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|
- Sat Oct 7 23:29:54 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
- -subjid 0050319 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050319/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
- subjid 0050319
- 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-623 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: 65993348 58374756 7618592 2163640 0 54764176
- -/+ buffers/cache: 3610580 62382768
- Swap: 0 0 0
- ########################################
- program versions used
- $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
- $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
- mri_convert.bin -all-info
- ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
- mri_convert.bin --version
- stable6
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
- ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:29:54-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-623 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-6.0.0/0050319
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050319/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/orig/001.mgz
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050319/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/orig/001.mgz
- $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
- reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050319/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-6.0.0/0050319/mri/orig/001.mgz...
- #--------------------------------------------
- #@# MotionCor Sat Oct 7 23:29:56 CEST 2017
- Found 1 runs
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/rawavg.mgz
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/orig.mgz --conform
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/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-6.0.0/0050319/mri/orig.mgz...
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Sat Oct 7 23:30:04 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/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-623 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
- Sat Oct 7 23:30:04 CEST 2017
- Program nu_correct, built from:
- Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
- /usr/bin/bc
- tmpdir is ./tmp.mri_nu_correct.mni.7541
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7541/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.7541/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.7541/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 23:30:06 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.7541/nu0.mnc ./tmp.mri_nu_correct.mni.7541/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7541/0/ -iterations 1000 -distance 50
- [ntraut@tars-623:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/] [2017-10-07 23:30:06] 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.7541/0/ ./tmp.mri_nu_correct.mni.7541/nu0.mnc ./tmp.mri_nu_correct.mni.7541/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
- Number of iterations: 31
- CV of field change: 0.000986388
-
-
-
- mri_convert ./tmp.mri_nu_correct.mni.7541/nu1.mnc orig_nu.mgz --like orig.mgz --conform
- mri_convert.bin ./tmp.mri_nu_correct.mni.7541/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.7541/nu1.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -1)
- k_ras = (0, 1, 0)
- INFO: transform src into the like-volume: orig.mgz
- changing data type from float to uchar (noscale = 0)...
- MRIchangeType: Building histogram
- writing to orig_nu.mgz...
-
-
- Sat Oct 7 23:31:07 CEST 2017
- mri_nu_correct.mni done
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- talairach_avi log file is transforms/talairach_avi.log...
- Started at Sat Oct 7 23:31:07 CEST 2017
- Ended at Sat Oct 7 23:31:40 CEST 2017
- talairach_avi done
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Sat Oct 7 23:31:42 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4401, pval=0.1049 >= 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-6.0.0/0050319/mri/transforms/talairach_avi.log
- tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/transforms/talairach_avi.log
- TalAviQA: 0.97975
- z-score: 0
- #--------------------------------------------
- #@# Nu Intensity Correction Sat Oct 7 23:31:42 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-6.0.0/0050319/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-623 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
- Sat Oct 7 23:31:42 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.8867
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8867/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.8867/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.8867/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 23:31:44 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.8867/nu0.mnc ./tmp.mri_nu_correct.mni.8867/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8867/0/
- [ntraut@tars-623:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/] [2017-10-07 23:31:44] 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.8867/0/ ./tmp.mri_nu_correct.mni.8867/nu0.mnc ./tmp.mri_nu_correct.mni.8867/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
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- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 30
- CV of field change: 0.000987107
-
-
- --------------------------------------------------------
- Iteration 2 Sat Oct 7 23:32:27 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.8867/nu1.mnc ./tmp.mri_nu_correct.mni.8867/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.8867/1/
- [ntraut@tars-623:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/] [2017-10-07 23:32:27] 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.8867/1/ ./tmp.mri_nu_correct.mni.8867/nu1.mnc ./tmp.mri_nu_correct.mni.8867/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
- Number of iterations: 13
- CV of field change: 0.000988729
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.8867/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.8867/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-6.0.0/0050319/mri
- cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.8867/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.8867/ones.mgz
- sysname Linux
- hostname tars-623
- machine x86_64
- user ntraut
- input ./tmp.mri_nu_correct.mni.8867/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.8867/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.8867/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.8867/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8867/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.8867/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.8867/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8867/input.mean.dat
- sysname Linux
- hostname tars-623
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.8867/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.8867/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8867/ones.mgz --i ./tmp.mri_nu_correct.mni.8867/nu2.mnc --sum ./tmp.mri_nu_correct.mni.8867/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8867/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.8867/ones.mgz --i ./tmp.mri_nu_correct.mni.8867/nu2.mnc --sum ./tmp.mri_nu_correct.mni.8867/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8867/output.mean.dat
- sysname Linux
- hostname tars-623
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.8867/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.8867/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.8867/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.8867/nu2.mnc ./tmp.mri_nu_correct.mni.8867/nu2.mnc mul .99810104679575800906
- Saving result to './tmp.mri_nu_correct.mni.8867/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.8867/nu2.mnc nu.mgz --like orig.mgz
- mri_convert.bin ./tmp.mri_nu_correct.mni.8867/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.8867/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -1)
- k_ras = (0, 1, 0)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 8 seconds.
