220 faces
- slice 200: 156170 vertices, 156236 faces
- slice 210: 156170 vertices, 156236 faces
- slice 220: 156170 vertices, 156236 faces
- slice 230: 156170 vertices, 156236 faces
- slice 240: 156170 vertices, 156236 faces
- slice 250: 156170 vertices, 156236 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...
- 156170 voxel in cpt #1: X=-66 [v=156170,e=468708,f=312472] located at (30.636024, -25.891964, 29.509291)
- For the whole surface: X=-66 [v=156170,e=468708,f=312472]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Sun Oct 8 07:58:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- #--------------------------------------------
- #@# Smooth1 rh Sun Oct 8 07:58:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- Waiting for PID 23775 of (23775 23778) to complete...
- Waiting for PID 23778 of (23775 23778) 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 (23775 23778) completed and logs appended.
- #--------------------------------------------
- #@# Inflation1 lh Sun Oct 8 07:58:55 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- #--------------------------------------------
- #@# Inflation1 rh Sun Oct 8 07:58:55 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Waiting for PID 23821 of (23821 23824) to complete...
- Waiting for PID 23824 of (23821 23824) to complete...
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- Not saving sulc
- Reading ../surf/lh.smoothwm.nofix
- avg radius = 49.3 mm, total surface area = 81268 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 1.4 minutes
-
step 000: RMS=0.157 (target=0.015)
step 005: RMS=0.118 (target=0.015)
step 010: RMS=0.087 (target=0.015)
step 015: RMS=0.073 (target=0.015)
step 020: RMS=0.062 (target=0.015)
step 025: RMS=0.054 (target=0.015)
step 030: RMS=0.047 (target=0.015)
step 035: RMS=0.042 (target=0.015)
step 040: RMS=0.039 (target=0.015)
step 045: RMS=0.036 (target=0.015)
step 050: RMS=0.035 (target=0.015)
step 055: RMS=0.033 (target=0.015)
step 060: RMS=0.033 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 94.883575
- mris_inflate stimesec 0.379942
- mris_inflate ru_maxrss 225172
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 32214
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 10864
- mris_inflate ru_oublock 10880
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 1657
- mris_inflate ru_nivcsw 4707
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Not saving sulc
- Reading ../surf/rh.smoothwm.nofix
- avg radius = 48.9 mm, total surface area = 82400 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.7 minutes
-
step 000: RMS=0.156 (target=0.015)
step 005: RMS=0.119 (target=0.015)
step 010: RMS=0.089 (target=0.015)
step 015: RMS=0.073 (target=0.015)
step 020: RMS=0.064 (target=0.015)
step 025: RMS=0.056 (target=0.015)
step 030: RMS=0.050 (target=0.015)
step 035: RMS=0.045 (target=0.015)
step 040: RMS=0.043 (target=0.015)
step 045: RMS=0.040 (target=0.015)
step 050: RMS=0.039 (target=0.015)
step 055: RMS=0.037 (target=0.015)
step 060: RMS=0.036 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 44.285267
- mris_inflate stimesec 0.104984
- mris_inflate ru_maxrss 227696
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 32331
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 11008
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2528
- mris_inflate ru_nivcsw 3472
- PIDs (23821 23824) completed and logs appended.
- #--------------------------------------------
- #@# QSphere lh Sun Oct 8 08:00:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- #--------------------------------------------
- #@# QSphere rh Sun Oct 8 08:00:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- Waiting for PID 23931 of (23931 23935) to complete...
- Waiting for PID 23935 of (23931 23935) to complete...
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.93 +- 0.56 (0.00-->5.87) (max @ vno 84155 --> 84168)
- face area 0.02 +- 0.03 (-0.04-->0.48)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.293...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.610, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.350, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.790, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.055, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.220, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.332, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.413, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.478, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.535, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.590, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.646, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.704, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.767, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.833, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.904, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.980, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.060, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.144, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.234, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.328, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.427, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.534, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.645, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.761, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.882, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.008, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.139, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.274, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.414, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.558, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.707, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.861, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.019, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.182, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.350, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.522, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.699, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.880, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.065, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.255, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.449, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.648, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.851, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.059, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.271, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.487, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.708, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.933, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.163, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.397, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.635, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.877, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.123, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.374, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.629, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.888, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.151, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.418, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.689, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.964, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.243, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 18424.49
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
- epoch 2 (K=40.0), pass 1, starting sse = 3228.84
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00006
- epoch 3 (K=160.0), pass 1, starting sse = 364.85
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.10/11 = 0.00879
- epoch 4 (K=640.0), pass 1, starting sse = 22.83
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.16/17 = 0.00939
- final distance error %28.29
- writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.15 hours
- mris_sphere utimesec 620.806623
- mris_sphere stimesec 0.679896
- mris_sphere ru_maxrss 225372
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 32269
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 10912
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 7446
- mris_sphere ru_nivcsw 21018
- FSRUNTIME@ mris_sphere 0.1525 hours 1 threads
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.92 +- 0.55 (0.00-->5.95) (max @ vno 118933 --> 118934)
- face area 0.02 +- 0.03 (-0.07-->0.64)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.288...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.705, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.443, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.882, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.144, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.304, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.405, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.481, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.540, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.593, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.643, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.694, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.749, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.809, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.874, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.943, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.017, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.096, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.180, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.269, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.363, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.462, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.566, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.675, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.789, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.909, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.033, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.162, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.296, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.436, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.580, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.729, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.882, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.040, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.203, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.370, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.541, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.717, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.898, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.083, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.272, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.466, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.664, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.867, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.074, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.286, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.501, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.722, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.946, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.175, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.409, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.646, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.888, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.134, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.384, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.639, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.897, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.160, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.427, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.697, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.972, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.251, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 18694.87
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
- epoch 2 (K=40.0), pass 1, starting sse = 3277.11
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
- epoch 3 (K=160.0), pass 1, starting sse = 363.59
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.08/11 = 0.00718
- epoch 4 (K=640.0), pass 1, starting sse = 22.94
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.23/23 = 0.01006
- final distance error %26.65
- writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.09 hours
- mris_sphere utimesec 309.462954
- mris_sphere stimesec 0.142978
- mris_sphere ru_maxrss 227892
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 32889
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 10992
- mris_sphere ru_oublock 11032
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 10472
- mris_sphere ru_nivcsw 24121
- FSRUNTIME@ mris_sphere 0.0860 hours 1 threads
- PIDs (23931 23935) completed and logs appended.
- #--------------------------------------------
- #@# Fix Topology Copy lh Sun Oct 8 08:09:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- #--------------------------------------------
- #@# Fix Topology Copy rh Sun Oct 8 08:09:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- #@# Fix Topology lh Sun Oct 8 08:09:28 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050490 lh
- #@# Fix Topology rh Sun Oct 8 08:09:28 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050490 rh
- Waiting for PID 24411 of (24411 24414) to complete...
- Waiting for PID 24414 of (24411 24414) to complete...
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050490 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=-68 (nv=154422, nf=308980, ne=463470, g=35)
- 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 14 iterations
- marking ambiguous vertices...
- 4176 ambiguous faces found in tessellation
- segmenting defects...
- 46 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 38 into 24
- 45 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.5872 (-4.7936)
- -vertex loglikelihood: -6.3859 (-3.1929)
- -normal dot loglikelihood: -3.5948 (-3.5948)
- -quad curv loglikelihood: -6.5552 (-3.2776)
- Total Loglikelihood : -26.1231
- CORRECTING DEFECT 0 (vertices=46, convex hull=68, v0=3510)
- After retessellation of defect 0 (v0=3510), euler #=-43 (151818,454253,302392) : difference with theory (-42) = 1
- CORRECTING DEFECT 1 (vertices=37, convex hull=71, v0=11236)
- After retessellation of defect 1 (v0=11236), euler #=-42 (151832,454321,302447) : difference with theory (-41) = 1
- CORRECTING DEFECT 2 (vertices=91, convex hull=136, v0=13002)
- After retessellation of defect 2 (v0=13002), euler #=-41 (151881,454528,302606) : difference with theory (-40) = 1
- CORRECTING DEFECT 3 (vertices=56, convex hull=80, v0=14142)
- After retessellation of defect 3 (v0=14142), euler #=-40 (151910,454648,302698) : difference with theory (-39) = 1
- CORRECTING DEFECT 4 (vertices=34, convex hull=69, v0=16438)
- After retessellation of defect 4 (v0=16438), euler #=-39 (151926,454723,302758) : difference with theory (-38) = 1
- CORRECTING DEFECT 5 (vertices=24, convex hull=26, v0=17225)
- After retessellation of defect 5 (v0=17225), euler #=-38 (151930,454741,302773) : difference with theory (-37) = 1
- CORRECTING DEFECT 6 (vertices=25, convex hull=51, v0=19189)
- After retessellation of defect 6 (v0=19189), euler #=-37 (151937,454782,302808) : difference with theory (-36) = 1
- CORRECTING DEFECT 7 (vertices=28, convex hull=66, v0=21241)
- After retessellation of defect 7 (v0=21241), euler #=-36 (151954,454859,302869) : difference with theory (-35) = 1
- CORRECTING DEFECT 8 (vertices=67, convex hull=61, v0=23912)
- After retessellation of defect 8 (v0=23912), euler #=-35 (151970,454932,302927) : difference with theory (-34) = 1
- CORRECTING DEFECT 9 (vertices=79, convex hull=108, v0=31040)
- After retessellation of defect 9 (v0=31040), euler #=-34 (151989,455035,303012) : difference with theory (-33) = 1
- CORRECTING DEFECT 10 (vertices=75, convex hull=99, v0=34905)
- After retessellation of defect 10 (v0=34905), euler #=-33 (152023,455178,303122) : difference with theory (-32) = 1
- CORRECTING DEFECT 11 (vertices=29, convex hull=75, v0=40424)
- After retessellation of defect 11 (v0=40424), euler #=-32 (152036,455244,303176) : difference with theory (-31) = 1
- CORRECTING DEFECT 12 (vertices=79, convex hull=105, v0=42010)
- After retessellation of defect 12 (v0=42010), euler #=-31 (152081,455421,303309) : difference with theory (-30) = 1
- CORRECTING DEFECT 13 (vertices=7, convex hull=23, v0=50580)
- After retessellation of defect 13 (v0=50580), euler #=-30 (152083,455433,303320) : difference with theory (-29) = 1
- CORRECTING DEFECT 14 (vertices=57, convex hull=88, v0=54783)
- After retessellation of defect 14 (v0=54783), euler #=-29 (152094,455504,303381) : difference with theory (-28) = 1
- CORRECTING DEFECT 15 (vertices=187, convex hull=102, v0=80080)
- After retessellation of defect 15 (v0=80080), euler #=-28 (152151,455718,303539) : difference with theory (-27) = 1
- CORRECTING DEFECT 16 (vertices=31, convex hull=62, v0=99704)
- After retessellation of defect 16 (v0=99704), euler #=-27 (152170,455802,303605) : difference with theory (-26) = 1
- CORRECTING DEFECT 17 (vertices=22, convex hull=30, v0=103019)
- After retessellation of defect 17 (v0=103019), euler #=-26 (152175,455824,303623) : difference with theory (-25) = 1
- CORRECTING DEFECT 18 (vertices=13, convex hull=19, v0=104465)
- After retessellation of defect 18 (v0=104465), euler #=-25 (152178,455834,303631) : difference with theory (-24) = 1
- CORRECTING DEFECT 19 (vertices=13, convex hull=19, v0=105204)
- After retessellation of defect 19 (v0=105204), euler #=-24 (152180,455847,303643) : difference with theory (-23) = 1
- CORRECTING DEFECT 20 (vertices=43, convex hull=61, v0=105408)
- After retessellation of defect 20 (v0=105408), euler #=-23 (152207,455954,303724) : difference with theory (-22) = 1
- CORRECTING DEFECT 21 (vertices=24, convex hull=26, v0=105626)
- After retessellation of defect 21 (v0=105626), euler #=-22 (152209,455969,303738) : difference with theory (-21) = 1
- CORRECTING DEFECT 22 (vertices=5, convex hull=15, v0=108538)
- After retessellation of defect 22 (v0=108538), euler #=-21 (152210,455975,303744) : difference with theory (-20) = 1
- CORRECTING DEFECT 23 (vertices=55, convex hull=82, v0=109655)
- After retessellation of defect 23 (v0=109655), euler #=-20 (152225,456051,303806) : difference with theory (-19) = 1
- CORRECTING DEFECT 24 (vertices=780, convex hull=370, v0=110411)
- After retessellation of defect 24 (v0=110411), euler #=-18 (152280,456401,304103) : difference with theory (-18) = 0
- CORRECTING DEFECT 25 (vertices=6, convex hull=26, v0=110595)
- After retessellation of defect 25 (v0=110595), euler #=-17 (152283,456417,304117) : difference with theory (-17) = 0
- CORRECTING DEFECT 26 (vertices=33, convex hull=57, v0=112627)
- After retessellation of defect 26 (v0=112627), euler #=-16 (152294,456472,304162) : difference with theory (-16) = 0
- CORRECTING DEFECT 27 (vertices=38, convex hull=56, v0=112639)
- After retessellation of defect 27 (v0=112639), euler #=-15 (152311,456544,304218) : difference with theory (-15) = 0
- CORRECTING DEFECT 28 (vertices=81, convex hull=66, v0=112740)
- After retessellation of defect 28 (v0=112740), euler #=-14 (152329,456623,304280) : difference with theory (-14) = 0
- CORRECTING DEFECT 29 (vertices=28, convex hull=69, v0=119476)
- After retessellation of defect 29 (v0=119476), euler #=-13 (152343,456694,304338) : difference with theory (-13) = 0
- CORRECTING DEFECT 30 (vertices=22, convex hull=16, v0=119945)
- After retessellation of defect 30 (v0=119945), euler #=-12 (152347,456709,304350) : difference with theory (-12) = 0
- CORRECTING DEFECT 31 (vertices=64, convex hull=72, v0=120325)
- After retessellation of defect 31 (v0=120325), euler #=-11 (152368,456799,304420) : difference with theory (-11) = 0
- CORRECTING DEFECT 32 (vertices=8, convex hull=18, v0=120971)
- After retessellation of defect 32 (v0=120971), euler #=-10 (152369,456806,304427) : difference with theory (-10) = 0
- CORRECTING DEFECT 33 (vertices=53, convex hull=88, v0=121871)
- After retessellation of defect 33 (v0=121871), euler #=-9 (152391,456909,304509) : difference with theory (-9) = 0
- CORRECTING DEFECT 34 (vertices=9, convex hull=50, v0=126521)
- After retessellation of defect 34 (v0=126521), euler #=-8 (152395,456936,304533) : difference with theory (-8) = 0
- CORRECTING DEFECT 35 (vertices=56, convex hull=90, v0=127703)
- After retessellation of defect 35 (v0=127703), euler #=-7 (152417,457039,304615) : difference with theory (-7) = 0
- CORRECTING DEFECT 36 (vertices=6, convex hull=22, v0=128501)
- After retessellation of defect 36 (v0=128501), euler #=-6 (152418,457048,304624) : difference with theory (-6) = 0
- CORRECTING DEFECT 37 (vertices=55, convex hull=68, v0=129154)
- After retessellation of defect 37 (v0=129154), euler #=-5 (152438,457135,304692) : difference with theory (-5) = 0
- CORRECTING DEFECT 38 (vertices=73, convex hull=75, v0=131150)
- After retessellation of defect 38 (v0=131150), euler #=-4 (152450,457203,304749) : difference with theory (-4) = 0
- CORRECTING DEFECT 39 (vertices=27, convex hull=51, v0=134424)
- After retessellation of defect 39 (v0=134424), euler #=-3 (152465,457269,304801) : difference with theory (-3) = 0
- CORRECTING DEFECT 40 (vertices=28, convex hull=75, v0=138410)
- After retessellation of defect 40 (v0=138410), euler #=-2 (152478,457339,304859) : difference with theory (-2) = 0
- CORRECTING DEFECT 41 (vertices=41, convex hull=63, v0=138663)
- After retessellation of defect 41 (v0=138663), euler #=-1 (152498,457425,304926) : difference with theory (-1) = 0
- CORRECTING DEFECT 42 (vertices=28, convex hull=60, v0=142328)
- After retessellation of defect 42 (v0=142328), euler #=0 (152510,457483,304973) : difference with theory (0) = 0
- CORRECTING DEFECT 43 (vertices=35, convex hull=73, v0=153694)
- After retessellation of defect 43 (v0=153694), euler #=1 (152523,457555,305033) : difference with theory (1) = 0
- CORRECTING DEFECT 44 (vertices=26, convex hull=24, v0=154156)
- After retessellation of defect 44 (v0=154156), euler #=2 (152526,457572,305048) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.23 (0.09-->8.73) (max @ vno 129768 --> 135089)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.23 (0.09-->8.73) (max @ vno 129768 --> 135089)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 145 mutations (36.4%), 253 crossovers (63.6%), 293 vertices were eliminated
- building final representation...
- 1896 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=152526, nf=305048, ne=457572, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 41.1 minutes
- 0 defective edges
- removing intersecting faces
- 000: 290 intersecting
- 001: 11 intersecting
- 002: 6 intersecting
- mris_fix_topology utimesec 2466.722001
- mris_fix_topology stimesec 1.328797
- mris_fix_topology ru_maxrss 494976
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 55521
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 10864
- mris_fix_topology ru_oublock 14680
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 757
- mris_fix_topology ru_nivcsw 13624
- FSRUNTIME@ mris_fix_topology lh 0.6852 hours 1 threads
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050490 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=-66 (nv=156170, nf=312472, ne=468708, g=34)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 3843 ambiguous faces found in tessellation
- segmenting defects...
- 43 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 24 into 23
- -merging segment 35 into 34
- 41 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.6031 (-4.8015)
- -vertex loglikelihood: -6.3247 (-3.1623)
- -normal dot loglikelihood: -3.6219 (-3.6219)
- -quad curv loglikelihood: -6.1991 (-3.0995)
- Total Loglikelihood : -25.7487
- CORRECTING DEFECT 0 (vertices=20, convex hull=30, v0=8661)
- After retessellation of defect 0 (v0=8661), euler #=-39 (153747,460080,306294) : difference with theory (-38) = 1
- CORRECTING DEFECT 1 (vertices=84, convex hull=122, v0=9725)
- After retessellation of defect 1 (v0=9725), euler #=-38 (153775,460225,306412) : difference with theory (-37) = 1
- CORRECTING DEFECT 2 (vertices=162, convex hull=133, v0=21761)
- After retessellation of defect 2 (v0=21761), euler #=-37 (153822,460422,306563) : difference with theory (-36) = 1
- CORRECTING DEFECT 3 (vertices=47, convex hull=48, v0=30542)
- After retessellation of defect 3 (v0=30542), euler #=-36 (153835,460478,306607) : difference with theory (-35) = 1
- CORRECTING DEFECT 4 (vertices=56, convex hull=86, v0=30774)
- After retessellation of defect 4 (v0=30774), euler #=-35 (153859,460586,306692) : difference with theory (-34) = 1
- CORRECTING DEFECT 5 (vertices=21, convex hull=47, v0=32745)
- After retessellation of defect 5 (v0=32745), euler #=-34 (153868,460629,306727) : difference with theory (-33) = 1
- CORRECTING DEFECT 6 (vertices=167, convex hull=124, v0=32873)
- After retessellation of defect 6 (v0=32873), euler #=-33 (153896,460769,306840) : difference with theory (-32) = 1
- CORRECTING DEFECT 7 (vertices=39, convex hull=30, v0=40113)
- After retessellation of defect 7 (v0=40113), euler #=-32 (153898,460783,306853) : difference with theory (-31) = 1
- CORRECTING DEFECT 8 (vertices=14, convex hull=25, v0=67187)
- After retessellation of defect 8 (v0=67187), euler #=-31 (153900,460798,306867) : difference with theory (-30) = 1
- CORRECTING DEFECT 9 (vertices=38, convex hull=68, v0=68584)
- After retessellation of defect 9 (v0=68584), euler #=-30 (153920,460886,306936) : difference with theory (-29) = 1
- CORRECTING DEFECT 10 (vertices=25, convex hull=35, v0=77304)
- After retessellation of defect 10 (v0=77304), euler #=-29 (153924,460908,306955) : difference with theory (-28) = 1
- CORRECTING DEFECT 11 (vertices=224, convex hull=100, v0=84346)
- After retessellation of defect 11 (v0=84346), euler #=-28 (153963,461072,307081) : difference with theory (-27) = 1
- CORRECTING DEFECT 12 (vertices=14, convex hull=22, v0=87916)
- After retessellation of defect 12 (v0=87916), euler #=-27 (153963,461080,307090) : difference with theory (-26) = 1
- CORRECTING DEFECT 13 (vertices=31, convex hull=18, v0=88005)
- After retessellation of defect 13 (v0=88005), euler #=-26 (153967,461095,307102) : difference with theory (-25) = 1
- CORRECTING DEFECT 14 (vertices=45, convex hull=26, v0=94952)
- After retessellation of defect 14 (v0=94952), euler #=-25 (153970,461109,307114) : difference with theory (-24) = 1
- CORRECTING DEFECT 15 (vertices=75, convex hull=116, v0=104106)
- After retessellation of defect 15 (v0=104106), euler #=-24 (154016,461300,307260) : difference with theory (-23) = 1
- CORRECTING DEFECT 16 (vertices=22, convex hull=52, v0=106306)
- After retessellation of defect 16 (v0=106306), euler #=-23 (154025,461351,307303) : difference with theory (-22) = 1
- CORRECTING DEFECT 17 (vertices=111, convex hull=106, v0=107727)
- After retessellation of defect 17 (v0=107727), euler #=-22 (154086,461587,307479) : difference with theory (-21) = 1
- CORRECTING DEFECT 18 (vertices=83, convex hull=80, v0=110027)
- After retessellation of defect 18 (v0=110027), euler #=-21 (154121,461729,307587) : difference with theory (-20) = 1
- CORRECTING DEFECT 19 (vertices=35, convex hull=72, v0=110656)
- After retessellation of defect 19 (v0=110656), euler #=-20 (154142,461823,307661) : difference with theory (-19) = 1
- CORRECTING DEFECT 20 (vertices=40, convex hull=62, v0=111626)
- After retessellation of defect 20 (v0=111626), euler #=-19 (154162,461905,307724) : difference with theory (-18) = 1
- CORRECTING DEFECT 21 (vertices=43, convex hull=56, v0=115443)
- After retessellation of defect 21 (v0=115443), euler #=-18 (154172,461961,307771) : difference with theory (-17) = 1
- CORRECTING DEFECT 22 (vertices=30, convex hull=73, v0=116026)
- After retessellation of defect 22 (v0=116026), euler #=-17 (154191,462048,307840) : difference with theory (-16) = 1
- CORRECTING DEFECT 23 (vertices=81, convex hull=129, v0=117715)
- After retessellation of defect 23 (v0=117715), euler #=-16 (154241,462259,308002) : difference with theory (-15) = 1
- CORRECTING DEFECT 24 (vertices=21, convex hull=52, v0=119264)
- After retessellation of defect 24 (v0=119264), euler #=-15 (154250,462306,308041) : difference with theory (-14) = 1
- CORRECTING DEFECT 25 (vertices=46, convex hull=45, v0=120144)
- After retessellation of defect 25 (v0=120144), euler #=-14 (154254,462336,308068) : difference with theory (-13) = 1
- CORRECTING DEFECT 26 (vertices=31, convex hull=23, v0=123648)
- After retessellation of defect 26 (v0=123648), euler #=-13 (154263,462368,308092) : difference with theory (-12) = 1
- CORRECTING DEFECT 27 (vertices=80, convex hull=114, v0=125516)
- After retessellation of defect 27 (v0=125516), euler #=-12 (154305,462551,308234) : difference with theory (-11) = 1
- CORRECTING DEFECT 28 (vertices=48, convex hull=77, v0=126194)
- After retessellation of defect 28 (v0=126194), euler #=-11 (154333,462668,308324) : difference with theory (-10) = 1
- CORRECTING DEFECT 29 (vertices=22, convex hull=24, v0=127194)
- After retessellation of defect 29 (v0=127194), euler #=-10 (154336,462685,308339) : difference with theory (-9) = 1
- CORRECTING DEFECT 30 (vertices=27, convex hull=77, v0=131397)
- After retessellation of defect 30 (v0=131397), euler #=-9 (154351,462758,308398) : difference with theory (-8) = 1
- CORRECTING DEFECT 31 (vertices=59, convex hull=82, v0=132258)
- After retessellation of defect 31 (v0=132258), euler #=-8 (154392,462919,308519) : difference with theory (-7) = 1
- CORRECTING DEFECT 32 (vertices=51, convex hull=74, v0=132340)
- After retessellation of defect 32 (v0=132340), euler #=-7 (154405,462988,308576) : difference with theory (-6) = 1
- CORRECTING DEFECT 33 (vertices=70, convex hull=59, v0=135476)
- After retessellation of defect 33 (v0=135476), euler #=-5 (154417,463050,308628) : difference with theory (-5) = 0
- CORRECTING DEFECT 34 (vertices=35, convex hull=75, v0=141339)
- After retessellation of defect 34 (v0=141339), euler #=-4 (154439,463147,308704) : difference with theory (-4) = 0
- CORRECTING DEFECT 35 (vertices=72, convex hull=105, v0=143500)
- After retessellation of defect 35 (v0=143500), euler #=-3 (154467,463278,308808) : difference with theory (-3) = 0
- CORRECTING DEFECT 36 (vertices=214, convex hull=61, v0=144665)
- After retessellation of defect 36 (v0=144665), euler #=-2 (154489,463372,308881) : difference with theory (-2) = 0
- CORRECTING DEFECT 37 (vertices=15, convex hull=29, v0=144765)
- After retessellation of defect 37 (v0=144765), euler #=-1 (154493,463394,308900) : difference with theory (-1) = 0
- CORRECTING DEFECT 38 (vertices=29, convex hull=57, v0=149173)
- After retessellation of defect 38 (v0=149173), euler #=0 (154502,463440,308938) : difference with theory (0) = 0
- CORRECTING DEFECT 39 (vertices=68, convex hull=89, v0=151834)
- After retessellation of defect 39 (v0=151834), euler #=1 (154516,463517,309002) : difference with theory (1) = 0
- CORRECTING DEFECT 40 (vertices=29, convex hull=71, v0=154483)
- After retessellation of defect 40 (v0=154483), euler #=2 (154525,463569,309046) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.23 (0.02-->11.96) (max @ vno 24078 --> 24098)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.23 (0.02-->11.96) (max @ vno 24078 --> 24098)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 116 mutations (33.8%), 227 crossovers (66.2%), 56 vertices were eliminated
- building final representation...
- 1645 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=154525, nf=309046, ne=463569, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 19.3 minutes
- 0 defective edges
- removing intersecting faces
- 000: 214 intersecting
- 001: 7 intersecting
- mris_fix_topology utimesec 1158.689852
- mris_fix_topology stimesec 0.152976
- mris_fix_topology ru_maxrss 480300
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 56172
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 0
- mris_fix_topology ru_oublock 14768
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 926
- mris_fix_topology ru_nivcsw 6161
- FSRUNTIME@ mris_fix_topology rh 0.3220 hours 1 threads
- PIDs (24411 24414) completed and logs appended.
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 152526 - 457572 + 305048 = 2 --> 0 holes
- F =2V-4: 305048 = 305052-4 (0)
- 2E=3F: 915144 = 915144 (0)
- total defect index = 0
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 154525 - 463569 + 309046 = 2 --> 0 holes
- F =2V-4: 309046 = 309050-4 (0)
- 2E=3F: 927138 = 927138 (0)
- total defect index = 0
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 31 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 5 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Sun Oct 8 08:50:47 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050490 lh
- #--------------------------------------------
- #@# Make White Surf rh Sun Oct 8 08:50:47 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050490 rh
- Waiting for PID 26267 of (26267 26270) to complete...
- Waiting for PID 26270 of (26267 26270) to complete...
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050490 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-6.0.0/0050490/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- 18861 bright wm thresholded.
- 604 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.orig...
- computing class statistics...
- border white: 281912 voxels (1.68%)
- border gray 319696 voxels (1.91%)
- WM (96.0): 96.5 +- 9.0 [70.0 --> 110.0]
- GM (68.0) : 68.0 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 52.8 (was 70)
- setting MAX_BORDER_WHITE to 110.0 (was 105)
- setting MIN_BORDER_WHITE to 63.0 (was 85)
- setting MAX_CSF to 42.5 (was 40)
- setting MAX_GRAY to 92.0 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 32.3 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.03-->3.75) (max @ vno 128964 --> 129768)
- face area 0.28 +- 0.12 (0.00-->2.43)
- mean absolute distance = 0.65 +- 0.75
- 4960 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=101+-7.8, GM=63+-8.7
- mean inside = 91.3, mean outside = 71.7
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=76.6, 25 (25) missing vertices, mean dist 0.3 [0.5 (%36.6)->0.7 (%63.4))]
- %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.25 (0.10-->4.02) (max @ vno 108380 --> 108379)
- face area 0.28 +- 0.13 (0.00-->2.43)
- mean absolute distance = 0.32 +- 0.52
- 3673 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3948342.0, rms=10.643
- 001: dt: 0.5000, sse=2215870.8, rms=7.431 (30.187%)
- 002: dt: 0.5000, sse=1517707.1, rms=5.616 (24.423%)
- 003: dt: 0.5000, sse=1205458.2, rms=4.573 (18.571%)
- 004: dt: 0.5000, sse=1065336.0, rms=4.017 (12.166%)
- 005: dt: 0.5000, sse=1009239.8, rms=3.766 (6.229%)
- 006: dt: 0.5000, sse=984131.8, rms=3.647 (3.167%)
- rms = 3.60, time step reduction 1 of 3 to 0.250...
- 007: dt: 0.5000, sse=975687.3, rms=3.602 (1.229%)
- 008: dt: 0.2500, sse=758159.9, rms=2.249 (37.571%)
- 009: dt: 0.2500, sse=713704.2, rms=1.864 (17.114%)
- 010: dt: 0.2500, sse=702277.5, rms=1.750 (6.092%)
- 011: dt: 0.2500, sse=696095.1, rms=1.687 (3.623%)
- rms = 1.65, time step reduction 2 of 3 to 0.125...
- 012: dt: 0.2500, sse=693576.9, rms=1.655 (1.924%)
- 013: dt: 0.1250, sse=687262.2, rms=1.586 (4.163%)
- rms = 1.58, time step reduction 3 of 3 to 0.062...
- 014: dt: 0.1250, sse=686718.0, rms=1.577 (0.556%)
- positioning took 3.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=79.7, 35 (6) missing vertices, mean dist -0.2 [0.4 (%72.0)->0.2 (%28.0))]
- %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.24 (0.05-->4.27) (max @ vno 108380 --> 108379)
- face area 0.35 +- 0.16 (0.00-->3.33)
- mean absolute distance = 0.26 +- 0.39
- 4820 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1402305.9, rms=4.628
- 015: dt: 0.5000, sse=1063699.5, rms=3.118 (32.617%)
- rms = 3.32, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.2500, sse=932639.1, rms=2.322 (25.550%)
- 017: dt: 0.2500, sse=868844.9, rms=1.787 (23.019%)
- 018: dt: 0.2500, sse=846297.3, rms=1.553 (13.098%)
- 019: dt: 0.2500, sse=838407.1, rms=1.463 (5.774%)
- 020: dt: 0.2500, sse=834537.9, rms=1.411 (3.570%)
- rms = 1.38, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=832683.9, rms=1.382 (2.048%)
- 022: dt: 0.1250, sse=827700.6, rms=1.329 (3.855%)
- rms = 1.32, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=827477.4, rms=1.325 (0.327%)
- positioning took 2.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- mean border=81.5, 34 (3) missing vertices, mean dist -0.1 [0.3 (%63.3)->0.2 (%36.7))]
- %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.24 (0.03-->4.54) (max @ vno 108380 --> 108379)
- face area 0.34 +- 0.16 (0.00-->3.39)
- mean absolute distance = 0.26 +- 0.36
- 4318 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=977428.7, rms=2.743
- 024: dt: 0.5000, sse=963890.4, rms=2.645 (3.575%)
- rms = 3.06, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=848681.8, rms=1.750 (33.832%)
- 026: dt: 0.2500, sse=813081.6, rms=1.371 (21.694%)
- 027: dt: 0.2500, sse=805593.6, rms=1.271 (7.274%)
- rms = 1.26, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.2500, sse=803831.7, rms=1.263 (0.640%)
- 029: dt: 0.1250, sse=799307.2, rms=1.197 (5.217%)
- rms = 1.20, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=799544.6, rms=1.200 (-0.282%)
- positioning took 1.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=82.3, 36 (2) missing vertices, mean dist -0.0 [0.3 (%54.5)->0.2 (%45.5))]
- %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white.preaparc...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=832190.4, rms=1.690
- rms = 1.85, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.2500, sse=790050.7, rms=1.183 (30.029%)
- 032: dt: 0.2500, sse=772827.8, rms=0.902 (23.745%)
- rms = 0.90, time step reduction 2 of 3 to 0.125...
- rms = 0.90, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=772043.2, rms=0.898 (0.450%)
- positioning took 0.6 minutes
- generating cortex label...
- 8 non-cortical segments detected
- only using segment with 8327 vertices
- erasing segment 1 (vno[0] = 94701)
- erasing segment 2 (vno[0] = 104655)
- erasing segment 3 (vno[0] = 107495)
- erasing segment 4 (vno[0] = 108417)
- erasing segment 5 (vno[0] = 108419)
- erasing segment 6 (vno[0] = 111556)
- erasing segment 7 (vno[0] = 120208)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.area
- vertex spacing 0.90 +- 0.25 (0.03-->4.57) (max @ vno 108379 --> 108380)
- face area 0.34 +- 0.16 (0.00-->3.40)
- refinement took 10.5 minutes
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050490 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-6.0.0/0050490/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- 18861 bright wm thresholded.
- 604 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.orig...
- computing class statistics...
- border white: 281912 voxels (1.68%)
- border gray 319696 voxels (1.91%)
- WM (96.0): 96.5 +- 9.0 [70.0 --> 110.0]
- GM (68.0) : 68.0 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 54.8 (was 70)
- setting MAX_BORDER_WHITE to 111.0 (was 105)
- setting MIN_BORDER_WHITE to 65.0 (was 85)
- setting MAX_CSF to 44.5 (was 40)
- setting MAX_GRAY to 93.0 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 54.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 34.3 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.02-->4.31) (max @ vno 22887 --> 24077)
- face area 0.28 +- 0.12 (0.00-->3.78)
- mean absolute distance = 0.64 +- 0.78
- 4173 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=102+-7.8, GM=65+-7.8
- mean inside = 91.7, mean outside = 72.4
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=78.4, 37 (37) missing vertices, mean dist 0.2 [0.5 (%39.8)->0.7 (%60.2))]
- %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.25 (0.08-->4.08) (max @ vno 24076 --> 24077)
- face area 0.28 +- 0.13 (0.00-->3.53)
- mean absolute distance = 0.33 +- 0.55
- 4122 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3681038.8, rms=10.121
- 001: dt: 0.5000, sse=2018981.1, rms=6.886 (31.966%)
- 002: dt: 0.5000, sse=1404970.1, rms=5.181 (24.754%)
- 003: dt: 0.5000, sse=1155562.6, rms=4.307 (16.886%)
- 004: dt: 0.5000, sse=1050026.1, rms=3.862 (10.324%)
- 005: dt: 0.5000, sse=1004668.8, rms=3.662 (5.172%)
- 006: dt: 0.5000, sse=985681.0, rms=3.567 (2.597%)
- rms = 3.54, time step reduction 1 of 3 to 0.250...
- 007: dt: 0.5000, sse=979759.2, rms=3.539 (0.793%)
- 008: dt: 0.2500, sse=766301.7, rms=2.195 (37.971%)
- 009: dt: 0.2500, sse=722744.2, rms=1.833 (16.485%)
- 010: dt: 0.2500, sse=712956.4, rms=1.732 (5.503%)
- 011: dt: 0.2500, sse=711361.0, rms=1.678 (3.117%)
- rms = 1.65, time step reduction 2 of 3 to 0.125...
- 012: dt: 0.2500, sse=705002.7, rms=1.653 (1.484%)
- 013: dt: 0.1250, sse=697310.4, rms=1.565 (5.356%)
- rms = 1.56, time step reduction 3 of 3 to 0.062...
- 014: dt: 0.1250, sse=696356.0, rms=1.556 (0.567%)
- positioning took 3.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=81.2, 64 (8) missing vertices, mean dist -0.2 [0.4 (%70.1)->0.2 (%29.9))]
- %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.24 (0.10-->3.95) (max @ vno 24076 --> 24077)
- face area 0.35 +- 0.16 (0.00-->4.44)
- mean absolute distance = 0.27 +- 0.44
- 4580 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1339157.5, rms=4.340
- 015: dt: 0.5000, sse=1049365.1, rms=2.990 (31.106%)
- rms = 3.21, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.2500, sse=926084.8, rms=2.210 (26.082%)
- 017: dt: 0.2500, sse=872998.6, rms=1.712 (22.536%)
- 018: dt: 0.2500, sse=848322.8, rms=1.513 (11.635%)
- 019: dt: 0.2500, sse=842345.5, rms=1.443 (4.601%)
- rms = 1.40, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=840730.0, rms=1.403 (2.807%)
- 021: dt: 0.1250, sse=834935.8, rms=1.348 (3.929%)
- rms = 1.34, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=834365.7, rms=1.342 (0.418%)
- positioning took 1.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=83.0, 68 (2) missing vertices, mean dist -0.1 [0.3 (%62.5)->0.2 (%37.5))]
- %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.24 (0.09-->3.99) (max @ vno 24098 --> 25235)
- face area 0.34 +- 0.15 (0.00-->4.29)
- mean absolute distance = 0.26 +- 0.38
- 4275 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=989596.1, rms=2.760
- 023: dt: 0.5000, sse=968723.0, rms=2.559 (7.288%)
- rms = 2.97, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=854671.8, rms=1.737 (32.115%)
- 025: dt: 0.2500, sse=826022.1, rms=1.372 (20.997%)
- 026: dt: 0.2500, sse=813133.7, rms=1.281 (6.670%)
- rms = 1.27, time step reduction 2 of 3 to 0.125...
- 027: dt: 0.2500, sse=811753.1, rms=1.266 (1.169%)
- 028: dt: 0.1250, sse=806791.3, rms=1.205 (4.810%)
- rms = 1.21, time step reduction 3 of 3 to 0.062...
- 029: dt: 0.1250, sse=807784.2, rms=1.206 (-0.110%)
- positioning took 1.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=83.7, 78 (0) missing vertices, mean dist -0.0 [0.3 (%53.6)->0.2 (%46.4))]
- %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white.preaparc...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=836678.6, rms=1.658
- rms = 1.83, time step reduction 1 of 3 to 0.250...
- 030: dt: 0.2500, sse=796564.9, rms=1.181 (28.789%)
- 031: dt: 0.2500, sse=781054.4, rms=0.930 (21.261%)
- rms = 0.93, time step reduction 2 of 3 to 0.125...
- 032: dt: 0.2500, sse=815665.3, rms=0.930 (0.016%)
- rms = 0.92, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=778004.3, rms=0.922 (0.880%)
- positioning took 0.5 minutes
- generating cortex label...
- 5 non-cortical segments detected
- only using segment with 7731 vertices
- erasing segment 1 (vno[0] = 109559)
- erasing segment 2 (vno[0] = 117438)
- erasing segment 3 (vno[0] = 124558)
- erasing segment 4 (vno[0] = 154232)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.area
- vertex spacing 0.90 +- 0.24 (0.02-->4.01) (max @ vno 24098 --> 25235)
- face area 0.34 +- 0.15 (0.00-->4.30)
- refinement took 10.3 minutes
- PIDs (26267 26270) completed and logs appended.