- mapping (15, 113) to ( 3, 110)
-
-
- Sat Oct 7 23:33:43 CEST 2017
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Sat Oct 7 23:33:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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
- 1.06239 -0.09901 0.06539 -128.10837;
- 0.10058 1.05458 -0.12130 -150.51035;
- -0.04485 0.16808 1.09476 -91.06519;
- 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 = 14
- Starting OpenSpline(): npoints = 14
- 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 74 (74), valley at 15 (15)
- csf peak at 37, setting threshold to 61
- 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 73 (73), valley at 15 (15)
- csf peak at 37, setting threshold to 61
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 1 minutes and 46 seconds.
- #--------------------------------------------
- #@# Skull Stripping Sat Oct 7 23:35:30 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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=15.0
- skull bounding box = (51, 52, 27) --> (209, 197, 214)
- using (104, 100, 121) as brain centroid...
- mean wm in atlas = 108, using box (85,82,98) --> (123, 117,144) to find MRI wm
- before smoothing, mri peak at 105
- robust fit to distribution - 105 +- 6.2
- after smoothing, mri peak at 105, scaling input intensities by 1.029
- scaling channel 0 by 1.02857
- initial log_p = -4.493
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.504074 @ (-9.091, -9.091, -9.091)
- max log p = -4.467091 @ (4.545, 4.545, 13.636)
- max log p = -4.404317 @ (2.273, -2.273, -6.818)
- max log p = -4.397723 @ (1.136, 1.136, -1.136)
- max log p = -4.369512 @ (-0.568, 0.568, 1.705)
- max log p = -4.369512 @ (0.000, 0.000, 0.000)
- Found translation: (-1.7, -5.1, -1.7): log p = -4.370
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.153, old_max_log_p =-4.370 (thresh=-4.4)
- 1.05669 0.17480 0.11491 -47.56803;
- -0.13912 1.20774 -0.19839 11.74174;
- -0.14032 0.11896 1.06209 -8.45724;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.153, old_max_log_p =-4.153 (thresh=-4.1)
- 1.05669 0.17480 0.11491 -47.56803;
- -0.13912 1.20774 -0.19839 11.74174;
- -0.14032 0.11896 1.06209 -8.45724;
- 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=-4.058, old_max_log_p =-4.153 (thresh=-4.1)
- 1.01096 0.08245 0.05486 -21.87748;
- -0.07185 1.26166 -0.20232 -4.00617;
- -0.07494 0.13755 1.12812 -30.72715;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.058, old_max_log_p =-4.058 (thresh=-4.1)
- 1.02992 0.08399 0.05589 -24.62909;
- -0.07427 1.26548 -0.16530 -8.56256;
- -0.07255 0.09619 1.13413 -25.86841;
- 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=-4.038, old_max_log_p =-4.058 (thresh=-4.1)
- 1.02806 0.07349 0.05733 -23.53991;
- -0.06381 1.25895 -0.19194 -6.32524;
- -0.07418 0.12692 1.12708 -29.19730;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.038, old_max_log_p =-4.038 (thresh=-4.0)
- 1.02806 0.07349 0.05733 -23.53991;
- -0.06381 1.25895 -0.19194 -6.32524;
- -0.07418 0.12692 1.12708 -29.19730;
- 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
- 1.02806 0.07349 0.05733 -23.53991;
- -0.06381 1.25895 -0.19194 -6.32524;
- -0.07418 0.12692 1.12708 -29.19730;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3243
- Quasinewton: input matrix
- 1.02806 0.07349 0.05733 -23.53991;
- -0.06381 1.25895 -0.19194 -6.32524;
- -0.07418 0.12692 1.12708 -29.19730;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.02806 0.07349 0.05733 -23.53991;
- -0.06381 1.25895 -0.19194 -6.32524;
- -0.07418 0.12692 1.12708 -29.19730;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -4.038 (old=-4.493)
- transform before final EM align:
- 1.02806 0.07349 0.05733 -23.53991;
- -0.06381 1.25895 -0.19194 -6.32524;
- -0.07418 0.12692 1.12708 -29.19730;
- 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
- 1.02806 0.07349 0.05733 -23.53991;
- -0.06381 1.25895 -0.19194 -6.32524;
- -0.07418 0.12692 1.12708 -29.19730;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 364799
- Quasinewton: input matrix
- 1.02806 0.07349 0.05733 -23.53991;
- -0.06381 1.25895 -0.19194 -6.32524;
- -0.07418 0.12692 1.12708 -29.19730;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 010: -log(p) = 4.5 tol 0.000000
- final transform:
- 1.02806 0.07349 0.05733 -23.53991;
- -0.06381 1.25895 -0.19194 -6.32524;
- -0.07418 0.12692 1.12708 -29.19730;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach_with_skull.lta...