- #--------------------------------------------
- #@# Smooth2 lh Sun Oct 8 09:01:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
- #--------------------------------------------
- #@# Smooth2 rh Sun Oct 8 09:01:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
- Waiting for PID 27028 of (27028 27031) to complete...
- Waiting for PID 27031 of (27028 27031) 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 (27028 27031) completed and logs appended.
- #--------------------------------------------
- #@# Inflation2 lh Sun Oct 8 09:01:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- #--------------------------------------------
- #@# Inflation2 rh Sun Oct 8 09:01:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Waiting for PID 27076 of (27076 27079) to complete...
- Waiting for PID 27079 of (27076 27079) to complete...
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- Reading ../surf/lh.smoothwm
- avg radius = 49.4 mm, total surface area = 93935 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.181 (target=0.015)
step 005: RMS=0.125 (target=0.015)
step 010: RMS=0.092 (target=0.015)
step 015: RMS=0.076 (target=0.015)
step 020: RMS=0.062 (target=0.015)
step 025: RMS=0.051 (target=0.015)
step 030: RMS=0.043 (target=0.015)
step 035: RMS=0.036 (target=0.015)
step 040: RMS=0.031 (target=0.015)
step 045: RMS=0.028 (target=0.015)
step 050: RMS=0.025 (target=0.015)
step 055: RMS=0.023 (target=0.015)
step 060: RMS=0.021 (target=0.015)
- inflation complete.
- inflation took 1.3 minutes
- mris_inflate utimesec 88.673519
- mris_inflate stimesec 0.200969
- mris_inflate ru_maxrss 222576
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 32205
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 10728
- mris_inflate ru_oublock 11944
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 1703
- mris_inflate ru_nivcsw 3580
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Reading ../surf/rh.smoothwm
- avg radius = 49.0 mm, total surface area = 94482 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.180 (target=0.015)
step 005: RMS=0.125 (target=0.015)
step 010: RMS=0.093 (target=0.015)
step 015: RMS=0.075 (target=0.015)
step 020: RMS=0.062 (target=0.015)
step 025: RMS=0.052 (target=0.015)
step 030: RMS=0.044 (target=0.015)
step 035: RMS=0.038 (target=0.015)
step 040: RMS=0.032 (target=0.015)
step 045: RMS=0.028 (target=0.015)
step 050: RMS=0.026 (target=0.015)
step 055: RMS=0.024 (target=0.015)
step 060: RMS=0.022 (target=0.015)
- inflation complete.
- inflation took 0.7 minutes
- mris_inflate utimesec 43.261423
- mris_inflate stimesec 0.089986
- mris_inflate ru_maxrss 225400
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 32907
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 10872
- mris_inflate ru_oublock 12096
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2562
- mris_inflate ru_nivcsw 3387
- PIDs (27076 27079) completed and logs appended.
- #--------------------------------------------
- #@# Curv .H and .K lh Sun Oct 8 09:02:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 09:02:46 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf
- reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 27190 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- Waiting for PID 27193 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- Waiting for PID 27196 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- Waiting for PID 27199 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- Waiting for PID 27202 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- Waiting for PID 27205 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- Waiting for PID 27208 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- Waiting for PID 27211 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- Waiting for PID 27214 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- Waiting for PID 27217 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- Waiting for PID 27220 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- Waiting for PID 27223 of (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) to complete...
- mris_curvature -w lh.white.preaparc
- total integrated curvature = 3.839*4pi (48.242) --> -3 handles
- ICI = 199.2, FI = 1873.6, variation=30233.165
- writing Gaussian curvature to ./lh.white.preaparc.K...done.
- writing mean curvature to ./lh.white.preaparc.H...done.
- rm -f lh.white.H
- ln -s lh.white.preaparc.H lh.white.H
- rm -f lh.white.K
- ln -s lh.white.preaparc.K lh.white.K
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 202 vertices thresholded to be in k1 ~ [-0.18 0.30], k2 ~ [-0.10 0.04]
- total integrated curvature = 0.616*4pi (7.746) --> 0 handles
- ICI = 1.5, FI = 10.8, variation=175.575
- 140 vertices thresholded to be in [-0.01 0.01]
- writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 152 vertices thresholded to be in [-0.11 0.13]
- done.
- writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022
- done.
- mris_curvature -w rh.white.preaparc
- total integrated curvature = 2.485*4pi (31.224) --> -1 handles
- ICI = 202.4, FI = 1972.0, variation=31573.021
- 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
- 187 vertices thresholded to be in k1 ~ [-0.23 0.93], k2 ~ [-0.13 0.05]
- total integrated curvature = 0.547*4pi (6.868) --> 0 handles
- ICI = 1.5, FI = 10.2, variation=169.057
- 152 vertices thresholded to be in [-0.04 0.01]
- writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 120 vertices thresholded to be in [-0.12 0.20]
- done.
- writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.022
- done.
- PIDs (27190 27193 27196 27199 27202 27205 27208 27211 27214 27217 27220 27223) completed and logs appended.
- #-----------------------------------------
- #@# Curvature Stats lh Sun Oct 8 09:04:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050490 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 [ 0050490/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 [ 283 ]
- Gb_filter = 0
- WARN: S lookup min: -0.234448
- WARN: S explicit min: 0.000000 vertex = 43
- #-----------------------------------------
- #@# Curvature Stats rh Sun Oct 8 09:04:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050490 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 [ 0050490/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 [ 287 ]
- Gb_filter = 0
- WARN: S lookup min: -0.330693
- WARN: S explicit min: 0.000000 vertex = 237
- #--------------------------------------------
- #@# Sphere lh Sun Oct 8 09:04:40 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- #--------------------------------------------
- #@# Sphere rh Sun Oct 8 09:04:40 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- Waiting for PID 27422 of (27422 27425) to complete...
- Waiting for PID 27425 of (27422 27425) to complete...
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0.272...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- singular matrix in quadratic form
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %19.33
- pass 1: epoch 2 of 3 starting distance error %19.31
- unfolding complete - removing small folds...
- starting distance error %19.25
- removing remaining folds...
- final distance error %19.27
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 91 negative triangles
- 179: dt=0.9900, 91 negative triangles
- 180: dt=0.9900, 47 negative triangles
- 181: dt=0.9900, 22 negative triangles
- 182: dt=0.9900, 13 negative triangles
- 183: dt=0.9900, 9 negative triangles
- 184: dt=0.9900, 7 negative triangles
- 185: dt=0.9900, 9 negative triangles
- 186: dt=0.9900, 6 negative triangles
- 187: dt=0.9900, 3 negative triangles
- 188: dt=0.9900, 3 negative triangles
- 189: dt=0.9900, 1 negative triangles
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.92 hours
- mris_sphere utimesec 3320.394223
- mris_sphere stimesec 0.904862
- mris_sphere ru_maxrss 313524
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 55072
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 10776
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 146566
- mris_sphere ru_nivcsw 275958
- FSRUNTIME@ mris_sphere 0.9223 hours 1 threads
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0.269...
- 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 %19.95
- pass 1: epoch 2 of 3 starting distance error %19.91
- unfolding complete - removing small folds...
- starting distance error %19.85
- removing remaining folds...
- final distance error %19.87
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 176 negative triangles
- 201: dt=0.9900, 176 negative triangles
- 202: dt=0.9900, 81 negative triangles
- 203: dt=0.9900, 76 negative triangles
- 204: dt=0.9900, 56 negative triangles
- 205: dt=0.9900, 54 negative triangles
- 206: dt=0.9900, 42 negative triangles
- 207: dt=0.9900, 41 negative triangles
- 208: dt=0.9900, 45 negative triangles
- 209: dt=0.9900, 41 negative triangles
- 210: dt=0.9900, 41 negative triangles
- 211: dt=0.9900, 37 negative triangles
- 212: dt=0.9900, 44 negative triangles
- 213: dt=0.9900, 44 negative triangles
- 214: dt=0.9900, 38 negative triangles
- 215: dt=0.9900, 33 negative triangles
- 216: dt=0.9900, 39 negative triangles
- 217: dt=0.9900, 37 negative triangles
- 218: dt=0.9900, 33 negative triangles
- 219: dt=0.9900, 27 negative triangles
- 220: dt=0.9900, 38 negative triangles
- 221: dt=0.9900, 31 negative triangles
- 222: dt=0.9900, 30 negative triangles
- 223: dt=0.9900, 35 negative triangles
- 224: dt=0.9900, 29 negative triangles
- 225: dt=0.9900, 32 negative triangles
- 226: dt=0.9900, 25 negative triangles
- 227: dt=0.9900, 26 negative triangles
- 228: dt=0.9900, 24 negative triangles
- 229: dt=0.9900, 24 negative triangles
- 230: dt=0.9900, 19 negative triangles
- 231: dt=0.9900, 25 negative triangles
- 232: dt=0.9900, 19 negative triangles
- 233: dt=0.9900, 16 negative triangles
- 234: dt=0.9900, 22 negative triangles
- 235: dt=0.9900, 15 negative triangles
- 236: dt=0.9900, 11 negative triangles
- 237: dt=0.9900, 12 negative triangles
- 238: dt=0.9900, 10 negative triangles
- 239: dt=0.9900, 13 negative triangles
- 240: dt=0.9900, 10 negative triangles
- 241: dt=0.9900, 8 negative triangles
- 242: dt=0.9900, 11 negative triangles
- 243: dt=0.9900, 13 negative triangles
- 244: dt=0.9900, 10 negative triangles
- 245: dt=0.9900, 7 negative triangles
- 246: dt=0.9900, 10 negative triangles
- 247: dt=0.9900, 8 negative triangles
- 248: dt=0.9900, 12 negative triangles
- 249: dt=0.9900, 10 negative triangles
- 250: dt=0.9900, 5 negative triangles
- 251: dt=0.9900, 9 negative triangles
- 252: dt=0.9900, 7 negative triangles
- 253: dt=0.9900, 10 negative triangles
- 254: dt=0.9900, 9 negative triangles
- 255: dt=0.9900, 4 negative triangles
- 256: dt=0.9900, 8 negative triangles
- 257: dt=0.9900, 4 negative triangles
- 258: dt=0.9900, 9 negative triangles
- 259: dt=0.9900, 8 negative triangles
- 260: dt=0.9900, 6 negative triangles
- 261: dt=0.9900, 2 negative triangles
- 262: dt=0.9900, 2 negative triangles
- 263: dt=0.9900, 2 negative triangles
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.75 hours
- mris_sphere utimesec 7472.463012
- mris_sphere stimesec 5.569153
- mris_sphere ru_maxrss 317228
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 55998
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 10928
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 110276
- mris_sphere ru_nivcsw 341591
- FSRUNTIME@ mris_sphere 1.7467 hours 1 threads
- PIDs (27422 27425) completed and logs appended.
- #--------------------------------------------
- #@# Surf Reg lh Sun Oct 8 10:49:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 10:49:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 31524 of (31524 31527) to complete...
- Waiting for PID 31527 of (31524 31527) to complete...
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 5.580
- curvature mean = 0.022, std = 0.818
- curvature mean = 0.016, std = 0.855
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 361896.5, tmin=1.1238
- d=32.00 min @ (0.00, 8.00, 0.00) sse = 289369.9, tmin=2.2698
- d=16.00 min @ (4.00, 0.00, -4.00) sse = 262620.3, tmin=3.4242
- d=8.00 min @ (-2.00, 0.00, 0.00) sse = 259453.7, tmin=4.6244
- d=4.00 min @ (1.00, 0.00, 1.00) sse = 257551.5, tmin=5.8339
- d=2.00 min @ (-0.50, 0.00, 0.00) sse = 257465.1, tmin=7.0473
- d=1.00 min @ (0.25, 0.25, 0.00) sse = 257283.9, tmin=8.2474
- tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 9.44 min
- curvature mean = -0.006, std = 0.830
- curvature mean = 0.007, std = 0.945
- curvature mean = -0.010, std = 0.840
- curvature mean = 0.003, std = 0.977
- curvature mean = -0.012, std = 0.841
- curvature mean = 0.001, std = 0.991
- 2 Reading smoothwm
- curvature mean = -0.026, std = 0.284
- curvature mean = 0.038, std = 0.246
- curvature mean = 0.064, std = 0.340
- curvature mean = 0.035, std = 0.302
- curvature mean = 0.039, std = 0.534
- curvature mean = 0.034, std = 0.329
- curvature mean = 0.021, std = 0.682
- curvature mean = 0.034, std = 0.340
- curvature mean = 0.007, std = 0.794
- MRISregister() return, current seed 0
- -01: dt=0.0000, 25 negative triangles
- 117: dt=0.9900, 25 negative triangles
- expanding nbhd size to 1
- 118: dt=0.9900, 29 negative triangles
- 119: dt=0.9900, 25 negative triangles
- 120: dt=0.9900, 23 negative triangles
- 121: dt=0.9900, 23 negative triangles
- 122: dt=0.9900, 22 negative triangles
- 123: dt=0.9900, 18 negative triangles
- 124: dt=0.9900, 14 negative triangles
- 125: dt=0.9900, 15 negative triangles
- 126: dt=0.9900, 13 negative triangles
- 127: dt=0.9900, 11 negative triangles
- 128: dt=0.9900, 11 negative triangles
- 129: dt=0.9900, 9 negative triangles
- 130: dt=0.9900, 5 negative triangles
- 131: dt=0.9900, 5 negative triangles
- 132: dt=0.9900, 2 negative triangles
- 133: dt=0.9900, 1 negative triangles
- 134: dt=0.9900, 1 negative triangles
- writing registered surface to ../surf/lh.sphere.reg...
- registration took 1.34 hours
- mris_register utimesec 4806.365321
- mris_register stimesec 1.869715
- mris_register ru_maxrss 277188
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 39770
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 10816
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 405322
- mris_register ru_nivcsw 251630
- FSRUNTIME@ mris_register 1.3353 hours 1 threads
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 5.698
- curvature mean = 0.019, std = 0.817
- curvature mean = 0.017, std = 0.852
- Starting MRISrigidBodyAlignGlobal()
- d=32.00 min @ (8.00, -8.00, 0.00) sse = 369997.8, tmin=5.0650
- d=16.00 min @ (-4.00, 0.00, -4.00) sse = 348248.9, tmin=7.6121
- d=8.00 min @ (0.00, 2.00, 2.00) sse = 345031.7, tmin=10.1948
- d=4.00 min @ (0.00, -1.00, -1.00) sse = 343818.1, tmin=12.8257
- d=2.00 min @ (0.00, 0.50, 0.00) sse = 343675.9, tmin=15.4552
- d=1.00 min @ (-0.25, -0.25, 0.00) sse = 343638.3, tmin=18.0755
- d=0.50 min @ (0.12, 0.00, 0.12) sse = 343614.6, tmin=20.6925
- 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 20.69 min
- curvature mean = -0.008, std = 0.810
- curvature mean = 0.007, std = 0.941
- curvature mean = -0.014, std = 0.815
- curvature mean = 0.003, std = 0.976
- curvature mean = -0.017, std = 0.813
- curvature mean = 0.001, std = 0.990
- 2 Reading smoothwm
- curvature mean = -0.027, std = 0.293
- curvature mean = 0.030, std = 0.235
- curvature mean = 0.065, std = 0.332
- curvature mean = 0.028, std = 0.292
- curvature mean = 0.041, std = 0.514
- curvature mean = 0.027, std = 0.318
- curvature mean = 0.024, std = 0.655
- curvature mean = 0.027, std = 0.329
- curvature mean = 0.008, std = 0.766
- MRISregister() return, current seed 0
- -01: dt=0.0000, 85 negative triangles
- 123: dt=0.9900, 85 negative triangles
- expanding nbhd size to 1
- 124: dt=0.9900, 98 negative triangles
- 125: dt=0.9900, 71 negative triangles
- 126: dt=0.9900, 51 negative triangles
- 127: dt=0.9900, 41 negative triangles
- 128: dt=0.9900, 35 negative triangles
- 129: dt=0.9900, 35 negative triangles
- 130: dt=0.9900, 28 negative triangles
- 131: dt=0.9900, 27 negative triangles
- 132: dt=0.9900, 23 negative triangles
- 133: dt=0.9900, 20 negative triangles
- 134: dt=0.9900, 22 negative triangles
- 135: dt=0.9900, 21 negative triangles
- 136: dt=0.9900, 16 negative triangles
- 137: dt=0.9900, 16 negative triangles
- 138: dt=0.9900, 10 negative triangles
- 139: dt=0.9900, 13 negative triangles
- 140: dt=0.9900, 11 negative triangles
- 141: dt=0.9900, 7 negative triangles
- 142: dt=0.9900, 7 negative triangles
- 143: dt=0.9900, 3 negative triangles
- 144: dt=0.9900, 8 negative triangles
- 145: dt=0.9900, 5 negative triangles
- 146: dt=0.9900, 4 negative triangles
- 147: dt=0.9900, 3 negative triangles
- 148: dt=0.9900, 3 negative triangles
- 149: dt=0.9900, 1 negative triangles
- 150: dt=0.9900, 5 negative triangles
- 151: dt=0.9900, 1 negative triangles
- 152: dt=0.9900, 3 negative triangles
- 153: dt=0.9900, 1 negative triangles
- 154: dt=0.9900, 2 negative triangles
- 155: dt=0.9900, 1 negative triangles
- 156: dt=0.9900, 2 negative triangles
- 157: dt=0.9900, 2 negative triangles
- 158: dt=0.9900, 2 negative triangles
- 159: dt=0.9405, 3 negative triangles
- 160: dt=0.9405, 3 negative triangles
- 161: dt=0.9405, 2 negative triangles
- 162: dt=0.9405, 1 negative triangles
- 163: dt=0.9405, 1 negative triangles
- 164: dt=0.9405, 1 negative triangles
- 165: dt=0.9405, 1 negative triangles
- 166: dt=0.9405, 1 negative triangles
- writing registered surface to ../surf/rh.sphere.reg...
- registration took 3.04 hours
- mris_register utimesec 12482.820322
- mris_register stimesec 9.242594
- mris_register ru_maxrss 281244
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 40733
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 10872
- mris_register ru_oublock 10968
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 252257
- mris_register ru_nivcsw 396536
- FSRUNTIME@ mris_register 3.0416 hours 1 threads
- PIDs (31524 31527) completed and logs appended.
- #--------------------------------------------
- #@# Jacobian white lh Sun Oct 8 13:51:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# Jacobian white rh Sun Oct 8 13:51:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- Waiting for PID 5119 of (5119 5122) to complete...
- Waiting for PID 5122 of (5119 5122) 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 (5119 5122) completed and logs appended.
- #--------------------------------------------
- #@# AvgCurv lh Sun Oct 8 13:52:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 13:52:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 5172 of (5172 5175) to complete...
- Waiting for PID 5175 of (5172 5175) 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 (5172 5175) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc lh Sun Oct 8 13:52:06 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 13:52:06 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 5219 of (5219 5222) to complete...
- Waiting for PID 5222 of (5219 5222) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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...
- 1409 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3415 changed, 152526 examined...
- 001: 827 changed, 14385 examined...
- 002: 216 changed, 4587 examined...
- 003: 59 changed, 1277 examined...
- 004: 25 changed, 369 examined...
- 005: 11 changed, 150 examined...
- 006: 4 changed, 66 examined...
- 007: 4 changed, 26 examined...
- 008: 0 changed, 23 examined...
- 289 labels changed using aseg
- 000: 136 total segments, 93 labels (383 vertices) changed
- 001: 44 total segments, 2 labels (7 vertices) changed
- 002: 42 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 4 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1346 vertices marked for relabeling...
- 1346 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 30 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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...
- 1173 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2988 changed, 154525 examined...
- 001: 734 changed, 12982 examined...
- 002: 179 changed, 4072 examined...
- 003: 52 changed, 1096 examined...
- 004: 18 changed, 324 examined...
- 005: 6 changed, 110 examined...