- mri_em_register utimesec 1072.745917
- mri_em_register stimesec 1.017845
- 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 157570
- 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 240
- mri_em_register ru_nivcsw 2985
- registration took 9 minutes and 24 seconds.
- mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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=130 y=122 z=119 r=65
- first estimation of the main basin volume: 1165084 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 14 found in the rest of the brain
- global maximum in x=101, y=104, z=88, Imax=255
- CSF=16, WM_intensity=110, WM_VARIANCE=5
- WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
- preflooding height equal to 10 percent
- done.
- Analyze...
- main basin size=7788518563 voxels, voxel volume =1.000
- = 7788518563 mmm3 = 7788518.400 cm3
- done.
- PostAnalyze...Basin Prior
- 48 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=129,y=123, z=115, r=8954 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 44792
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1106423531
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1122542633
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1123922611
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1070350834
- OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1075366306
- Problem with the least square interpolation in GM_MIN calculation.
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 4, 6, 42, 67
- after analyzing : 4, 30, 42, 39
- RIGHT_CER
- before analyzing : 3, 4, 47, 69
- after analyzing : 3, 32, 47, 41
- LEFT_CER
- before analyzing : 3, 4, 45, 72
- after analyzing : 3, 31, 45, 41
- RIGHT_BRAIN
- before analyzing : 4, 6, 40, 67
- after analyzing : 4, 28, 40, 37
- LEFT_BRAIN
- before analyzing : 4, 6, 42, 67
- after analyzing : 4, 30, 42, 39
- OTHER
- before analyzing : 3, 6, 74, 92
- after analyzing : 3, 51, 74, 61
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...65 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.010
- curvature mean = 70.183, std = 7.300
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 9.58, sigma = 18.21
- after rotation: sse = 9.58, sigma = 18.21
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 11.93, its var is 29.40
- before Erosion-Dilatation 12.27% of inacurate vertices
- after Erosion-Dilatation 18.56% 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...31 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1595430 voxels, voxel volume = 1.000 mm3
- = 1595430 mmm3 = 1595.430 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- mri_watershed utimesec 20.505882
- mri_watershed stimesec 0.413937
- mri_watershed ru_maxrss 818060
- mri_watershed ru_ixrss 0
- mri_watershed ru_idrss 0
- mri_watershed ru_isrss 0
- mri_watershed ru_minflt 211189
- mri_watershed ru_majflt 0
- mri_watershed ru_nswap 0
- mri_watershed ru_inblock 4120
- mri_watershed ru_oublock 2504
- mri_watershed ru_msgsnd 0
- mri_watershed ru_msgrcv 0
- mri_watershed ru_nsignals 0
- mri_watershed ru_nvcsw 1408
- mri_watershed ru_nivcsw 91
- mri_watershed done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Sat Oct 7 23:45:15 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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=25.0
- skull bounding box = (60, 61, 36) --> (199, 171, 203)
- using (106, 98, 120) as brain centroid...