- 006: 2 changed, 36 examined...
- 007: 0 changed, 11 examined...
- 173 labels changed using aseg
- 000: 104 total segments, 67 labels (332 vertices) changed
- 001: 40 total segments, 3 labels (3 vertices) changed
- 002: 37 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 4 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1485 vertices marked for relabeling...
- 1485 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 15 seconds.
- PIDs (5219 5222) completed and logs appended.
- #--------------------------------------------
- #@# Make Pial Surf lh Sun Oct 8 13:52:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050490 lh
- #--------------------------------------------
- #@# Make Pial Surf rh Sun Oct 8 13:52:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050490 rh
- Waiting for PID 5286 of (5286 5289) to complete...
- Waiting for PID 5289 of (5286 5289) to complete...
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050490 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-6.0.0/0050490/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- 18861 bright wm thresholded.
- 604 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.orig...
- computing class statistics...
- border white: 281912 voxels (1.68%)
- border gray 319696 voxels (1.91%)
- WM (96.0): 96.5 +- 9.0 [70.0 --> 110.0]
- GM (68.0) : 68.0 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 52.8 (was 70)
- setting MAX_BORDER_WHITE to 110.0 (was 105)
- setting MIN_BORDER_WHITE to 63.0 (was 85)
- setting MAX_CSF to 42.5 (was 40)
- setting MAX_GRAY to 92.0 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 32.3 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=101+-7.8, GM=63+-8.7
- mean inside = 91.3, mean outside = 71.7
- 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 +- 0.25 (0.03-->4.57) (max @ vno 108379 --> 108380)
- face area 0.34 +- 0.16 (0.00-->3.39)
- mean absolute distance = 0.53 +- 0.74
- 3617 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 157 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- deleting segment 6 with 22 points - only 0.00% unknown
- deleting segment 7 with 9 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- mean border=76.2, 35 (35) missing vertices, mean dist 0.3 [0.6 (%16.4)->0.5 (%83.6))]
- %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.93 +- 0.26 (0.11-->4.72) (max @ vno 108380 --> 108379)
- face area 0.34 +- 0.16 (0.00-->3.48)
- mean absolute distance = 0.33 +- 0.53
- 3795 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2568560.0, rms=7.898
- 001: dt: 0.5000, sse=1411311.5, rms=4.776 (39.529%)
- 002: dt: 0.5000, sse=1143989.6, rms=3.724 (22.026%)
- 003: dt: 0.5000, sse=1108550.8, rms=3.568 (4.177%)
- 004: dt: 0.5000, sse=1072233.8, rms=3.397 (4.807%)
- rms = 3.50, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.2500, sse=905890.7, rms=2.356 (30.627%)
- 006: dt: 0.2500, sse=848154.8, rms=1.850 (21.482%)
- 007: dt: 0.2500, sse=831939.7, rms=1.694 (8.435%)
- rms = 1.65, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=828308.0, rms=1.652 (2.475%)
- 009: dt: 0.1250, sse=822237.9, rms=1.586 (3.986%)
- rms = 1.58, time step reduction 3 of 3 to 0.062...
- 010: dt: 0.1250, sse=821997.2, rms=1.577 (0.570%)
- positioning took 1.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 3 with 103 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 20 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- mean border=79.5, 54 (11) missing vertices, mean dist -0.2 [0.4 (%73.0)->0.2 (%27.0))]
- %80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.25 (0.08-->5.07) (max @ vno 108380 --> 108379)
- face area 0.36 +- 0.17 (0.00-->4.11)
- mean absolute distance = 0.26 +- 0.40
- 4406 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1425067.8, rms=4.641
- 011: dt: 0.5000, sse=1071937.8, rms=3.064 (33.986%)
- rms = 3.24, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.2500, sse=947613.4, rms=2.277 (25.684%)
- 013: dt: 0.2500, sse=881596.7, rms=1.718 (24.548%)
- 014: dt: 0.2500, sse=859537.2, rms=1.469 (14.485%)
- 015: dt: 0.2500, sse=851964.0, rms=1.380 (6.076%)
- rms = 1.34, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=850602.8, rms=1.341 (2.854%)
- 017: dt: 0.1250, sse=844464.9, rms=1.282 (4.346%)
- rms = 1.28, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=844237.9, rms=1.281 (0.108%)
- positioning took 1.5 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 6 points - only 0.00% unknown
- deleting segment 1 with 107 points - only 0.00% unknown
- deleting segment 2 with 7 points - only 0.00% unknown
- deleting segment 3 with 20 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- mean border=81.4, 67 (10) missing vertices, mean dist -0.1 [0.3 (%63.9)->0.2 (%36.1))]
- %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.91 +- 0.25 (0.08-->5.05) (max @ vno 108380 --> 108379)
- face area 0.35 +- 0.16 (0.00-->4.19)
- mean absolute distance = 0.26 +- 0.36
- 4304 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=993206.5, rms=2.775
- 019: dt: 0.5000, sse=982003.6, rms=2.645 (4.673%)
- rms = 3.03, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=860322.1, rms=1.747 (33.944%)
- 021: dt: 0.2500, sse=823729.1, rms=1.350 (22.761%)
- 022: dt: 0.2500, sse=817866.4, rms=1.248 (7.543%)
- rms = 1.24, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=812990.2, rms=1.237 (0.880%)
- 024: dt: 0.1250, sse=808936.6, rms=1.172 (5.218%)
- rms = 1.18, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=808296.8, rms=1.176 (-0.272%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 3 with 102 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- deleting segment 6 with 20 points - only 0.00% unknown
- deleting segment 7 with 7 points - only 0.00% unknown
- mean border=82.2, 73 (8) missing vertices, mean dist -0.0 [0.3 (%54.7)->0.2 (%45.3))]
- %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=839374.1, rms=1.672
- rms = 1.84, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=796976.4, rms=1.162 (30.487%)
- 027: dt: 0.2500, sse=780269.6, rms=0.887 (23.692%)
- rms = 0.89, time step reduction 2 of 3 to 0.125...
- rms = 0.88, time step reduction 3 of 3 to 0.062...
- 028: dt: 0.1250, sse=779187.8, rms=0.883 (0.457%)
- positioning took 0.8 minutes
- generating cortex label...
- 8 non-cortical segments detected
- only using segment with 8328 vertices
- erasing segment 1 (vno[0] = 94701)
- erasing segment 2 (vno[0] = 104655)
- erasing segment 3 (vno[0] = 107495)
- erasing segment 4 (vno[0] = 108417)
- erasing segment 5 (vno[0] = 109348)
- erasing segment 6 (vno[0] = 111556)
- erasing segment 7 (vno[0] = 120208)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.area
- vertex spacing 0.90 +- 0.26 (0.03-->5.19) (max @ vno 108379 --> 108380)
- face area 0.34 +- 0.16 (0.00-->4.20)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=51.3, 58 (58) missing vertices, mean dist 1.7 [0.2 (%0.0)->3.0 (%100.0))]
- %13 local maxima, %43 large gradients and %40 min vals, 686 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=29762172.0, rms=31.523
- 001: dt: 0.0500, sse=26197402.0, rms=29.523 (6.345%)
- 002: dt: 0.0500, sse=23621610.0, rms=27.989 (5.196%)
- 003: dt: 0.0500, sse=21639090.0, rms=26.748 (4.433%)
- 004: dt: 0.0500, sse=20031638.0, rms=25.698 (3.926%)
- 005: dt: 0.0500, sse=18679012.0, rms=24.780 (3.573%)
- 006: dt: 0.0500, sse=17509580.0, rms=23.958 (3.318%)
- 007: dt: 0.0500, sse=16477574.0, rms=23.208 (3.130%)
- 008: dt: 0.0500, sse=15552422.0, rms=22.514 (2.988%)
- 009: dt: 0.0500, sse=14712902.0, rms=21.866 (2.880%)
- 010: dt: 0.0500, sse=13946098.0, rms=21.256 (2.788%)
- positioning took 1.7 minutes
- mean border=51.1, 48 (33) missing vertices, mean dist 1.4 [0.0 (%0.0)->2.4 (%100.0))]
- %13 local maxima, %43 large gradients and %40 min vals, 643 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=14593958.0, rms=21.777
- 011: dt: 0.0500, sse=13886399.0, rms=21.213 (2.591%)
- 012: dt: 0.0500, sse=13233426.0, rms=20.678 (2.519%)
- 013: dt: 0.0500, sse=12628352.0, rms=20.170 (2.456%)
- 014: dt: 0.0500, sse=12067110.0, rms=19.687 (2.394%)
- 015: dt: 0.0500, sse=11546334.0, rms=19.228 (2.332%)
- 016: dt: 0.0500, sse=11061937.0, rms=18.791 (2.273%)
- 017: dt: 0.0500, sse=10611011.0, rms=18.375 (2.216%)
- 018: dt: 0.0500, sse=10191678.0, rms=17.979 (2.155%)
- 019: dt: 0.0500, sse=9801357.0, rms=17.602 (2.095%)
- 020: dt: 0.0500, sse=9437904.0, rms=17.244 (2.035%)
- positioning took 1.7 minutes
- mean border=51.0, 72 (28) missing vertices, mean dist 1.2 [0.1 (%0.8)->2.1 (%99.2))]
- %14 local maxima, %43 large gradients and %39 min vals, 599 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=9549234.0, rms=17.363
- 021: dt: 0.0500, sse=9205318.0, rms=17.019 (1.979%)
- 022: dt: 0.0500, sse=8885649.0, rms=16.693 (1.915%)
- 023: dt: 0.0500, sse=8586732.0, rms=16.382 (1.861%)
- 024: dt: 0.0500, sse=8308631.0, rms=16.088 (1.798%)
- 025: dt: 0.0500, sse=8049604.5, rms=15.809 (1.736%)
- 026: dt: 0.0500, sse=7807815.0, rms=15.543 (1.679%)
- 027: dt: 0.0500, sse=7580886.5, rms=15.290 (1.630%)
- 028: dt: 0.0500, sse=7366054.5, rms=15.046 (1.595%)
- 029: dt: 0.0500, sse=7162448.5, rms=14.811 (1.562%)
- 030: dt: 0.0500, sse=6969210.5, rms=14.584 (1.530%)
- positioning took 1.7 minutes
- mean border=51.0, 100 (25) missing vertices, mean dist 1.1 [0.1 (%7.6)->1.9 (%92.4))]
- %14 local maxima, %43 large gradients and %39 min vals, 566 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=7054325.0, rms=14.686
- 031: dt: 0.5000, sse=5695360.0, rms=12.994 (11.519%)
- 032: dt: 0.5000, sse=4759852.0, rms=11.680 (10.117%)
- 033: dt: 0.5000, sse=4037138.0, rms=10.554 (9.642%)
- 034: dt: 0.5000, sse=3461212.5, rms=9.555 (9.462%)
- 035: dt: 0.5000, sse=2991665.0, rms=8.658 (9.394%)
- 036: dt: 0.5000, sse=2602582.5, rms=7.834 (9.517%)
- 037: dt: 0.5000, sse=2276125.8, rms=7.073 (9.713%)
- 038: dt: 0.5000, sse=2023942.0, rms=6.419 (9.238%)
- 039: dt: 0.5000, sse=1823200.0, rms=5.853 (8.817%)
- 040: dt: 0.5000, sse=1683072.8, rms=5.419 (7.429%)
- 041: dt: 0.5000, sse=1578122.5, rms=5.073 (6.379%)
- 042: dt: 0.5000, sse=1513598.6, rms=4.842 (4.542%)
- 043: dt: 0.5000, sse=1466469.2, rms=4.674 (3.485%)
- 044: dt: 0.5000, sse=1441205.2, rms=4.575 (2.116%)
- 045: dt: 0.5000, sse=1422256.1, rms=4.505 (1.527%)
- rms = 4.46, time step reduction 1 of 3 to 0.250...
- 046: dt: 0.5000, sse=1410498.1, rms=4.456 (1.093%)
- 047: dt: 0.2500, sse=1342691.6, rms=4.134 (7.230%)
- 048: dt: 0.2500, sse=1325339.0, rms=4.058 (1.832%)
- rms = 4.05, time step reduction 2 of 3 to 0.125...
- 049: dt: 0.2500, sse=1325086.1, rms=4.054 (0.095%)
- rms = 4.02, time step reduction 3 of 3 to 0.062...
- 050: dt: 0.1250, sse=1317554.4, rms=4.017 (0.912%)
- positioning took 3.8 minutes
- mean border=50.0, 2327 (16) missing vertices, mean dist 0.1 [0.2 (%48.0)->0.6 (%52.0))]
- %25 local maxima, %35 large gradients and %34 min vals, 328 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=1581280.1, rms=4.218
- 051: dt: 0.5000, sse=1455028.8, rms=3.671 (12.966%)
- 052: dt: 0.5000, sse=1422030.5, rms=3.553 (3.198%)
- rms = 3.55, time step reduction 1 of 3 to 0.250...
- 053: dt: 0.5000, sse=1419740.2, rms=3.552 (0.035%)
- 054: dt: 0.2500, sse=1340842.5, rms=3.065 (13.706%)
- 055: dt: 0.2500, sse=1319575.1, rms=2.943 (3.996%)
- rms = 2.93, time step reduction 2 of 3 to 0.125...
- 056: dt: 0.2500, sse=1317783.6, rms=2.931 (0.408%)
- 057: dt: 0.1250, sse=1309214.0, rms=2.873 (1.985%)
- rms = 2.86, time step reduction 3 of 3 to 0.062...
- 058: dt: 0.1250, sse=1307431.9, rms=2.864 (0.313%)
- positioning took 1.4 minutes
- mean border=49.3, 2697 (15) missing vertices, mean dist 0.1 [0.2 (%49.4)->0.5 (%50.6))]
- %35 local maxima, %26 large gradients and %33 min vals, 362 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=1363939.2, rms=3.164
- rms = 3.26, time step reduction 1 of 3 to 0.250...
- 059: dt: 0.2500, sse=1338844.4, rms=3.016 (4.664%)
- 060: dt: 0.2500, sse=1325213.6, rms=2.941 (2.503%)
- rms = 2.91, time step reduction 2 of 3 to 0.125...
- 061: dt: 0.2500, sse=1318807.9, rms=2.911 (0.999%)
- 062: dt: 0.1250, sse=1310227.8, rms=2.855 (1.926%)
- rms = 2.84, time step reduction 3 of 3 to 0.062...
- 063: dt: 0.1250, sse=1307132.4, rms=2.840 (0.533%)
- positioning took 1.1 minutes
- mean border=48.7, 4966 (15) missing vertices, mean dist 0.1 [0.2 (%48.6)->0.4 (%51.4))]
- %39 local maxima, %21 large gradients and %32 min vals, 362 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-6.0.0/0050490/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1333719.9, rms=2.982
- rms = 3.08, time step reduction 1 of 3 to 0.250...
- 064: dt: 0.2500, sse=1318192.0, rms=2.888 (3.177%)
- 065: dt: 0.2500, sse=1304756.8, rms=2.822 (2.269%)
- rms = 2.79, time step reduction 2 of 3 to 0.125...
- 066: dt: 0.2500, sse=1297994.8, rms=2.790 (1.132%)
- 067: dt: 0.1250, sse=1288483.9, rms=2.728 (2.238%)
- rms = 2.71, time step reduction 3 of 3 to 0.062...
- 068: dt: 0.1250, sse=1284379.2, rms=2.707 (0.768%)
- positioning took 1.1 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.area.pial
- vertex spacing 1.03 +- 0.46 (0.07-->8.70) (max @ vno 104403 --> 104383)
- face area 0.42 +- 0.34 (0.00-->7.75)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 152526 vertices processed
- 25000 of 152526 vertices processed
- 50000 of 152526 vertices processed
- 75000 of 152526 vertices processed
- 100000 of 152526 vertices processed
- 125000 of 152526 vertices processed
- 150000 of 152526 vertices processed
- 0 of 152526 vertices processed
- 25000 of 152526 vertices processed
- 50000 of 152526 vertices processed
- 75000 of 152526 vertices processed
- 100000 of 152526 vertices processed
- 125000 of 152526 vertices processed
- 150000 of 152526 vertices processed
- thickness calculation complete, 709:1254 truncations.
- 28305 vertices at 0 distance
- 100548 vertices at 1 distance
- 97151 vertices at 2 distance
- 43359 vertices at 3 distance
- 14735 vertices at 4 distance
- 4848 vertices at 5 distance
- 1660 vertices at 6 distance
- 712 vertices at 7 distance
- 282 vertices at 8 distance
- 151 vertices at 9 distance
- 77 vertices at 10 distance
- 49 vertices at 11 distance
- 52 vertices at 12 distance
- 35 vertices at 13 distance
- 34 vertices at 14 distance
- 27 vertices at 15 distance
- 25 vertices at 16 distance
- 20 vertices at 17 distance
- 17 vertices at 18 distance
- 10 vertices at 19 distance
- 9 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.thickness
- positioning took 23.1 minutes
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050490 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-6.0.0/0050490/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- 18861 bright wm thresholded.
- 604 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.orig...
- computing class statistics...
- border white: 281912 voxels (1.68%)
- border gray 319696 voxels (1.91%)
- WM (96.0): 96.5 +- 9.0 [70.0 --> 110.0]
- GM (68.0) : 68.0 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 54.8 (was 70)
- setting MAX_BORDER_WHITE to 111.0 (was 105)
- setting MIN_BORDER_WHITE to 65.0 (was 85)
- setting MAX_CSF to 44.5 (was 40)
- setting MAX_GRAY to 93.0 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 54.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 34.3 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=102+-7.8, GM=65+-7.8
- mean inside = 91.7, mean outside = 72.4
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.24 (0.02-->4.01) (max @ vno 24098 --> 25235)
- face area 0.34 +- 0.15 (0.00-->4.28)
- mean absolute distance = 0.53 +- 0.78
- 3586 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- deleting segment 4 with 237 points - only 0.00% unknown
- deleting segment 5 with 35 points - only 0.00% unknown
- deleting segment 6 with 11 points - only 0.00% unknown
- mean border=78.1, 63 (63) missing vertices, mean dist 0.3 [0.6 (%17.5)->0.5 (%82.5))]
- %69 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.25 (0.05-->3.98) (max @ vno 123731 --> 123723)
- face area 0.34 +- 0.16 (0.00-->3.81)
- mean absolute distance = 0.33 +- 0.57
- 3741 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2379276.2, rms=7.415
- 001: dt: 0.5000, sse=1392713.5, rms=4.632 (37.528%)
- 002: dt: 0.5000, sse=1139185.1, rms=3.638 (21.465%)
- 003: dt: 0.5000, sse=1118103.0, rms=3.514 (3.419%)
- 004: dt: 0.5000, sse=1066665.0, rms=3.315 (5.660%)
- rms = 3.44, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.2500, sse=903378.0, rms=2.291 (30.880%)
- 006: dt: 0.2500, sse=847913.1, rms=1.800 (21.444%)
- 007: dt: 0.2500, sse=834445.1, rms=1.646 (8.535%)
- rms = 1.61, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=828903.8, rms=1.613 (2.046%)
- 009: dt: 0.1250, sse=823342.8, rms=1.547 (4.072%)
- rms = 1.54, time step reduction 3 of 3 to 0.062...