- mean wm in atlas = 107, using box (89,85,99) --> (123, 111,140) to find MRI wm
- before smoothing, mri peak at 104
- robust fit to distribution - 105 +- 4.6
- after smoothing, mri peak at 105, scaling input intensities by 1.019
- scaling channel 0 by 1.01905
- initial log_p = -4.131
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -3.976174 @ (-9.091, -9.091, -9.091)
- max log p = -3.932662 @ (4.545, 4.545, 4.545)
- max log p = -3.911404 @ (2.273, -6.818, -2.273)
- max log p = -3.911404 @ (0.000, 0.000, 0.000)
- max log p = -3.885872 @ (0.568, 1.705, -0.568)
- max log p = -3.885872 @ (0.000, 0.000, 0.000)
- Found translation: (-1.7, -9.7, -7.4): log p = -3.886
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.819, old_max_log_p =-3.886 (thresh=-3.9)
- 1.05669 0.15727 0.11961 -42.76127;
- -0.13912 1.05429 -0.15727 26.45312;
- -0.13053 0.12941 0.98296 -5.38631;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.774, old_max_log_p =-3.819 (thresh=-3.8)
- 0.98587 0.01694 0.12868 -17.49874;
- -0.00000 1.06580 -0.14032 5.12338;
- -0.14032 0.13912 1.05669 -13.69862;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.774, old_max_log_p =-3.774 (thresh=-3.8)
- 0.98587 0.01694 0.12868 -17.49874;
- -0.00000 1.06580 -0.14032 5.12338;
- -0.14032 0.13912 1.05669 -13.69862;
- 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=-3.659, old_max_log_p =-3.774 (thresh=-3.8)
- 1.00374 0.05162 0.12768 -25.74955;
- -0.02949 1.07875 -0.18103 10.07085;
- -0.13976 0.17182 1.03137 -16.87796;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.652, old_max_log_p =-3.659 (thresh=-3.7)
- 1.02667 0.04683 0.09563 -24.44817;
- -0.03004 1.09897 -0.18442 6.14800;
- -0.10484 0.17017 1.01559 -21.29082;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.633, old_max_log_p =-3.652 (thresh=-3.6)
- 1.02133 0.09020 0.12008 -32.08664;
- -0.05656 1.08312 -0.25452 19.82244;
- -0.13749 0.23552 0.97898 -19.11014;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.633, old_max_log_p =-3.633 (thresh=-3.6)
- 1.02133 0.09020 0.12008 -32.08664;
- -0.05656 1.08312 -0.25452 19.82244;
- -0.13749 0.23552 0.97898 -19.11014;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.622, old_max_log_p =-3.633 (thresh=-3.6)
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05556;
- -0.13749 0.23552 0.97898 -19.11014;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.622, old_max_log_p =-3.622 (thresh=-3.6)
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05556;
- -0.13749 0.23552 0.97898 -19.11014;
- 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
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05556;
- -0.13749 0.23552 0.97898 -19.11014;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2830
- Quasinewton: input matrix
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05556;
- -0.13749 0.23552 0.97898 -19.11014;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05556;
- -0.13749 0.23552 0.97898 -19.11014;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.622 (old=-4.131)
- transform before final EM align:
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05556;
- -0.13749 0.23552 0.97898 -19.11014;
- 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
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05556;
- -0.13749 0.23552 0.97898 -19.11014;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 315557
- Quasinewton: input matrix
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05556;
- -0.13749 0.23552 0.97898 -19.11014;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 013: -log(p) = 4.1 tol 0.000000
- final transform:
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05556;
- -0.13749 0.23552 0.97898 -19.11014;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach.lta...
- mri_em_register utimesec 1377.143642
- mri_em_register stimesec 1.362792
- mri_em_register ru_maxrss 599052
- mri_em_register ru_ixrss 0
- mri_em_register ru_idrss 0
- mri_em_register ru_isrss 0
- mri_em_register ru_minflt 158983
- mri_em_register ru_majflt 0
- mri_em_register ru_nswap 0
- mri_em_register ru_inblock 0
- mri_em_register ru_oublock 24
- mri_em_register ru_msgsnd 0
- mri_em_register ru_msgrcv 0
- mri_em_register ru_nsignals 0
- mri_em_register ru_nvcsw 312
- mri_em_register ru_nivcsw 9057
- registration took 11 minutes and 45 seconds.
- #--------------------------------------
- #@# CA Normalize Sat Oct 7 23:57:00 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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=25.0
- skull bounding box = (60, 61, 36) --> (199, 171, 203)
- using (106, 98, 120) as brain centroid...
- mean wm in atlas = 107, using box (89,85,99) --> (123, 111,140) to find MRI wm
- before smoothing, mri peak at 104
- robust fit to distribution - 105 +- 4.6
- after smoothing, mri peak at 105, scaling input intensities by 1.019
- scaling channel 0 by 1.01905
- using 246344 sample points...