- 010: dt: 0.1250, sse=822787.3, rms=1.539 (0.519%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 1 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 40 points - only 0.00% unknown
- deleting segment 4 with 38 points - only 0.00% unknown
- deleting segment 6 with 12 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- mean border=81.1, 64 (10) missing vertices, mean dist -0.2 [0.4 (%70.9)->0.2 (%29.1))]
- %78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.25 (0.07-->4.13) (max @ vno 55092 --> 55093)
- face area 0.36 +- 0.17 (0.00-->4.49)
- mean absolute distance = 0.28 +- 0.44
- 4038 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1354921.1, rms=4.343
- 011: dt: 0.5000, sse=1060712.9, rms=2.917 (32.823%)
- rms = 3.12, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.2500, sse=935119.1, rms=2.156 (26.107%)
- 013: dt: 0.2500, sse=876738.8, rms=1.643 (23.776%)
- 014: dt: 0.2500, sse=857526.8, rms=1.441 (12.328%)
- 015: dt: 0.2500, sse=853807.1, rms=1.371 (4.841%)
- rms = 1.34, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=849497.9, rms=1.342 (2.119%)
- 017: dt: 0.1250, sse=845816.0, rms=1.287 (4.059%)
- rms = 1.28, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=845187.2, rms=1.283 (0.346%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 51 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- deleting segment 5 with 39 points - only 0.00% unknown
- deleting segment 6 with 43 points - only 0.00% unknown
- deleting segment 7 with 8 points - only 0.00% unknown
- deleting segment 8 with 7 points - only 0.00% unknown
- mean border=82.9, 77 (5) missing vertices, mean dist -0.1 [0.3 (%62.8)->0.2 (%37.2))]
- %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.07-->4.51) (max @ vno 111330 --> 110402)
- face area 0.34 +- 0.16 (0.00-->5.02)
- mean absolute distance = 0.26 +- 0.37
- 4165 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=996523.7, rms=2.757
- 019: dt: 0.5000, sse=968235.1, rms=2.546 (7.641%)
- rms = 2.93, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=861039.8, rms=1.717 (32.566%)
- 021: dt: 0.2500, sse=826542.8, rms=1.343 (21.765%)
- 022: dt: 0.2500, sse=818970.1, rms=1.251 (6.876%)
- rms = 1.24, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=817362.1, rms=1.236 (1.184%)
- 024: dt: 0.1250, sse=812619.4, rms=1.176 (4.904%)
- rms = 1.18, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=812121.3, rms=1.175 (0.027%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 99 points - only 0.00% unknown
- deleting segment 2 with 38 points - only 0.00% unknown
- deleting segment 3 with 45 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- mean border=83.6, 101 (4) missing vertices, mean dist -0.0 [0.3 (%54.0)->0.2 (%46.0))]
- %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=841924.2, rms=1.652
- rms = 1.78, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=801637.6, rms=1.167 (29.348%)
- 027: dt: 0.2500, sse=787579.9, rms=0.892 (23.588%)
- rms = 0.90, time step reduction 2 of 3 to 0.125...
- rms = 0.89, time step reduction 3 of 3 to 0.062...
- 028: dt: 0.1250, sse=784410.8, rms=0.888 (0.455%)
- positioning took 0.5 minutes
- generating cortex label...
- 7 non-cortical segments detected
- only using segment with 7688 vertices
- erasing segment 1 (vno[0] = 70657)
- erasing segment 2 (vno[0] = 96781)
- erasing segment 3 (vno[0] = 100810)
- erasing segment 4 (vno[0] = 117438)
- erasing segment 5 (vno[0] = 124558)
- erasing segment 6 (vno[0] = 154232)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.area
- vertex spacing 0.90 +- 0.25 (0.02-->4.59) (max @ vno 110402 --> 111330)
- face area 0.34 +- 0.16 (0.00-->5.04)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=53.6, 65 (65) missing vertices, mean dist 1.6 [1.9 (%0.0)->2.9 (%100.0))]
- %13 local maxima, %41 large gradients and %42 min vals, 738 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=28591284.0, rms=30.667
- 001: dt: 0.0500, sse=25126148.0, rms=28.695 (6.430%)
- 002: dt: 0.0500, sse=22636180.0, rms=27.190 (5.246%)
- 003: dt: 0.0500, sse=20726322.0, rms=25.976 (4.464%)
- 004: dt: 0.0500, sse=19182336.0, rms=24.952 (3.944%)
- 005: dt: 0.0500, sse=17887744.0, rms=24.059 (3.578%)
- 006: dt: 0.0500, sse=16771449.0, rms=23.262 (3.314%)
- 007: dt: 0.0500, sse=15788946.0, rms=22.537 (3.117%)
- 008: dt: 0.0500, sse=14910352.0, rms=21.868 (2.968%)
- 009: dt: 0.0500, sse=14115389.0, rms=21.244 (2.851%)
- 010: dt: 0.0500, sse=13390797.0, rms=20.660 (2.752%)
- positioning took 1.1 minutes
- mean border=53.5, 47 (28) missing vertices, mean dist 1.3 [0.7 (%0.0)->2.3 (%100.0))]
- %14 local maxima, %41 large gradients and %41 min vals, 700 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=14114317.0, rms=21.246
- 011: dt: 0.0500, sse=13446091.0, rms=20.708 (2.534%)
- 012: dt: 0.0500, sse=12830051.0, rms=20.199 (2.459%)
- 013: dt: 0.0500, sse=12260551.0, rms=19.716 (2.389%)
- 014: dt: 0.0500, sse=11732908.0, rms=19.258 (2.323%)
- 015: dt: 0.0500, sse=11243536.0, rms=18.824 (2.257%)
- 016: dt: 0.0500, sse=10788885.0, rms=18.410 (2.195%)
- 017: dt: 0.0500, sse=10366025.0, rms=18.017 (2.134%)
- 018: dt: 0.0500, sse=9972790.0, rms=17.644 (2.072%)
- 019: dt: 0.0500, sse=9606747.0, rms=17.289 (2.011%)
- 020: dt: 0.0500, sse=9265819.0, rms=16.952 (1.951%)
- positioning took 1.1 minutes
- mean border=53.3, 69 (18) missing vertices, mean dist 1.2 [0.1 (%1.1)->2.0 (%98.9))]
- %14 local maxima, %41 large gradients and %41 min vals, 690 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=9382395.0, rms=17.075
- 021: dt: 0.0500, sse=9057217.0, rms=16.749 (1.907%)
- 022: dt: 0.0500, sse=8754779.0, rms=16.441 (1.844%)
- 023: dt: 0.0500, sse=8471255.0, rms=16.146 (1.794%)
- 024: dt: 0.0500, sse=8207091.5, rms=15.866 (1.733%)
- 025: dt: 0.0500, sse=7960495.0, rms=15.600 (1.675%)
- 026: dt: 0.0500, sse=7729750.5, rms=15.347 (1.622%)
- 027: dt: 0.0500, sse=7512824.5, rms=15.105 (1.576%)
- 028: dt: 0.0500, sse=7307445.5, rms=14.873 (1.540%)
- 029: dt: 0.0500, sse=7112433.0, rms=14.648 (1.509%)
- 030: dt: 0.0500, sse=6927000.5, rms=14.431 (1.480%)
- positioning took 1.1 minutes
- mean border=53.3, 91 (17) missing vertices, mean dist 1.0 [0.1 (%9.9)->1.9 (%90.1))]
- %14 local maxima, %41 large gradients and %41 min vals, 661 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=7007615.0, rms=14.526
- 031: dt: 0.5000, sse=5685522.5, rms=12.889 (11.275%)
- 032: dt: 0.5000, sse=4774513.5, rms=11.618 (9.861%)
- 033: dt: 0.5000, sse=4069952.0, rms=10.530 (9.359%)
- 034: dt: 0.5000, sse=3506505.2, rms=9.566 (9.159%)
- 035: dt: 0.5000, sse=3032196.8, rms=8.673 (9.336%)
- 036: dt: 0.5000, sse=2642254.5, rms=7.861 (9.364%)
- 037: dt: 0.5000, sse=2315803.2, rms=7.114 (9.502%)
- 038: dt: 0.5000, sse=2057048.2, rms=6.459 (9.210%)
- 039: dt: 0.5000, sse=1861106.2, rms=5.916 (8.401%)
- 040: dt: 0.5000, sse=1721930.5, rms=5.496 (7.091%)
- 041: dt: 0.5000, sse=1619535.8, rms=5.168 (5.974%)
- 042: dt: 0.5000, sse=1551382.2, rms=4.933 (4.545%)
- 043: dt: 0.5000, sse=1501293.8, rms=4.757 (3.563%)
- 044: dt: 0.5000, sse=1469673.2, rms=4.639 (2.494%)
- 045: dt: 0.5000, sse=1447026.2, rms=4.555 (1.814%)
- 046: dt: 0.5000, sse=1431843.6, rms=4.495 (1.310%)
- rms = 4.46, time step reduction 1 of 3 to 0.250...
- 047: dt: 0.5000, sse=1421239.4, rms=4.455 (0.882%)
- 048: dt: 0.2500, sse=1356744.0, rms=4.149 (6.865%)
- 049: dt: 0.2500, sse=1338394.5, rms=4.072 (1.865%)
- rms = 4.07, time step reduction 2 of 3 to 0.125...
- rms = 4.05, time step reduction 3 of 3 to 0.062...
- 050: dt: 0.1250, sse=1334714.6, rms=4.054 (0.437%)
- positioning took 3.0 minutes
- mean border=52.2, 2709 (2) missing vertices, mean dist 0.2 [0.2 (%46.8)->0.7 (%53.2))]
- %25 local maxima, %33 large gradients and %36 min vals, 323 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=1646132.1, rms=4.453
- 051: dt: 0.5000, sse=1516327.1, rms=3.929 (11.773%)
- 052: dt: 0.5000, sse=1457182.1, rms=3.696 (5.927%)
- rms = 3.68, time step reduction 1 of 3 to 0.250...
- 053: dt: 0.5000, sse=1451123.4, rms=3.675 (0.554%)
- 054: dt: 0.2500, sse=1363523.4, rms=3.170 (13.762%)
- 055: dt: 0.2500, sse=1339227.8, rms=3.034 (4.269%)
- rms = 3.01, time step reduction 2 of 3 to 0.125...
- 056: dt: 0.2500, sse=1334617.8, rms=3.007 (0.908%)
- 057: dt: 0.1250, sse=1322336.6, rms=2.929 (2.594%)
- rms = 2.91, time step reduction 3 of 3 to 0.062...
- 058: dt: 0.1250, sse=1318630.8, rms=2.908 (0.714%)
- positioning took 1.4 minutes
- mean border=51.4, 2983 (2) missing vertices, mean dist 0.1 [0.2 (%46.6)->0.5 (%53.4))]
- %34 local maxima, %24 large gradients and %35 min vals, 366 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=1393568.2, rms=3.275
- rms = 3.32, time step reduction 1 of 3 to 0.250...
- 059: dt: 0.2500, sse=1362484.8, rms=3.101 (5.307%)
- 060: dt: 0.2500, sse=1342400.1, rms=2.990 (3.593%)
- rms = 2.95, time step reduction 2 of 3 to 0.125...
- 061: dt: 0.2500, sse=1334520.8, rms=2.952 (1.272%)
- 062: dt: 0.1250, sse=1323991.2, rms=2.885 (2.278%)
- rms = 2.86, time step reduction 3 of 3 to 0.062...
- 063: dt: 0.1250, sse=1319919.6, rms=2.864 (0.723%)
- positioning took 1.1 minutes
- mean border=50.9, 5447 (2) missing vertices, mean dist 0.1 [0.2 (%45.6)->0.4 (%54.4))]
- %39 local maxima, %19 large gradients and %34 min vals, 371 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-6.0.0/0050490/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=1349689.9, rms=3.016
- rms = 3.11, time step reduction 1 of 3 to 0.250...
- 064: dt: 0.2500, sse=1331967.5, rms=2.910 (3.531%)
- 065: dt: 0.2500, sse=1317083.9, rms=2.834 (2.613%)
- rms = 2.81, time step reduction 2 of 3 to 0.125...
- 066: dt: 0.2500, sse=1310877.5, rms=2.807 (0.961%)
- 067: dt: 0.1250, sse=1299727.8, rms=2.735 (2.560%)
- rms = 2.71, time step reduction 3 of 3 to 0.062...
- 068: dt: 0.1250, sse=1295306.6, rms=2.712 (0.831%)
- positioning took 1.1 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.area.pial
- vertex spacing 1.03 +- 0.46 (0.04-->7.33) (max @ vno 106470 --> 105422)
- face area 0.42 +- 0.33 (0.00-->5.92)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 154525 vertices processed
- 25000 of 154525 vertices processed
- 50000 of 154525 vertices processed
- 75000 of 154525 vertices processed
- 100000 of 154525 vertices processed
- 125000 of 154525 vertices processed
- 150000 of 154525 vertices processed
- 0 of 154525 vertices processed
- 25000 of 154525 vertices processed
- 50000 of 154525 vertices processed
- 75000 of 154525 vertices processed
- 100000 of 154525 vertices processed
- 125000 of 154525 vertices processed
- 150000 of 154525 vertices processed
- thickness calculation complete, 734:1585 truncations.
- 31621 vertices at 0 distance
- 103576 vertices at 1 distance
- 95035 vertices at 2 distance
- 43210 vertices at 3 distance
- 14846 vertices at 4 distance
- 4800 vertices at 5 distance
- 1698 vertices at 6 distance
- 692 vertices at 7 distance
- 258 vertices at 8 distance
- 108 vertices at 9 distance
- 84 vertices at 10 distance
- 48 vertices at 11 distance
- 38 vertices at 12 distance
- 34 vertices at 13 distance
- 16 vertices at 14 distance
- 21 vertices at 15 distance
- 20 vertices at 16 distance
- 12 vertices at 17 distance
- 13 vertices at 18 distance
- 10 vertices at 19 distance
- 32 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.thickness
- positioning took 17.7 minutes
- PIDs (5286 5289) completed and logs appended.
- #--------------------------------------------
- #@# Surf Volume lh Sun Oct 8 14:15:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label
- Total face volume 297729
- Total vertex volume 293320 (mask=0)
- #@# 0050490 lh 293320
-
- vertexvol Done
- #--------------------------------------------
- #@# Surf Volume rh Sun Oct 8 14:15:52 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label
- Total face volume 297991
- Total vertex volume 293786 (mask=0)
- #@# 0050490 rh 293786
-
- vertexvol Done
- #--------------------------------------------
- #@# Cortical ribbon mask Sun Oct 8 14:16:00 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490
- 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 = 311
- writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/ribbon.mgz
- mris_volmask took 19.25 minutes
- writing ribbon files
- #-----------------------------------------
- #@# Parcellation Stats lh Sun Oct 8 14:35:15 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 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 0050490 lh pial
- #-----------------------------------------
- #@# Parcellation Stats rh Sun Oct 8 14:35:15 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 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 0050490 rh pial
- Waiting for PID 6925 of (6925 6929 6934 6937) to complete...
- Waiting for PID 6929 of (6925 6929 6934 6937) to complete...
- Waiting for PID 6934 of (6925 6929 6934 6937) to complete...
- Waiting for PID 6937 of (6925 6929 6934 6937) 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 0050490 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297729
- Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 1452 1028 2661 2.640 0.489 0.110 0.025 10 1.3 bankssts
- 1130 742 2422 2.880 0.730 0.148 0.029 17 1.3 caudalanteriorcingulate
- 3987 2675 8257 2.798 0.629 0.123 0.036 45 6.4 caudalmiddlefrontal
- 2750 1882 3901 1.982 0.482 0.148 0.036 38 4.1 cuneus
- 527 361 1926 3.722 0.757 0.122 0.044 7 0.8 entorhinal
- 6037 4214 13566 2.775 0.717 0.124 0.032 72 8.0 fusiform
- 7306 5107 14077 2.448 0.647 0.130 0.028 93 8.9 inferiorparietal
- 5250 3743 14228 3.160 0.694 0.135 0.038 74 8.5 inferiortemporal
- 1625 1077 2893 2.389 0.953 0.133 0.037 23 2.1 isthmuscingulate
- 8572 5758 14417 2.165 0.614 0.141 0.036 115 11.9 lateraloccipital
- 4121 2871 8747 2.819 0.621 0.135 0.034 57 6.0 lateralorbitofrontal
- 5026 3521 7675 2.113 0.587 0.138 0.039 63 7.5 lingual
- 2518 1726 5388 2.614 0.821 0.132 0.035 42 3.5 medialorbitofrontal
- 4865 3382 11099 2.763 0.741 0.128 0.030 63 6.2 middletemporal
- 1080 714 2323 2.786 0.693 0.092 0.016 6 0.7 parahippocampal
- 2692 1803 5201 2.585 0.593 0.125 0.032 27 3.4 paracentral
- 2462 1711 5337 2.710 0.502 0.119 0.029 26 2.8 parsopercularis
- 1105 746 2897 2.829 0.617 0.134 0.044 17 1.8 parsorbitalis
- 1988 1334 4133 2.681 0.549 0.117 0.025 20 1.7 parstriangularis
- 1967 1360 1953 1.626 0.396 0.124 0.026 16 2.2 pericalcarine
- 6782 4518 11402 2.222 0.709 0.125 0.031 80 8.9 postcentral
- 2283 1560 4441 2.516 0.933 0.137 0.028 32 2.8 posteriorcingulate
- 7533 4881 14542 2.755 0.678 0.116 0.030 67 9.1 precentral
- 6155 4311 11223 2.453 0.594 0.134 0.033 73 8.3 precuneus
- 1364 933 3496 3.236 0.762 0.157 0.039 27 2.0 rostralanteriorcingulate
- 9697 6739 20612 2.573 0.626 0.138 0.036 156 14.1 rostralmiddlefrontal
- 13821 9483 32681 2.994 0.655 0.129 0.032 168 17.6 superiorfrontal
- 8771 5953 15975 2.371 0.615 0.130 0.031 103 10.3 superiorparietal
- 6992 4684 16370 3.002 0.714 0.111 0.025 72 6.9 superiortemporal
- 7552 5288 15015 2.530 0.621 0.128 0.030 91 9.1 supramarginal
- 468 316 1392 2.784 0.834 0.164 0.067 11 1.3 frontalpole
- 723 555 2833 3.643 0.897 0.132 0.026 10 0.9 temporalpole
- 833 537 1339 2.590 0.518 0.130 0.029 9 0.9 transversetemporal
- 4113 2847 8890 3.098 0.720 0.129 0.037 42 6.3 insula
- mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050490 lh pial
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297729
- Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 1452 1003 2661 2.640 0.489 0.133 0.039 21 2.5 bankssts
- 1130 910 2422 2.880 0.730 0.157 0.039 39 1.6 caudalanteriorcingulate
- 3987 3193 8257 2.798 0.629 0.141 0.035 49 6.0 caudalmiddlefrontal
- 2750 2164 3901 1.982 0.482 0.143 0.035 42 4.4 cuneus
- 527 711 1926 3.722 0.757 0.212 0.052 6 1.2 entorhinal
- 6037 5415 13566 2.775 0.717 0.156 0.040 87 11.3 fusiform
- 7306 6359 14077 2.448 0.647 0.154 0.036 100 11.7 inferiorparietal
- 5250 4952 14228 3.160 0.694 0.164 0.043 93 10.3 inferiortemporal
- 1625 1304 2893 2.389 0.953 0.140 0.038 28 2.4 isthmuscingulate
- 8572 7293 14417 2.165 0.614 0.150 0.034 136 13.5 lateraloccipital
- 4121 3369 8747 2.819 0.621 0.147 0.038 65 7.1 lateralorbitofrontal
- 5026 4030 7675 2.113 0.587 0.141 0.036 74 8.2 lingual
- 2518 2321 5388 2.614 0.821 0.166 0.040 31 4.8 medialorbitofrontal
- 4865 4403 11099 2.763 0.741 0.156 0.039 70 8.7 middletemporal
- 1080 996 2323 2.786 0.693 0.140 0.033 9 1.7 parahippocampal
- 2692 2168 5201 2.585 0.593 0.137 0.033 31 4.1 paracentral
- 2462 2186 5337 2.710 0.502 0.154 0.033 26 3.9 parsopercularis
- 1105 1187 2897 2.829 0.617 0.187 0.041 15 2.2 parsorbitalis
- 1988 1672 4133 2.681 0.549 0.153 0.035 25 3.2 parstriangularis
- 1967 1123 1953 1.626 0.396 0.115 0.028 21 2.6 pericalcarine
- 6782 5650 11402 2.222 0.709 0.140 0.032 77 10.1 postcentral
- 2283 1905 4441 2.516 0.933 0.157 0.041 83 4.1 posteriorcingulate
- 7533 5488 14542 2.755 0.678 0.115 0.028 83 9.4 precentral
- 6155 4731 11223 2.453 0.594 0.148 0.040 113 11.1 precuneus
- 1364 1236 3496 3.236 0.762 0.171 0.049 33 2.9 rostralanteriorcingulate
- 9697 8887 20612 2.573 0.626 0.171 0.039 153 17.5 rostralmiddlefrontal
- 13821 11893 32681 2.994 0.655 0.152 0.039 216 24.2 superiorfrontal
- 8771 7229 15975 2.371 0.615 0.148 0.036 121 14.1 superiorparietal
- 6992 5936 16370 3.002 0.714 0.136 0.030 71 9.2 superiortemporal
- 7552 6549 15015 2.530 0.621 0.154 0.037 113 12.9 supramarginal
- 468 613 1392 2.784 0.834 0.242 0.059 8 1.4 frontalpole
- 723 988 2833 3.643 0.897 0.205 0.038 9 1.4 temporalpole
- 833 523 1339 2.590 0.518 0.108 0.028 7 1.0 transversetemporal
- 4113 2707 8890 3.098 0.720 0.138 0.043 79 8.0 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 0050490 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297991
- Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 1359 1001 2708 2.833 0.532 0.109 0.018 10 1.0 bankssts
- 1530 1019 3131 2.595 0.732 0.134 0.025 25 1.5 caudalanteriorcingulate
- 3447 2402 7266 2.704 0.639 0.125 0.027 36 3.8 caudalmiddlefrontal
- 2755 1846 3927 2.065 0.530 0.152 0.040 37 4.6 cuneus
- 751 478 2815 3.328 1.029 0.130 0.051 11 1.7 entorhinal
- 5943 4104 14178 2.905 0.792 0.132 0.036 79 8.2 fusiform
- 10788 7450 21775 2.585 0.647 0.128 0.030 127 12.8 inferiorparietal
- 5597 3803 13810 3.081 0.844 0.124 0.034 63 7.0 inferiortemporal
- 1375 911 2858 2.659 1.074 0.137 0.038 21 1.9 isthmuscingulate
- 9417 6261 15954 2.365 0.633 0.142 0.037 125 13.5 lateraloccipital
- 4059 2763 8200 2.645 0.626 0.130 0.035 60 5.3 lateralorbitofrontal
- 4842 3413 7321 2.031 0.608 0.142 0.038 64 7.6 lingual
- 2960 2070 6043 2.429 0.785 0.135 0.039 52 4.5 medialorbitofrontal
- 5427 3778 13797 3.042 0.646 0.119 0.027 66 5.6 middletemporal
- 1221 803 2591 2.817 0.646 0.109 0.024 10 1.1 parahippocampal
- 2458 1655 4340 2.473 0.492 0.111 0.030 21 2.8 paracentral
- 1717 1199 3677 2.733 0.561 0.109 0.020 18 1.3 parsopercularis
- 1340 945 3241 2.677 0.786 0.142 0.033 23 1.7 parsorbitalis
- 1923 1356 3861 2.403 0.563 0.124 0.025 25 1.8 parstriangularis
- 2217 1520 2262 1.698 0.464 0.125 0.027 23 2.4 pericalcarine
- 5982 3857 9758 2.277 0.724 0.116 0.026 60 6.2 postcentral
- 1900 1305 3423 2.369 0.730 0.147 0.037 30 2.8 posteriorcingulate
- 8693 5674 16188 2.650 0.685 0.113 0.026 74 9.2 precentral
- 6796 4767 12237 2.464 0.602 0.131 0.033 85 9.0 precuneus
- 1213 834 2865 2.834 0.661 0.128 0.032 17 1.6 rostralanteriorcingulate
- 9558 6521 18653 2.312 0.671 0.134 0.037 184 14.0 rostralmiddlefrontal
- 13200 8958 29919 2.788 0.715 0.130 0.033 207 17.4 superiorfrontal
- 9310 6213 16864 2.369 0.635 0.130 0.034 113 13.1 superiorparietal
- 6018 4002 13607 2.963 0.641 0.107 0.027 61 6.0 superiortemporal
- 6437 4324 12621 2.676 0.555 0.121 0.031 70 7.8 supramarginal
- 573 379 1752 2.987 0.695 0.179 0.071 23 1.8 frontalpole
- 686 520 2652 3.467 0.838 0.154 0.042 15 1.2 temporalpole
- 566 329 1082 3.080 0.574 0.110 0.033 6 0.8 transversetemporal
- 3990 2677 8366 3.154 0.773 0.126 0.034 52 5.4 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 0050490 rh pial
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297991
- Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 1359 929 2708 2.833 0.532 0.129 0.036 20 2.0 bankssts
- 1530 1303 3131 2.595 0.732 0.146 0.036 28 2.2 caudalanteriorcingulate
- 3447 2793 7266 2.704 0.639 0.142 0.033 41 5.2 caudalmiddlefrontal
- 2755 2109 3927 2.065 0.530 0.137 0.034 42 4.1 cuneus
- 751 1002 2815 3.328 1.029 0.193 0.042 8 1.5 entorhinal
- 5943 5499 14178 2.905 0.792 0.155 0.038 88 10.2 fusiform
- 10788 8967 21775 2.585 0.647 0.141 0.032 152 15.5 inferiorparietal
- 5597 4875 13810 3.081 0.844 0.149 0.039 88 9.9 inferiortemporal
- 1375 1171 2858 2.659 1.074 0.161 0.040 31 2.4 isthmuscingulate
- 9417 7273 15954 2.365 0.633 0.137 0.037 132 15.6 lateraloccipital
- 4059 3491 8200 2.645 0.626 0.169 0.043 66 8.1 lateralorbitofrontal
- 4842 3899 7321 2.031 0.608 0.140 0.035 61 7.5 lingual
- 2960 2774 6043 2.429 0.785 0.175 0.043 44 5.8 medialorbitofrontal
- 5427 5209 13797 3.042 0.646 0.157 0.033 72 8.6 middletemporal
- 1221 1032 2591 2.817 0.646 0.137 0.030 15 1.8 parahippocampal
- 2458 1841 4340 2.473 0.492 0.122 0.027 31 3.0 paracentral
- 1717 1516 3677 2.733 0.561 0.152 0.032 22 2.5 parsopercularis
- 1340 1433 3241 2.677 0.786 0.193 0.042 21 2.6 parsorbitalis
- 1923 1821 3861 2.403 0.563 0.165 0.035 24 3.1 parstriangularis
- 2217 1296 2262 1.698 0.464 0.119 0.033 29 3.2 pericalcarine
- 5982 4681 9758 2.277 0.724 0.127 0.030 53 7.8 postcentral
- 1900 1535 3423 2.369 0.730 0.160 0.044 41 3.7 posteriorcingulate
- 8693 6265 16188 2.650 0.685 0.113 0.025 91 10.0 precentral
- 6796 5168 12237 2.464 0.602 0.146 0.039 104 11.8 precuneus
- 1213 1143 2865 2.834 0.661 0.164 0.040 13 2.1 rostralanteriorcingulate
- 9558 9130 18653 2.312 0.671 0.181 0.044 140 19.8 rostralmiddlefrontal
- 13200 11970 29919 2.788 0.715 0.164 0.041 195 24.3 superiorfrontal
- 9310 7647 16864 2.369 0.635 0.143 0.034 117 14.1 superiorparietal
- 6018 5043 13607 2.963 0.641 0.140 0.032 77 8.7 superiortemporal
- 6437 4970 12621 2.676 0.555 0.136 0.034 77 9.7 supramarginal
- 573 790 1752 2.987 0.695 0.236 0.049 7 1.6 frontalpole
- 686 996 2652 3.467 0.838 0.241 0.048 8 1.7 temporalpole
- 566 388 1082 3.080 0.574 0.101 0.024 3 0.6 transversetemporal
- 3990 2454 8366 3.154 0.773 0.132 0.038 83 6.1 insula
- PIDs (6925 6929 6934 6937) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 2 lh Sun Oct 8 14:37:42 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 14:37:42 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 7046 of (7046 7049) to complete...
- Waiting for PID 7049 of (7046 7049) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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...
- 7 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9715 changed, 152526 examined...
- 001: 2311 changed, 38077 examined...
- 002: 662 changed, 11921 examined...
- 003: 253 changed, 3765 examined...
- 004: 130 changed, 1497 examined...
- 005: 62 changed, 723 examined...
- 006: 37 changed, 362 examined...
- 007: 23 changed, 212 examined...
- 008: 14 changed, 119 examined...
- 009: 4 changed, 69 examined...
- 010: 2 changed, 22 examined...
- 011: 0 changed, 14 examined...
- 0 labels changed using aseg
- 000: 283 total segments, 194 labels (2687 vertices) changed
- 001: 94 total segments, 6 labels (27 vertices) changed
- 002: 88 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 29 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 662 vertices marked for relabeling...
- 662 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 0 minutes and 20 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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...
- 0 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9915 changed, 154525 examined...
- 001: 2243 changed, 39162 examined...
- 002: 642 changed, 11781 examined...
- 003: 291 changed, 3635 examined...
- 004: 149 changed, 1654 examined...
- 005: 90 changed, 838 examined...
- 006: 40 changed, 487 examined...
- 007: 11 changed, 212 examined...
- 008: 4 changed, 71 examined...
- 009: 3 changed, 22 examined...
- 010: 0 changed, 19 examined...
- 1 labels changed using aseg
- 000: 275 total segments, 188 labels (2584 vertices) changed
- 001: 97 total segments, 10 labels (25 vertices) changed
- 002: 87 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 50 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1098 vertices marked for relabeling...
- 1098 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 0 minutes and 36 seconds.
- PIDs (7046 7049) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Sun Oct 8 14:38:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 lh white
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Sun Oct 8 14:38:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 rh white
- Waiting for PID 7125 of (7125 7128) to complete...
- Waiting for PID 7128 of (7125 7128) 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 0050490 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297729
- Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 1566 1101 3361 2.448 0.695 0.145 0.042 28 2.7 G&S_frontomargin
- 2008 1429 4160 2.425 0.664 0.142 0.034 25 2.7 G&S_occipital_inf
- 1977 1282 3753 2.413 0.552 0.136 0.047 28 4.0 G&S_paracentral
- 1795 1203 4090 2.933 0.635 0.126 0.027 19 2.0 G&S_subcentral
- 1019 698 2831 2.723 0.772 0.154 0.051 21 2.1 G&S_transv_frontopol
- 2761 1910 6184 2.969 0.662 0.132 0.031 38 3.5 G&S_cingul-Ant
- 1635 1142 3549 2.937 0.538 0.130 0.026 16 1.9 G&S_cingul-Mid-Ant
- 1696 1176 3317 2.726 0.717 0.127 0.027 17 1.8 G&S_cingul-Mid-Post
- 759 529 2148 3.175 0.857 0.155 0.042 13 1.2 G_cingul-Post-dorsal
- 307 194 751 2.943 0.800 0.138 0.046 4 0.5 G_cingul-Post-ventral
- 2467 1695 3778 1.980 0.542 0.154 0.037 37 3.7 G_cuneus
- 1452 971 3707 2.885 0.495 0.138 0.040 22 2.3 G_front_inf-Opercular
- 439 289 1002 2.505 0.489 0.135 0.058 9 0.8 G_front_inf-Orbital
- 1212 780 3197 2.869 0.575 0.125 0.030 17 1.3 G_front_inf-Triangul
- 5307 3589 13466 2.801 0.647 0.153 0.049 115 11.1 G_front_middle
- 9689 6544 25607 3.070 0.690 0.137 0.037 143 14.0 G_front_sup
- 883 621 2070 3.095 0.873 0.159 0.059 15 2.2 G_Ins_lg&S_cent_ins
- 978 691 3223 3.603 0.744 0.150 0.047 15 1.9 G_insular_short
- 2611 1733 5689 2.445 0.715 0.145 0.039 43 3.8 G_occipital_middle
- 1861 1234 3188 2.212 0.556 0.141 0.032 25 2.3 G_occipital_sup
- 2642 1793 6850 2.937 0.799 0.139 0.039 43 4.2 G_oc-temp_lat-fusifor
- 3428 2411 5622 2.055 0.611 0.148 0.047 50 6.1 G_oc-temp_med-Lingual
- 1243 804 3536 3.202 0.810 0.101 0.023 10 1.1 G_oc-temp_med-Parahip
- 2707 1900 7468 2.951 0.679 0.143 0.040 47 4.4 G_orbital
- 3150 2211 8185 2.759 0.713 0.148 0.038 60 4.9 G_pariet_inf-Angular
- 3910 2738 8759 2.546 0.655 0.133 0.033 55 5.2 G_pariet_inf-Supramar
- 3468 2321 7344 2.485 0.694 0.139 0.036 54 4.7 G_parietal_sup
- 2515 1608 4529 2.267 0.660 0.138 0.038 38 3.7 G_postcentral
- 2701 1668 6887 3.056 0.649 0.120 0.038 33 3.7 G_precentral
- 2841 2062 6700 2.511 0.681 0.152 0.043 47 4.9 G_precuneus
- 940 643 2473 2.746 0.776 0.165 0.059 23 2.4 G_rectus
- 172 119 399 3.772 0.579 0.078 0.017 1 0.1 G_subcallosal
- 606 343 1072 2.664 0.572 0.117 0.031 7 0.7 G_temp_sup-G_T_transv
- 2298 1491 7795 3.422 0.690 0.137 0.038 41 3.0 G_temp_sup-Lateral
- 1053 709 2829 3.536 0.704 0.074 0.016 4 0.7 G_temp_sup-Plan_polar
- 1305 941 2614 2.498 0.705 0.128 0.029 17 1.6 G_temp_sup-Plan_tempo
- 2672 1889 8494 3.287 0.747 0.151 0.049 49 5.5 G_temporal_inf
- 2424 1711 6910 2.916 0.777 0.147 0.040 44 4.2 G_temporal_middle
- 363 245 533 2.514 0.372 0.094 0.015 2 0.2 Lat_Fis-ant-Horizont
- 315 236 532 2.555 0.495 0.110 0.016 2 0.2 Lat_Fis-ant-Vertical
- 1255 853 1691 2.555 0.589 0.115 0.024 9 1.2 Lat_Fis-post
- 2455 1549 3480 2.027 0.505 0.148 0.042 39 4.1 Pole_occipital
- 1752 1314 6109 3.268 0.766 0.151 0.040 32 3.0 Pole_temporal
- 2388 1661 2732 1.916 0.658 0.121 0.027 18 2.8 S_calcarine
- 3456 2289 4041 2.036 0.637 0.106 0.024 21 3.4 S_central
- 1210 835 1779 2.357 0.559 0.123 0.024 10 1.3 S_cingul-Marginalis
- 509 352 853 3.013 0.349 0.100 0.020 2 0.4 S_circular_insula_ant
- 1687 1171 2747 2.925 0.472 0.089 0.015 7 1.1 S_circular_insula_inf
- 1943 1327 2933 2.846 0.520 0.106 0.021 9 1.8 S_circular_insula_sup
- 1251 858 2586 3.000 0.523 0.104 0.022 10 1.2 S_collat_transv_ant
- 517 355 619 2.015 0.395 0.125 0.025 4 0.5 S_collat_transv_post
- 2205 1549 3299 2.236 0.506 0.103 0.018 16 1.5 S_front_inf
- 1911 1302 2934 2.475 0.463 0.111 0.021 12 1.7 S_front_middle
- 3675 2594 6929 2.800 0.522 0.119 0.028 29 4.0 S_front_sup
- 648 456 931 2.484 0.393 0.106 0.018 4 0.5 S_interm_prim-Jensen
- 3334 2357 5226 2.386 0.462 0.124 0.024 28 3.3 S_intrapariet&P_trans
- 1048 728 1191 1.899 0.476 0.127 0.025 9 1.1 S_oc_middle&Lunatus
- 1536 1039 1982 2.046 0.430 0.111 0.020 10 1.2 S_oc_sup&transversal
- 768 542 1170 2.228 0.562 0.112 0.034 6 0.9 S_occipital_ant
- 1370 965 2197 2.683 0.482 0.098 0.016 8 1.0 S_oc-temp_lat
- 2774 1967 4116 2.358 0.486 0.110 0.022 19 2.4 S_oc-temp_med&Lingual
- 451 312 623 2.286 0.422 0.118 0.019 3 0.4 S_orbital_lateral
- 520 392 974 2.722 0.661 0.126 0.019 4 0.4 S_orbital_med-olfact
- 1488 1038 2748 2.714 0.617 0.124 0.028 14 1.8 S_orbital-H_Shaped
- 2399 1651 3502 2.325 0.512 0.113 0.025 18 2.4 S_parieto_occipital
- 1590 948 1450 1.980 0.951 0.129 0.022 27 1.2 S_pericallosal
- 3041 2075 4351 2.273 0.542 0.120 0.028 25 3.3 S_postcentral
- 1963 1358 3232 2.626 0.495 0.113 0.021 13 1.8 S_precentral-inf-part
- 1117 791 1718 2.484 0.606 0.110 0.021 7 1.0 S_precentral-sup-part
- 784 542 1304 2.452 0.859 0.124 0.024 8 0.7 S_suborbital
- 1189 831 1656 2.400 0.507 0.124 0.027 10 1.3 S_subparietal
- 1490 1077 2836 2.761 0.733 0.113 0.024 9 1.5 S_temporal_inf
- 6360 4427 10353 2.476 0.587 0.109 0.021 48 5.7 S_temporal_sup
- 292 203 424 2.537 0.477 0.117 0.018 3 0.2 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 0050490 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297991
- Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 1304 853 2188 2.086 0.730 0.151 0.051 43 3.2 G&S_frontomargin
- 1889 1295 3781 2.645 0.542 0.140 0.039 25 2.8 G&S_occipital_inf
- 1509 940 2648 2.368 0.608 0.119 0.035 15 2.1 G&S_paracentral
- 1305 846 3168 3.147 0.522 0.126 0.028 15 1.4 G&S_subcentral
- 1591 1071 3889 2.593 0.700 0.140 0.038 32 2.5 G&S_transv_frontopol
- 3491 2405 7049 2.565 0.655 0.130 0.031 47 4.5 G&S_cingul-Ant
- 1636 1151 3547 2.944 0.495 0.113 0.022 16 1.4 G&S_cingul-Mid-Ant
- 1599 1101 3106 2.654 0.589 0.132 0.036 17 2.2 G&S_cingul-Mid-Post
- 546 361 1523 3.066 0.923 0.167 0.050 12 1.0 G_cingul-Post-dorsal
- 346 238 784 2.529 0.727 0.160 0.050 7 0.7 G_cingul-Post-ventral
- 2454 1635 3572 2.012 0.557 0.152 0.040 36 3.9 G_cuneus
- 1228 831 3237 2.894 0.529 0.125 0.024 19 1.2 G_front_inf-Opercular
- 431 288 1190 2.856 0.490 0.145 0.031 9 0.6 G_front_inf-Orbital
- 751 534 1867 2.589 0.478 0.129 0.029 12 0.8 G_front_inf-Triangul
- 4543 3081 12387 2.810 0.678 0.151 0.046 111 8.1 G_front_middle
- 8770 5905 22615 2.903 0.747 0.141 0.041 181 14.4 G_front_sup
- 758 515 1700 3.147 0.952 0.139 0.043 10 1.1 G_Ins_lg&S_cent_ins
- 858 560 2523 3.460 0.870 0.148 0.051 15 1.7 G_insular_short
- 3032 2005 6716 2.700 0.730 0.149 0.041 47 4.7 G_occipital_middle
- 1968 1256 3650 2.363 0.620 0.152 0.054 35 4.8 G_occipital_sup
- 2942 1978 7820 3.002 0.801 0.150 0.046 53 5.0 G_oc-temp_lat-fusifor
- 3276 2294 5247 1.995 0.639 0.142 0.039 45 5.0 G_oc-temp_med-Lingual
- 1402 875 4200 3.156 0.806 0.116 0.039 15 2.2 G_oc-temp_med-Parahip
- 3003 2030 7863 2.776 0.705 0.146 0.043 70 4.7 G_orbital
- 4637 3087 11324 2.803 0.678 0.138 0.037 71 6.6 G_pariet_inf-Angular
- 2925 1881 6668 2.795 0.601 0.132 0.041 44 4.6 G_pariet_inf-Supramar
- 2810 1852 6706 2.610 0.746 0.133 0.037 40 4.0 G_parietal_sup
- 2146 1298 3804 2.276 0.640 0.122 0.031 28 2.6 G_postcentral
- 3587 2256 8378 2.780 0.785 0.118 0.032 40 4.6 G_precentral
- 2851 1999 6357 2.558 0.597 0.147 0.040 52 4.6 G_precuneus
- 873 608 2429 2.628 0.764 0.154 0.056 28 1.9 G_rectus
- 145 111 402 3.441 0.671 0.121 0.025 1 0.1 G_subcallosal
- 538 290 1075 2.923 0.514 0.090 0.033 5 0.7 G_temp_sup-G_T_transv
- 1975 1322 5939 3.232 0.655 0.137 0.041 35 3.1 G_temp_sup-Lateral
- 684 503 1964 3.357 0.667 0.094 0.019 4 0.6 G_temp_sup-Plan_polar
- 929 646 2021 2.826 0.524 0.100 0.023 6 0.8 G_temp_sup-Plan_tempo
- 2883 1930 9151 3.311 0.872 0.138 0.044 44 4.5 G_temporal_inf
- 3255 2215 9844 3.202 0.651 0.128 0.031 49 3.9 G_temporal_middle
- 362 255 433 2.030 0.567 0.097 0.012 2 0.1 Lat_Fis-ant-Horizont
- 242 184 356 2.104 0.432 0.102 0.016 1 0.1 Lat_Fis-ant-Vertical
- 1487 1016 2372 2.923 0.619 0.101 0.021 7 1.2 Lat_Fis-post
- 4202 2724 6171 2.031 0.530 0.143 0.038 57 6.6 Pole_occipital
- 2055 1458 6898 3.169 0.763 0.141 0.045 41 3.5 Pole_temporal
- 2295 1569 2815 2.106 0.747 0.124 0.027 21 2.6 S_calcarine
- 3571 2427 4159 2.011 0.539 0.106 0.021 23 3.1 S_central
- 1460 993 2211 2.305 0.487 0.108 0.027 12 1.4 S_cingul-Marginalis
- 748 519 1218 2.869 0.432 0.109 0.023 3 0.8 S_circular_insula_ant
- 1603 1058 2357 2.718 0.586 0.081 0.014 6 1.0 S_circular_insula_inf
- 1481 1007 2493 2.908 0.580 0.110 0.022 8 1.4 S_circular_insula_sup
- 1159 798 2561 3.172 0.779 0.100 0.021 7 0.9 S_collat_transv_ant
- 655 448 780 2.394 0.547 0.147 0.035 7 0.8 S_collat_transv_post
- 1690 1178 2545 2.231 0.499 0.120 0.027 17 1.7 S_front_inf
- 2678 1873 3635 1.988 0.486 0.108 0.021 19 2.1 S_front_middle
- 3124 2174 5185 2.400 0.553 0.119 0.024 26 3.2 S_front_sup
- 797 547 1061 2.459 0.392 0.092 0.015 3 0.6 S_interm_prim-Jensen
- 4411 3047 6130 2.225 0.499 0.116 0.024 36 4.2 S_intrapariet&P_trans
- 1070 763 1404 2.190 0.378 0.126 0.028 8 1.1 S_oc_middle&Lunatus
- 1622 1150 2103 2.108 0.392 0.127 0.024 14 1.6 S_oc_sup&transversal
- 920 631 1402 2.505 0.513 0.125 0.025 7 1.0 S_occipital_ant
- 1756 1217 2890 2.648 0.602 0.101 0.022 10 1.6 S_oc-temp_lat
- 2310 1680 3390 2.345 0.619 0.118 0.022 19 2.1 S_oc-temp_med&Lingual
- 548 366 654 1.931 0.471 0.133 0.025 6 0.6 S_orbital_lateral
- 682 475 1088 2.566 0.852 0.124 0.040 10 1.0 S_orbital_med-olfact
- 1515 1065 2532 2.350 0.485 0.125 0.025 18 1.5 S_orbital-H_Shaped
- 2457 1715 3419 2.312 0.521 0.113 0.024 19 2.6 S_parieto_occipital
- 1723 1103 1651 1.894 0.732 0.125 0.019 24 1.1 S_pericallosal
- 2406 1622 3265 2.248 0.474 0.129 0.028 24 2.7 S_postcentral
- 1522 1071 2636 2.772 0.477 0.102 0.018 9 1.0 S_precentral-inf-part
- 1791 1262 2842 2.723 0.443 0.095 0.016 7 1.3 S_precentral-sup-part
- 508 351 667 2.218 0.802 0.115 0.016 4 0.3 S_suborbital
- 1680 1209 3067 2.629 0.691 0.137 0.031 18 2.2 S_subparietal
- 1273 895 2126 2.788 0.789 0.108 0.019 8 1.0 S_temporal_inf
- 7181 5104 12593 2.679 0.598 0.109 0.020 53 5.8 S_temporal_sup
- 221 147 345 3.032 0.567 0.166 0.030 4 0.3 S_temporal_transverse
- PIDs (7125 7128) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 3 lh Sun Oct 8 14:39:54 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 14:39:54 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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 7203 of (7203 7206) to complete...