- INFO: compute sample coordinates transform
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05556;
- -0.13749 0.23552 0.97898 -19.11014;
- 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 (124, 64, 36) --> (196, 179, 201)
- Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
- 0 of 3802 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (67, 62, 36) --> (136, 175, 200)
- Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
- 1 of 3038 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (133, 135, 51) --> (180, 175, 106)
- Left_Cerebellum_White_Matter: limiting intensities to 105.0 --> 132.0
- 84 of 157 (53.5%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (89, 135, 47) --> (134, 173, 103)
- Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 132.0
- 0 of 175 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (113, 133, 78) --> (146, 193, 117)
- Brain_Stem: limiting intensities to 104.0 --> 132.0
- 127 of 209 (60.8%) samples deleted
- using 7381 total control points for intensity normalization...
- bias field = 0.937 +- 0.053
- 2 of 7169 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (124, 64, 36) --> (196, 179, 201)
- Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 0 of 4512 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (67, 62, 36) --> (136, 175, 200)
- Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 5 of 3709 (0.1%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (133, 135, 51) --> (180, 175, 106)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 119 of 303 (39.3%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (89, 135, 47) --> (134, 173, 103)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 238 of 269 (88.5%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (113, 133, 78) --> (146, 193, 117)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 153 of 356 (43.0%) samples deleted
- using 9149 total control points for intensity normalization...
- bias field = 1.036 +- 0.057
- 8 of 8545 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (124, 64, 36) --> (196, 179, 201)
- Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
- 2 of 4585 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (67, 62, 36) --> (136, 175, 200)
- Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 1 of 3849 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (133, 135, 51) --> (180, 175, 106)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 217 of 354 (61.3%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (89, 135, 47) --> (134, 173, 103)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 304 of 332 (91.6%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (113, 133, 78) --> (146, 193, 117)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 243 of 403 (60.3%) samples deleted
- using 9523 total control points for intensity normalization...
- bias field = 1.033 +- 0.053
- 20 of 8638 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 1 minutes and 37 seconds.
- #--------------------------------------
- #@# CA Reg Sat Oct 7 23:58:37 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri
- mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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) = 1.16 (predicted orig area = 6.9)
- 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=0.874, neg=0, invalid=762
- 0001: dt=246.444890, rms=0.772 (11.723%), neg=0, invalid=762
- 0002: dt=161.211356, rms=0.742 (3.865%), neg=0, invalid=762
- 0003: dt=240.330852, rms=0.729 (1.700%), neg=0, invalid=762
- 0004: dt=153.700787, rms=0.723 (0.869%), neg=0, invalid=762
- 0005: dt=295.936000, rms=0.718 (0.762%), neg=0, invalid=762
- 0006: dt=129.472000, rms=0.714 (0.531%), neg=0, invalid=762
- 0007: dt=517.888000, rms=0.709 (0.650%), neg=0, invalid=762
- 0008: dt=110.976000, rms=0.706 (0.408%), neg=0, invalid=762
- 0009: dt=1183.744000, rms=0.701 (0.700%), neg=0, invalid=762
- 0010: dt=92.480000, rms=0.699 (0.391%), neg=0, invalid=762
- 0011: dt=517.888000, rms=0.697 (0.197%), neg=0, invalid=762
- 0012: dt=517.888000, rms=0.697 (-0.205%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.698, neg=0, invalid=762
- 0013: dt=221.952000, rms=0.695 (0.419%), neg=0, invalid=762
- 0014: dt=129.472000, rms=0.694 (0.066%), neg=0, invalid=762
- 0015: dt=129.472000, rms=0.694 (0.067%), neg=0, invalid=762
- 0016: dt=129.472000, rms=0.693 (0.113%), neg=0, invalid=762
- 0017: dt=129.472000, rms=0.692 (0.149%), neg=0, invalid=762
- 0018: dt=129.472000, rms=0.691 (0.181%), neg=0, invalid=762
- 0019: dt=129.472000, rms=0.689 (0.184%), neg=0, invalid=762
- 0020: dt=129.472000, rms=0.688 (0.187%), neg=0, invalid=762
- 0021: dt=129.472000, rms=0.687 (0.179%), neg=0, invalid=762
- 0022: dt=129.472000, rms=0.686 (0.174%), neg=0, invalid=762
- 0023: dt=129.472000, rms=0.685 (0.174%), neg=0, invalid=762
- 0024: dt=129.472000, rms=0.683 (0.163%), neg=0, invalid=762
- 0025: dt=129.472000, rms=0.682 (0.153%), neg=0, invalid=762
- 0026: dt=129.472000, rms=0.681 (0.162%), neg=0, invalid=762
- 0027: dt=129.472000, rms=0.680 (0.162%), neg=0, invalid=762
- 0028: dt=129.472000, rms=0.679 (0.154%), neg=0, invalid=762
- 0029: dt=129.472000, rms=0.678 (0.152%), neg=0, invalid=762
- 0030: dt=129.472000, rms=0.677 (0.140%), neg=0, invalid=762
- 0031: dt=129.472000, rms=0.676 (0.137%), neg=0, invalid=762
- 0032: dt=129.472000, rms=0.675 (0.132%), neg=0, invalid=762
- 0033: dt=129.472000, rms=0.674 (0.137%), neg=0, invalid=762
- 0034: dt=129.472000, rms=0.674 (0.122%), neg=0, invalid=762
- 0035: dt=129.472000, rms=0.673 (0.109%), neg=0, invalid=762
- 0036: dt=1479.680000, rms=0.672 (0.088%), neg=0, invalid=762
- 0037: dt=1479.680000, rms=0.672 (-3.139%), neg=0, invalid=762
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.677, neg=0, invalid=762
- 0038: dt=124.416000, rms=0.671 (0.950%), neg=0, invalid=762
- 0039: dt=218.453333, rms=0.661 (1.451%), neg=0, invalid=762
- 0040: dt=56.808989, rms=0.657 (0.615%), neg=0, invalid=762
- 0041: dt=331.776000, rms=0.653 (0.668%), neg=0, invalid=762
- 0042: dt=82.944000, rms=0.648 (0.674%), neg=0, invalid=762
- 0043: dt=69.632000, rms=0.647 (0.177%), neg=0, invalid=762
- 0044: dt=69.632000, rms=0.646 (0.153%), neg=0, invalid=762
- 0045: dt=69.632000, rms=0.645 (0.232%), neg=0, invalid=762
- 0046: dt=69.632000, rms=0.643 (0.347%), neg=0, invalid=762
- 0047: dt=69.632000, rms=0.640 (0.375%), neg=0, invalid=762
- 0048: dt=69.632000, rms=0.638 (0.387%), neg=0, invalid=762
- 0049: dt=69.632000, rms=0.635 (0.380%), neg=0, invalid=762
- 0050: dt=69.632000, rms=0.633 (0.345%), neg=0, invalid=762
- 0051: dt=69.632000, rms=0.631 (0.352%), neg=0, invalid=762
- 0052: dt=69.632000, rms=0.629 (0.298%), neg=0, invalid=762
- 0053: dt=69.632000, rms=0.627 (0.294%), neg=0, invalid=762
- 0054: dt=69.632000, rms=0.626 (0.230%), neg=0, invalid=762
- 0055: dt=69.632000, rms=0.624 (0.210%), neg=0, invalid=762
- 0056: dt=69.632000, rms=0.623 (0.218%), neg=0, invalid=762
- 0057: dt=69.632000, rms=0.622 (0.188%), neg=0, invalid=762
- 0058: dt=69.632000, rms=0.621 (0.156%), neg=0, invalid=762
- 0059: dt=69.632000, rms=0.620 (0.127%), neg=0, invalid=762
- 0060: dt=69.632000, rms=0.619 (0.124%), neg=0, invalid=762
- 0061: dt=69.632000, rms=0.618 (0.127%), neg=0, invalid=762
- 0062: dt=69.632000, rms=0.618 (0.131%), neg=0, invalid=762
- 0063: dt=69.632000, rms=0.617 (0.098%), neg=0, invalid=762
- 0064: dt=69.632000, rms=0.617 (0.069%), neg=0, invalid=762
- 0065: dt=124.416000, rms=0.617 (0.015%), neg=0, invalid=762
- 0066: dt=124.416000, rms=0.617 (-0.011%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.617, neg=0, invalid=762
- 0067: dt=117.960784, rms=0.615 (0.413%), neg=0, invalid=762
- 0068: dt=82.944000, rms=0.614 (0.103%), neg=0, invalid=762
- 0069: dt=82.944000, rms=0.613 (0.070%), neg=0, invalid=762
- 0070: dt=82.944000, rms=0.613 (0.081%), neg=0, invalid=762
- 0071: dt=82.944000, rms=0.612 (0.085%), neg=0, invalid=762
- 0072: dt=82.944000, rms=0.612 (0.024%), neg=0, invalid=762
- 0073: dt=82.944000, rms=0.612 (0.034%), neg=0, invalid=762
- 0074: dt=82.944000, rms=0.612 (-0.002%), neg=0, invalid=762
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.638, neg=0, invalid=762
- 0075: dt=2.800000, rms=0.637 (0.090%), neg=0, invalid=762