- Waiting for PID 7206 of (7203 7206) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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...
- 1281 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2119 changed, 152526 examined...
- 001: 464 changed, 9900 examined...
- 002: 125 changed, 2681 examined...
- 003: 44 changed, 734 examined...
- 004: 19 changed, 267 examined...
- 005: 19 changed, 110 examined...
- 006: 12 changed, 99 examined...
- 007: 14 changed, 72 examined...
- 008: 12 changed, 77 examined...
- 009: 9 changed, 47 examined...
- 010: 10 changed, 50 examined...
- 011: 11 changed, 57 examined...
- 012: 7 changed, 53 examined...
- 013: 5 changed, 34 examined...
- 014: 3 changed, 27 examined...
- 015: 2 changed, 18 examined...
- 016: 1 changed, 12 examined...
- 017: 3 changed, 10 examined...
- 018: 1 changed, 9 examined...
- 019: 1 changed, 7 examined...
- 020: 0 changed, 9 examined...
- 236 labels changed using aseg
- 000: 56 total segments, 23 labels (143 vertices) changed
- 001: 34 total segments, 1 labels (1 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 10 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 578 vertices marked for relabeling...
- 578 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas.annot...
- classification took 0 minutes and 31 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050490 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...
- 1246 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2119 changed, 154525 examined...
- 001: 522 changed, 9999 examined...
- 002: 143 changed, 2839 examined...
- 003: 66 changed, 886 examined...
- 004: 28 changed, 374 examined...
- 005: 18 changed, 158 examined...
- 006: 11 changed, 97 examined...
- 007: 6 changed, 57 examined...
- 008: 4 changed, 40 examined...
- 009: 8 changed, 22 examined...
- 010: 8 changed, 33 examined...
- 011: 4 changed, 34 examined...
- 012: 5 changed, 25 examined...
- 013: 4 changed, 29 examined...
- 014: 7 changed, 26 examined...
- 015: 1 changed, 35 examined...
- 016: 0 changed, 7 examined...
- 223 labels changed using aseg
- 000: 54 total segments, 21 labels (742 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 9 filter iterations complete (10 requested, 0 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 347 vertices marked for relabeling...
- 347 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas.annot...
- classification took 0 minutes and 16 seconds.
- PIDs (7203 7206) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Sun Oct 8 14:40:25 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 lh white
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Sun Oct 8 14:40:25 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 rh white
- Waiting for PID 7288 of (7288 7291) to complete...
- Waiting for PID 7291 of (7288 7291) 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 0050490 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297729
- Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 1944 1287 4067 2.912 0.665 0.135 0.026 24 2.1 caudalanteriorcingulate
- 4290 2882 8854 2.783 0.627 0.123 0.035 48 6.7 caudalmiddlefrontal
- 3586 2446 5233 2.074 0.531 0.139 0.033 45 4.6 cuneus
- 530 351 1805 3.603 0.784 0.118 0.039 6 0.8 entorhinal
- 5500 3840 11951 2.739 0.707 0.123 0.030 63 6.8 fusiform
- 7364 5173 14392 2.455 0.661 0.129 0.029 91 8.8 inferiorparietal
- 5364 3817 14686 3.159 0.707 0.134 0.038 76 8.5 inferiortemporal
- 1577 1059 2881 2.436 0.946 0.136 0.038 23 2.1 isthmuscingulate
- 8724 5826 14688 2.169 0.621 0.140 0.035 115 11.9 lateraloccipital
- 4470 3165 10463 2.861 0.704 0.145 0.041 73 7.8 lateralorbitofrontal
- 5107 3568 7778 2.110 0.585 0.138 0.039 65 7.8 lingual
- 1978 1379 4382 2.647 0.856 0.142 0.040 34 3.2 medialorbitofrontal
- 6257 4367 13832 2.768 0.709 0.127 0.030 77 8.1 middletemporal
- 1163 773 2466 2.764 0.694 0.094 0.016 7 0.7 parahippocampal
- 3240 2158 6245 2.609 0.591 0.123 0.031 31 3.9 paracentral
- 2284 1590 4809 2.714 0.495 0.122 0.030 25 2.7 parsopercularis
- 1109 740 2133 2.541 0.495 0.117 0.033 12 1.4 parsorbitalis
- 2412 1613 5094 2.647 0.561 0.110 0.023 23 2.0 parstriangularis
- 2016 1393 2026 1.629 0.397 0.125 0.026 17 2.3 pericalcarine
- 7709 5125 12867 2.243 0.703 0.123 0.031 89 9.8 postcentral
- 2488 1685 4731 2.533 0.923 0.135 0.028 34 3.0 posteriorcingulate
- 7444 4788 14391 2.779 0.673 0.115 0.030 66 9.1 precentral
- 5979 4214 11418 2.469 0.605 0.137 0.034 74 8.3 precuneus
- 1826 1239 4301 3.164 0.768 0.145 0.037 31 2.5 rostralanteriorcingulate
- 6509 4523 13797 2.583 0.623 0.139 0.036 98 9.1 rostralmiddlefrontal
- 15443 10625 36838 2.910 0.681 0.132 0.034 217 21.3 superiorfrontal
- 7019 4780 12710 2.378 0.609 0.130 0.031 82 8.5 superiorparietal
- 8920 6088 21925 3.018 0.746 0.115 0.027 98 9.5 superiortemporal
- 6960 4879 13404 2.502 0.605 0.129 0.030 83 8.4 supramarginal
- 802 510 1282 2.597 0.510 0.129 0.029 9 0.9 transversetemporal
- 3537 2479 7869 3.129 0.687 0.127 0.033 32 4.9 insula
- mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050490 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 297991
- Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 1618 1085 3296 2.588 0.724 0.135 0.025 26 1.6 caudalanteriorcingulate
- 3635 2522 7603 2.700 0.632 0.125 0.028 38 4.1 caudalmiddlefrontal
- 3262 2196 4950 2.132 0.564 0.147 0.037 41 5.2 cuneus
- 699 448 2553 3.259 1.062 0.124 0.046 9 1.4 entorhinal
- 5507 3802 12583 2.877 0.782 0.129 0.035 69 7.4 fusiform
- 10802 7444 21968 2.587 0.644 0.129 0.030 129 13.0 inferiorparietal
- 6139 4185 15589 3.075 0.848 0.126 0.035 73 8.0 inferiortemporal
- 1366 910 2896 2.681 1.061 0.140 0.040 22 1.9 isthmuscingulate
- 9492 6286 16217 2.358 0.640 0.143 0.038 128 13.8 lateraloccipital
- 4595 3115 9287 2.534 0.706 0.140 0.041 90 7.5 lateralorbitofrontal
- 4790 3386 7273 2.034 0.602 0.143 0.038 63 7.6 lingual
- 1857 1318 4273 2.542 0.849 0.134 0.040 37 2.7 medialorbitofrontal
- 6593 4615 16177 3.023 0.637 0.119 0.026 77 6.6 middletemporal
- 1246 819 2592 2.812 0.633 0.111 0.024 11 1.1 parahippocampal
- 2639 1752 4841 2.517 0.516 0.114 0.031 23 3.0 paracentral
- 1962 1362 4040 2.675 0.554 0.112 0.021 21 1.6 parsopercularis
- 1188 814 2788 2.831 0.670 0.125 0.027 18 1.4 parsorbitalis
- 1900 1332 3624 2.343 0.577 0.126 0.025 24 1.8 parstriangularis
- 2184 1493 2215 1.697 0.467 0.123 0.027 22 2.3 pericalcarine
- 6540 4234 10740 2.289 0.719 0.118 0.027 66 7.0 postcentral
- 1961 1343 3516 2.386 0.744 0.147 0.038 31 3.0 posteriorcingulate
- 8233 5353 15467 2.661 0.692 0.112 0.025 70 8.5 precentral
- 6932 4876 12631 2.464 0.602 0.132 0.033 88 9.2 precuneus
- 1477 1015 3276 2.785 0.664 0.129 0.030 20 1.8 rostralanteriorcingulate
- 6323 4352 12252 2.303 0.651 0.135 0.037 114 8.8 rostralmiddlefrontal
- 17338 11782 38512 2.701 0.729 0.131 0.035 297 24.6 superiorfrontal
- 7874 5231 13908 2.348 0.632 0.129 0.034 97 11.1 superiorparietal
- 7737 5249 18232 2.986 0.670 0.113 0.028 85 8.5 superiortemporal
- 6005 4033 11604 2.676 0.559 0.117 0.029 62 6.9 supramarginal
- 559 328 1081 3.074 0.561 0.107 0.032 6 0.8 transversetemporal
- 3622 2465 7801 3.194 0.765 0.125 0.033 36 4.5 insula
- PIDs (7288 7291) completed and logs appended.
- #-----------------------------------------
- #@# WM/GM Contrast lh Sun Oct 8 14:41:52 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- pctsurfcon --s 0050490 --lh-only
- #-----------------------------------------
- #@# WM/GM Contrast rh Sun Oct 8 14:41:52 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts
- pctsurfcon --s 0050490 --rh-only
- Waiting for PID 7371 of (7371 7375) to complete...
- Waiting for PID 7375 of (7371 7375) to complete...
- pctsurfcon --s 0050490 --lh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts/pctsurfcon.log
- Sun Oct 8 14:41:52 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-6.0.0/0050490/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-114 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-6.0.0/0050490/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.wm.mgh --regheader 0050490 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 119280
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.wm.mgh
- Dim: 152526 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.gm.mgh --projfrac 0.3 --regheader 0050490 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 134998
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.gm.mgh
- Dim: 152526 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7371/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/lh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.w-g.pct.mgh --annot 0050490 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/lh.w-g.pct.mgh --annot 0050490 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-114
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/lh.w-g.pct.mgh
- Vertex Area is 0.683006 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 0050490 --rh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/scripts/pctsurfcon.log
- Sun Oct 8 14:41:52 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-6.0.0/0050490/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-114 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-6.0.0/0050490/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.wm.mgh --regheader 0050490 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 120584
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.wm.mgh
- Dim: 154525 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.gm.mgh --projfrac 0.3 --regheader 0050490 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 136544
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.gm.mgh
- Dim: 154525 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/tmp.pctsurfcon.7375/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.w-g.pct.mgh --annot 0050490 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.w-g.pct.mgh --annot 0050490 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-114
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.w-g.pct.mgh
- Vertex Area is 0.677396 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 (7371 7375) completed and logs appended.
- #-----------------------------------------
- #@# Relabel Hypointensities Sun Oct 8 14:42:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
- reading input surface ../surf/lh.white...
- relabeling lh hypointensities...
- 1289 voxels changed to hypointensity...
- reading input surface ../surf/rh.white...
- relabeling rh hypointensities...
- 1862 voxels changed to hypointensity...
- 3168 hypointense voxels neighboring cortex changed
- #-----------------------------------------
- #@# AParc-to-ASeg aparc Sun Oct 8 14:43:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490
- mri_aparc2aseg --s 0050490 --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 14:43:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490
- mri_aparc2aseg --s 0050490 --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 14:43:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490
- mri_aparc2aseg --s 0050490 --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 7574 of (7574 7577 7580) to complete...
- Waiting for PID 7577 of (7574 7577 7580) to complete...
- Waiting for PID 7580 of (7574 7577 7580) to complete...
- mri_aparc2aseg --s 0050490 --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 0050490
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 7.14
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 106
- rescaling Left_Cerebral_Cortex from 61 --> 57
- rescaling Left_Lateral_Ventricle from 13 --> 14
- rescaling Left_Inf_Lat_Vent from 34 --> 28
- rescaling Left_Cerebellum_White_Matter from 86 --> 89
- rescaling Left_Cerebellum_Cortex from 60 --> 58
- rescaling Left_Thalamus from 94 --> 98
- rescaling Left_Thalamus_Proper from 84 --> 90
- rescaling Left_Caudate from 75 --> 66
- rescaling Left_Putamen from 80 --> 81
- rescaling Left_Pallidum from 98 --> 97
- rescaling Third_Ventricle from 25 --> 27
- rescaling Fourth_Ventricle from 22 --> 17
- rescaling Brain_Stem from 81 --> 86
- rescaling Left_Hippocampus from 57 --> 60
- rescaling Left_Amygdala from 56 --> 63
- rescaling CSF from 32 --> 37
- rescaling Left_Accumbens_area from 62 --> 60
- rescaling Left_VentralDC from 87 --> 92
- rescaling Right_Cerebral_White_Matter from 105 --> 104
- rescaling Right_Cerebral_Cortex from 58 --> 59
- rescaling Right_Lateral_Ventricle from 13 --> 16
- rescaling Right_Inf_Lat_Vent from 25 --> 25
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 59
- rescaling Right_Thalamus_Proper from 85 --> 92
- rescaling Right_Caudate from 62 --> 73
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 90
- rescaling Right_Hippocampus from 53 --> 59
- rescaling Right_Amygdala from 55 --> 62
- rescaling Right_Accumbens_area from 65 --> 71
- rescaling Right_VentralDC from 86 --> 96
- rescaling Fifth_Ventricle from 40 --> 33
- 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 = 582624
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 122 changed.
- pass 2: 9 changed.
- pass 3: 1 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aparc+aseg.mgz
- mri_aparc2aseg --s 0050490 --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 0050490
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 7.14
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 106
- rescaling Left_Cerebral_Cortex from 61 --> 57
- rescaling Left_Lateral_Ventricle from 13 --> 14
- rescaling Left_Inf_Lat_Vent from 34 --> 28
- rescaling Left_Cerebellum_White_Matter from 86 --> 89
- rescaling Left_Cerebellum_Cortex from 60 --> 58
- rescaling Left_Thalamus from 94 --> 98
- rescaling Left_Thalamus_Proper from 84 --> 90
- rescaling Left_Caudate from 75 --> 66
- rescaling Left_Putamen from 80 --> 81
- rescaling Left_Pallidum from 98 --> 97
- rescaling Third_Ventricle from 25 --> 27
- rescaling Fourth_Ventricle from 22 --> 17
- rescaling Brain_Stem from 81 --> 86
- rescaling Left_Hippocampus from 57 --> 60
- rescaling Left_Amygdala from 56 --> 63
- rescaling CSF from 32 --> 37
- rescaling Left_Accumbens_area from 62 --> 60
- rescaling Left_VentralDC from 87 --> 92
- rescaling Right_Cerebral_White_Matter from 105 --> 104
- rescaling Right_Cerebral_Cortex from 58 --> 59
- rescaling Right_Lateral_Ventricle from 13 --> 16
- rescaling Right_Inf_Lat_Vent from 25 --> 25
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 59
- rescaling Right_Thalamus_Proper from 85 --> 92
- rescaling Right_Caudate from 62 --> 73
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 90
- rescaling Right_Hippocampus from 53 --> 59
- rescaling Right_Amygdala from 55 --> 62
- rescaling Right_Accumbens_area from 65 --> 71
- rescaling Right_VentralDC from 86 --> 96
- rescaling Fifth_Ventricle from 40 --> 33
- 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 = 582670
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 122 changed.
- pass 2: 9 changed.
- pass 3: 1 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/aparc.a2009s+aseg.mgz
- mri_aparc2aseg --s 0050490 --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 0050490
- outvol mri/aparc.DKTatlas+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/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-6.0.0/0050490/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 7.14
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 106
- rescaling Left_Cerebral_Cortex from 61 --> 57
- rescaling Left_Lateral_Ventricle from 13 --> 14
- rescaling Left_Inf_Lat_Vent from 34 --> 28
- rescaling Left_Cerebellum_White_Matter from 86 --> 89
- rescaling Left_Cerebellum_Cortex from 60 --> 58
- rescaling Left_Thalamus from 94 --> 98
- rescaling Left_Thalamus_Proper from 84 --> 90
- rescaling Left_Caudate from 75 --> 66
- rescaling Left_Putamen from 80 --> 81
- rescaling Left_Pallidum from 98 --> 97
- rescaling Third_Ventricle from 25 --> 27
- rescaling Fourth_Ventricle from 22 --> 17
- rescaling Brain_Stem from 81 --> 86
- rescaling Left_Hippocampus from 57 --> 60
- rescaling Left_Amygdala from 56 --> 63
- rescaling CSF from 32 --> 37
- rescaling Left_Accumbens_area from 62 --> 60
- rescaling Left_VentralDC from 87 --> 92
- rescaling Right_Cerebral_White_Matter from 105 --> 104
- rescaling Right_Cerebral_Cortex from 58 --> 59
- rescaling Right_Lateral_Ventricle from 13 --> 16
- rescaling Right_Inf_Lat_Vent from 25 --> 25
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 59
- rescaling Right_Thalamus_Proper from 85 --> 92
- rescaling Right_Caudate from 62 --> 73
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 90
- rescaling Right_Hippocampus from 53 --> 59
- rescaling Right_Amygdala from 55 --> 62
- rescaling Right_Accumbens_area from 65 --> 71
- rescaling Right_VentralDC from 86 --> 96
- rescaling Fifth_Ventricle from 40 --> 33
- 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 = 582670
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 122 changed.
- pass 2: 9 changed.
- pass 3: 1 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
- PIDs (7574 7577 7580) completed and logs appended.
- #-----------------------------------------
- #@# APas-to-ASeg Sun Oct 8 14:52:35 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri
- apas2aseg --i aparc+aseg.mgz --o aseg.mgz
- Sun Oct 8 14:52:35 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-6.0.0/0050490/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-114 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-6.0.0/0050490/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-114
- 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 14:52:35 CEST 2017
- Ended at Sun Oct 8 14:52:48 CEST 2017
- Apas2aseg-Run-Time-Sec 13
-
- apas2aseg Done
- #--------------------------------------------
- #@# ASeg Stats Sun Oct 8 14:52:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490
- 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 0050490
- $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 0050490
- sysname Linux
- hostname tars-114
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1695813 mm^3 (det: 1.148774 )
- Computing euler number
- orig.nofix lheno = -68, rheno = -66
- orig.nofix lhholes = 35, rhholes = 34
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 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 14:56:56 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490
- mri_aparc2aseg --s 0050490 --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 0050490
- 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-6.0.0/0050490/mri/aparc+aseg.mgz
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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-6.0.0/0050490/mri/ribbon.mgz
- Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/ribbon.mgz
- Ripping vertices labeled as unkown
- Ripped 8979 vertices from left hemi
- Ripped 8477 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-6.0.0/0050490/mri/aseg.mgz
- Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 = 1084513
- Used brute-force search on 544 voxels
- Fixing Parahip LH WM
- Found 7 clusters
- 0 k 1.000000
- 1 k 1515.000000
- 2 k 1.000000
- 3 k 1.000000
- 4 k 11.000000
- 5 k 1.000000
- 6 k 4.000000
- Fixing Parahip RH WM
- Found 12 clusters
- 0 k 5.000000
- 1 k 2.000000
- 2 k 1.000000
- 3 k 1785.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 12.000000
- 8 k 1.000000
- 9 k 1.000000
- 10 k 2.000000
- 11 k 1.000000
- Writing output aseg to mri/wmparc.mgz
- mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050490 --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 0050490 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname tars-114
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1695813 mm^3 (det: 1.148774 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 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-6.0.0/0050490/label
- #--------------------------------------------
- #@# BA_exvivo Labels lh Sun Oct 8 15:17:50 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 9004 of (9004 9010 9016 9022 9027) to complete...
- Waiting for PID 9010 of (9004 9010 9016 9022 9027) to complete...
- Waiting for PID 9016 of (9004 9010 9016 9022 9027) to complete...
- Waiting for PID 9022 of (9004 9010 9016 9022 9027) to complete...
- Waiting for PID 9027 of (9004 9010 9016 9022 9027) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 382
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.label 4511
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 630
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.label 8539
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 208
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.label 4285
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 525
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.label 6508
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 645
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.label 6429
- mri_label2label: Done
- PIDs (9004 9010 9016 9022 9027) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 9088 of (9088 9094 9100 9106) to complete...
- Waiting for PID 9094 of (9088 9094 9100 9106) to complete...
- Waiting for PID 9100 of (9088 9094 9100 9106) to complete...
- Waiting for PID 9106 of (9088 9094 9100 9106) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 263
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.label 4333
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 2103
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.label 15692
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 324
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.label 4505
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 522
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.label 3944
- mri_label2label: Done
- PIDs (9088 9094 9100 9106) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 9146 of (9146 9152 9156 9163 9169) to complete...
- Waiting for PID 9152 of (9146 9152 9156 9163 9169) to complete...
- Waiting for PID 9156 of (9146 9152 9156 9163 9169) to complete...
- Waiting for PID 9163 of (9146 9152 9156 9163 9169) to complete...
- Waiting for PID 9169 of (9146 9152 9156 9163 9169) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 1479
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.label 6120
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 3642
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.label 11756
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 509
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.label 2527
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 107
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.label 1397
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 83
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.label 1282
- mri_label2label: Done
- PIDs (9146 9152 9156 9163 9169) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 9235 of (9235 9241 9247 9253 9257) to complete...
- Waiting for PID 9241 of (9235 9241 9247 9253 9257) to complete...
- Waiting for PID 9247 of (9235 9241 9247 9253 9257) to complete...
- Waiting for PID 9253 of (9235 9241 9247 9253 9257) to complete...
- Waiting for PID 9257 of (9235 9241 9247 9253 9257) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 81
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.thresh.label 1095
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 183
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.thresh.label 2275
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 44
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.thresh.label 1548
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 193
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.thresh.label 2189
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 313
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.thresh.label 2632
- mri_label2label: Done
- PIDs (9235 9241 9247 9253 9257) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 9300 of (9300 9306 9312 9320) to complete...
- Waiting for PID 9306 of (9300 9306 9312 9320) to complete...
- Waiting for PID 9312 of (9300 9306 9312 9320) to complete...
- Waiting for PID 9320 of (9300 9306 9312 9320) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 120
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.thresh.label 1669
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 1039
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.thresh.label 8074
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 131
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.thresh.label 2043
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 241
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.thresh.label 1392
- mri_label2label: Done
- PIDs (9300 9306 9312 9320) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 9379 of (9379 9385 9391 9397 9401) to complete...
- Waiting for PID 9385 of (9379 9385 9391 9397 9401) to complete...
- Waiting for PID 9391 of (9379 9385 9391 9397 9401) to complete...
- Waiting for PID 9397 of (9379 9385 9391 9397 9401) to complete...
- Waiting for PID 9401 of (9379 9385 9391 9397 9401) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 1035
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.thresh.label 4440
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 1605
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.thresh.label 4939
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 128
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.thresh.label 641
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 29
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.thresh.label 499
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 152526
- Number of reverse mapping hits = 20
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.thresh.label 470
- mri_label2label: Done
- PIDs (9379 9385 9391 9397 9401) completed and logs appended.
- mris_label2annot --s 0050490 --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-6.0.0/0050490/label
- cmdline mris_label2annot --s 0050490 --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-114
- machine x86_64
- user ntraut
- subject 0050490
- 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-6.0.0/0050490/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 107137 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/lh.BA_exvivo.annot
- mris_label2annot --s 0050490 --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-6.0.0/0050490/label
- cmdline mris_label2annot --s 0050490 --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-114
- machine x86_64
- user ntraut
- subject 0050490
- 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-6.0.0/0050490/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 125920 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 297729
- Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 1194 748 2269 2.363 0.572 0.147 0.045 21 2.0 BA1_exvivo
- 4295 2898 7035 2.317 0.592 0.123 0.028 42 4.7 BA2_exvivo
- 1110 750 1165 1.904 0.460 0.120 0.026 8 1.2 BA3a_exvivo
- 2670 1790 3991 1.980 0.728 0.117 0.031 31 3.6 BA3b_exvivo
- 2027 1262 3877 2.689 0.571 0.123 0.037 20 3.2 BA4a_exvivo
- 1451 894 2278 2.672 0.550 0.102 0.033 9 2.0 BA4p_exvivo
- 10985 7427 26094 2.961 0.667 0.119 0.029 114 12.3 BA6_exvivo
- 2346 1606 4827 2.765 0.521 0.127 0.030 25 2.8 BA44_exvivo
- 2870 1982 6426 2.602 0.615 0.123 0.026 37 2.7 BA45_exvivo
- 3684 2528 4362 1.710 0.467 0.134 0.032 43 5.0 V1_exvivo
- 9362 6361 14104 2.082 0.533 0.145 0.039 128 13.8 V2_exvivo
- 2125 1492 4515 2.502 0.747 0.127 0.032 21 2.7 MT_exvivo
- 609 386 1818 3.534 0.723 0.124 0.038 7 0.9 perirhinal_exvivo
- 661 478 1633 2.946 0.838 0.120 0.038 8 1.1 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 0050490 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 297729
- Total vertex volume 293320 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 760 473 1376 2.304 0.577 0.147 0.044 14 1.3 BA1_exvivo
- 1630 1106 2849 2.342 0.552 0.128 0.032 18 2.0 BA2_exvivo
- 918 611 860 1.839 0.407 0.127 0.028 7 1.1 BA3a_exvivo
- 1613 1066 1729 1.581 0.385 0.108 0.032 18 2.3 BA3b_exvivo
- 1966 1189 3509 2.697 0.582 0.118 0.037 19 3.1 BA4a_exvivo
- 1174 735 1752 2.541 0.509 0.109 0.038 8 1.8 BA4p_exvivo
- 6113 4075 14349 2.904 0.672 0.116 0.028 61 6.7 BA6_exvivo
- 1473 1014 3183 2.752 0.464 0.143 0.037 21 2.2 BA44_exvivo
- 1224 817 3319 2.812 0.619 0.129 0.032 17 1.3 BA45_exvivo
- 3931 2692 4709 1.719 0.465 0.135 0.034 47 5.5 V1_exvivo
- 4608 3128 6182 1.961 0.472 0.149 0.040 64 7.1 V2_exvivo
- 576 411 1602 2.826 0.871 0.134 0.043 7 1.0 MT_exvivo
- 292 190 1167 3.893 0.596 0.094 0.018 2 0.2 perirhinal_exvivo
- 328 224 829 3.104 0.827 0.086 0.018 2 0.3 entorhinal_exvivo
- #--------------------------------------------
- #@# BA_exvivo Labels rh Sun Oct 8 15:22:07 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 9542 of (9542 9548 9554 9560 9565) to complete...
- Waiting for PID 9548 of (9542 9548 9554 9560 9565) to complete...
- Waiting for PID 9554 of (9542 9548 9554 9560 9565) to complete...
- Waiting for PID 9560 of (9542 9548 9554 9560 9565) to complete...
- Waiting for PID 9565 of (9542 9548 9554 9560 9565) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 292
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.label 4254
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 344
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.label 7031
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 214
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.label 4194
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 296
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.label 4818
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 877
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.label 6624
- mri_label2label: Done
- PIDs (9542 9548 9554 9560 9565) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 9756 of (9756 9762 9768 9774) to complete...
- Waiting for PID 9762 of (9756 9762 9768 9774) to complete...
- Waiting for PID 9768 of (9756 9762 9768 9774) to complete...
- Waiting for PID 9774 of (9756 9762 9768 9774) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 469
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.label 4942
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 2119
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.label 14375
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 354
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.label 7266
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label --trgsubject 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 557
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.label 5912
- mri_label2label: Done
- PIDs (9756 9762 9768 9774) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 9864 of (9864 9870 9876 9882 9888) to complete...
- Waiting for PID 9870 of (9864 9870 9876 9882 9888) to complete...
- Waiting for PID 9876 of (9864 9870 9876 9882 9888) to complete...
- Waiting for PID 9882 of (9864 9870 9876 9882 9888) to complete...
- Waiting for PID 9888 of (9864 9870 9876 9882 9888) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 1731
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.label 6458
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 3809
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.label 11825
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 816
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.label 2748
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 189
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.label 1227
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 129
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.label 881
- mri_label2label: Done
- PIDs (9864 9870 9876 9882 9888) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 9949 of (9949 9955 9961 9966 9973) to complete...
- Waiting for PID 9955 of (9949 9955 9961 9966 9973) to complete...
- Waiting for PID 9961 of (9949 9955 9961 9966 9973) to complete...
- Waiting for PID 9966 of (9949 9955 9961 9966 9973) to complete...
- Waiting for PID 9973 of (9949 9955 9961 9966 9973) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 66
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.thresh.label 942
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 76
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.thresh.label 2764
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 77
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.thresh.label 1775
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 141
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.thresh.label 2324
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 167
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.thresh.label 1555
- mri_label2label: Done
- PIDs (9949 9955 9961 9966 9973) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 10019 of (10019 10025 10031 10037) to complete...
- Waiting for PID 10025 of (10019 10025 10031 10037) to complete...
- Waiting for PID 10031 of (10019 10025 10031 10037) to complete...
- Waiting for PID 10037 of (10019 10025 10031 10037) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 184
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.thresh.label 1673
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 1306
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.thresh.label 8265
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 77
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.thresh.label 1089
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 85
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.thresh.label 1263
- mri_label2label: Done
- PIDs (10019 10025 10031 10037) 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 0050490 --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 0050490 --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 0050490 --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 0050490 --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 0050490 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 10092 of (10092 10098 10104 10110 10114) to complete...
- Waiting for PID 10098 of (10092 10098 10104 10110 10114) to complete...
- Waiting for PID 10104 of (10092 10098 10104 10110 10114) to complete...
- Waiting for PID 10110 of (10092 10098 10104 10110 10114) to complete...
- Waiting for PID 10114 of (10092 10098 10104 10110 10114) 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 1061
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.thresh.label 4293
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 1719
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.thresh.label 5156
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 108
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.thresh.label 376
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 121
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.thresh.label 815
- 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 0050490 --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 = 0050490
- 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-6.0.0/0050490/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 154525
- Number of reverse mapping hits = 33
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.thresh.label 324
- mri_label2label: Done
- PIDs (10092 10098 10104 10110 10114) completed and logs appended.
- mris_label2annot --s 0050490 --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-6.0.0/0050490/label
- cmdline mris_label2annot --s 0050490 --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-114
- machine x86_64
- user ntraut
- subject 0050490
- 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-6.0.0/0050490/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 109634 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/label/rh.BA_exvivo.annot
- mris_label2annot --s 0050490 --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-6.0.0/0050490/label
- cmdline mris_label2annot --s 0050490 --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-114
- machine x86_64
- user ntraut
- subject 0050490
- 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-6.0.0/0050490/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 128814 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/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 0050490 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 297991
- Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 968 538 1898 2.469 0.628 0.121 0.036 13 1.3 BA1_exvivo
- 2850 1900 4708 2.380 0.548 0.132 0.031 33 3.3 BA2_exvivo
- 1204 807 1145 1.887 0.456 0.130 0.030 11 1.4 BA3a_exvivo
- 2076 1385 2804 1.830 0.554 0.105 0.022 18 1.9 BA3b_exvivo
- 1893 1192 3318 2.494 0.686 0.107 0.029 17 2.1 BA4a_exvivo
- 1588 1040 2307 2.327 0.552 0.107 0.026 10 1.8 BA4p_exvivo
- 10423 6999 24281 2.905 0.689 0.122 0.031 142 13.4 BA6_exvivo
- 3133 2165 6658 2.815 0.538 0.113 0.021 30 2.5 BA44_exvivo
- 3604 2505 7310 2.447 0.668 0.130 0.027 52 3.9 BA45_exvivo
- 4026 2726 5233 1.805 0.517 0.135 0.034 48 5.7 V1_exvivo
- 9382 6276 13978 2.117 0.575 0.144 0.038 123 14.1 V2_exvivo
- 2604 1800 4558 2.504 0.509 0.133 0.030 27 2.9 MT_exvivo
- 709 449 2716 3.430 0.947 0.128 0.048 11 1.4 perirhinal_exvivo
- 431 297 1095 2.890 0.667 0.099 0.025 3 0.5 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 0050490 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050490/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 297991
- Total vertex volume 293786 (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) = 1695813 mm^3 (det: 1.148774 )
- lhCtxGM: 292970.261 292529.000 diff= 441.3 pctdiff= 0.151
- rhCtxGM: 292492.913 292199.000 diff= 293.9 pctdiff= 0.100
- lhCtxWM: 249643.976 250178.000 diff= -534.0 pctdiff=-0.214
- rhCtxWM: 251828.606 252463.000 diff= -634.4 pctdiff=-0.252
- SubCortGMVol 65030.000
- SupraTentVol 1171402.756 (1169037.000) diff=2365.756 pctdiff=0.202
- SupraTentVolNotVent 1154839.756 (1152474.000) diff=2365.756 pctdiff=0.205
- BrainSegVol 1330254.000 (1327398.000) diff=2856.000 pctdiff=0.215
- BrainSegVolNotVent 1309200.000 (1308521.756) diff=678.244 pctdiff=0.052
- BrainSegVolNotVent 1309200.000
- CerebellumVol 156481.000
- VentChorVol 16563.000
- 3rd4th5thCSF 4491.000
- CSFVol 1635.000, OptChiasmVol 245.000
- MaskVol 1762497.000
- 597 359 1164 2.376 0.569 0.112 0.032 6 0.7 BA1_exvivo
- 1597 1030 2861 2.475 0.546 0.122 0.029 18 1.8 BA2_exvivo
- 1103 739 945 1.851 0.416 0.137 0.030 10 1.4 BA3a_exvivo
- 1650 1141 1903 1.667 0.366 0.098 0.018 11 1.2 BA3b_exvivo
- 1122 722 1876 2.341 0.664 0.134 0.043 15 1.9 BA4a_exvivo
- 1295 870 1856 2.331 0.578 0.109 0.026 8 1.4 BA4p_exvivo
- 6908 4578 15248 2.821 0.668 0.116 0.030 102 8.5 BA6_exvivo
- 816 559 2178 2.959 0.480 0.119 0.021 11 0.7 BA44_exvivo
- 888 645 2187 2.515 0.512 0.139 0.031 16 1.1 BA45_exvivo
- 3796 2578 4902 1.807 0.533 0.134 0.033 44 5.2 V1_exvivo
- 4862 3257 6697 1.979 0.544 0.145 0.037 65 7.3 V2_exvivo
- 360 254 697 2.530 0.459 0.146 0.034 4 0.5 MT_exvivo
- 438 266 1614 3.342 0.954 0.132 0.050 7 1.0 perirhinal_exvivo
- 279 188 707 2.958 0.565 0.081 0.020 1 0.2 entorhinal_exvivo
- Started at Sun Oct 8 01:15:11 CEST 2017
- Ended at Sun Oct 8 15:26:14 CEST 2017
- #@#%# recon-all-run-time-hours 14.184
- recon-all -s 0050490 finished without error at Sun Oct 8 15:26:14 CEST 2017
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