- 0076: dt=0.600000, rms=0.637 (0.002%), neg=0, invalid=762
- 0077: dt=0.600000, rms=0.637 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.638, neg=0, invalid=762
- 0078: dt=0.000000, rms=0.637 (0.077%), neg=0, invalid=762
- 0079: dt=0.000000, rms=0.637 (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=0.710, neg=0, invalid=762
- 0080: dt=5.757576, rms=0.686 (3.325%), neg=0, invalid=762
- 0081: dt=3.814815, rms=0.685 (0.210%), neg=0, invalid=762
- 0082: dt=3.814815, rms=0.685 (-0.054%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.685, neg=0, invalid=762
- 0083: dt=0.000000, rms=0.685 (0.069%), neg=0, invalid=762
- 0084: dt=0.000000, rms=0.685 (0.000%), neg=0, invalid=762
- setting smoothness coefficient to 5.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.748, neg=0, invalid=762
- 0085: dt=1.024000, rms=0.746 (0.362%), neg=0, invalid=762
- 0086: dt=1.983471, rms=0.741 (0.621%), neg=0, invalid=762
- 0087: dt=1.024000, rms=0.740 (0.074%), neg=0, invalid=762
- 0088: dt=1.024000, rms=0.739 (0.190%), neg=0, invalid=762
- 0089: dt=1.024000, rms=0.738 (0.123%), neg=0, invalid=762
- 0090: dt=1.024000, rms=0.738 (-0.116%), neg=0, invalid=762
- 0091: dt=0.000000, rms=0.738 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.738, neg=0, invalid=762
- 0092: dt=1.024000, rms=0.738 (0.124%), neg=0, invalid=762
- 0093: dt=1.536000, rms=0.737 (0.053%), neg=0, invalid=762
- 0094: dt=1.536000, rms=0.737 (-0.031%), 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=0.691, neg=0, invalid=762
- 0095: dt=0.867840, rms=0.672 (2.784%), neg=0, invalid=762
- 0096: dt=0.080000, rms=0.671 (0.152%), neg=0, invalid=762
- 0097: dt=0.080000, rms=0.671 (-0.069%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.671, neg=0, invalid=762
- 0098: dt=0.028000, rms=0.671 (0.086%), neg=0, invalid=762
- 0099: dt=0.007000, rms=0.671 (0.001%), neg=0, invalid=762
- 0100: dt=0.007000, rms=0.671 (-0.000%), neg=0, invalid=762
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.10027 (20)
- mri peak = 0.08612 (24)
- Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (1124 voxels, overlap=0.783)
- Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (1124 voxels, peak = 22), gca=22.5
- gca peak = 0.15565 (16)
- mri peak = 0.10756 (26)
- Right_Lateral_Ventricle (43): linear fit = 1.65 x + 0.0 (1272 voxels, overlap=0.325)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1272 voxels, peak = 26), gca=24.0
- gca peak = 0.26829 (96)
- mri peak = 0.08040 (91)
- Right_Pallidum (52): linear fit = 0.94 x + 0.0 (998 voxels, overlap=0.499)
- Right_Pallidum (52): linear fit = 0.94 x + 0.0 (998 voxels, peak = 90), gca=89.8
- gca peak = 0.20183 (93)
- mri peak = 0.06825 (83)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (894 voxels, overlap=0.240)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (894 voxels, peak = 82), gca=82.3
- gca peak = 0.21683 (55)
- mri peak = 0.07516 (66)
- Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (1089 voxels, overlap=0.036)
- Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (1089 voxels, peak = 65), gca=65.2
- gca peak = 0.30730 (58)
- mri peak = 0.06491 (65)
- Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (1009 voxels, overlap=0.207)
- Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (1009 voxels, peak = 68), gca=67.6
- gca peak = 0.11430 (101)
- mri peak = 0.08092 (103)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (63471 voxels, overlap=0.809)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (63471 voxels, peak = 105), gca=104.5
- gca peak = 0.12076 (102)
- mri peak = 0.09434 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (65890 voxels, overlap=0.779)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (65890 voxels, peak = 106), gca=105.6
- gca peak = 0.14995 (59)
- mri peak = 0.04121 (70)
- Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (23712 voxels, overlap=0.157)
- Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (23712 voxels, peak = 71), gca=70.5
- gca peak = 0.15082 (58)
- mri peak = 0.04022 (70)
- Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (26246 voxels, overlap=0.125)
- Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (26246 voxels, peak = 71), gca=71.1
- gca peak = 0.14161 (67)
- mri peak = 0.08091 (72)
- Right_Caudate (50): linear fit = 1.07 x + 0.0 (932 voxels, overlap=0.756)
- Right_Caudate (50): linear fit = 1.07 x + 0.0 (932 voxels, peak = 71), gca=71.4
- gca peak = 0.15243 (71)
- mri peak = 0.06910 (77)
- Left_Caudate (11): linear fit = 1.03 x + 0.0 (1053 voxels, overlap=0.913)
- Left_Caudate (11): linear fit = 1.03 x + 0.0 (1053 voxels, peak = 73), gca=73.5
- gca peak = 0.13336 (57)
- mri peak = 0.05647 (64)
- Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (23492 voxels, overlap=0.549)
- Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (23492 voxels, peak = 66), gca=66.4
- gca peak = 0.13252 (56)
- mri peak = 0.04951 (65)
- Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (26109 voxels, overlap=0.442)
- Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (26109 voxels, peak = 67), gca=67.5
- gca peak = 0.18181 (84)
- mri peak = 0.06340 (82)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (10410 voxels, overlap=0.977)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (10410 voxels, peak = 84), gca=84.0
- gca peak = 0.20573 (83)
- mri peak = 0.09744 (79)
- Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (9194 voxels, overlap=0.978)
- Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (9194 voxels, peak = 80), gca=80.1
- gca peak = 0.21969 (57)
- mri peak = 0.10658 (72)
- Left_Amygdala (18): linear fit = 1.23 x + 0.0 (440 voxels, overlap=0.032)
- Left_Amygdala (18): linear fit = 1.23 x + 0.0 (440 voxels, peak = 70), gca=69.8
- gca peak = 0.39313 (56)
- mri peak = 0.06597 (69)
- Right_Amygdala (54): linear fit = 1.27 x + 0.0 (578 voxels, overlap=0.032)
- Right_Amygdala (54): linear fit = 1.27 x + 0.0 (578 voxels, peak = 71), gca=71.4
- gca peak = 0.14181 (85)
- mri peak = 0.07328 (87)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5696 voxels, overlap=0.958)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5696 voxels, peak = 86), gca=86.3
- gca peak = 0.11978 (83)
- mri peak = 0.06886 (87)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4142 voxels, overlap=0.928)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4142 voxels, peak = 85), gca=85.1
- gca peak = 0.13399 (79)
- mri peak = 0.07004 (80)
- Left_Putamen (12): linear fit = 1.04 x + 0.0 (2528 voxels, overlap=0.919)
- Left_Putamen (12): linear fit = 1.04 x + 0.0 (2528 voxels, peak = 83), gca=82.6
- gca peak = 0.14159 (79)
- mri peak = 0.08488 (78)
- Right_Putamen (51): linear fit = 1.01 x + 0.0 (2554 voxels, overlap=0.973)
- Right_Putamen (51): linear fit = 1.01 x + 0.0 (2554 voxels, peak = 80), gca=80.2
- gca peak = 0.10025 (80)
- mri peak = 0.08533 (85)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (12397 voxels, overlap=0.402)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (12397 voxels, peak = 88), gca=87.6
- gca peak = 0.13281 (86)
- mri peak = 0.06893 (88)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1071 voxels, overlap=0.678)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1071 voxels, peak = 93), gca=93.3
- gca peak = 0.12801 (89)
- mri peak = 0.06354 (91)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1187 voxels, overlap=0.734)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1187 voxels, peak = 90), gca=90.3
- gca peak = 0.20494 (23)
- mri peak = 1.00000 (47)
- gca peak = 0.15061 (21)
- mri peak = 0.13483 (16)
- Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (296 voxels, overlap=0.533)
- Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (296 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 1.21 x + 0.0
- estimating mean wm scale to be 1.03 x + 0.0
- estimating mean csf scale to be 1.15 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=0.673, neg=0, invalid=762
- 0101: dt=92.648649, rms=0.662 (1.719%), neg=0, invalid=762
- 0102: dt=129.472000, rms=0.659 (0.330%), neg=0, invalid=762
- 0103: dt=443.904000, rms=0.655 (0.650%), neg=0, invalid=762
- 0104: dt=443.904000, rms=0.652 (0.410%), neg=0, invalid=762
- 0105: dt=129.472000, rms=0.651 (0.289%), neg=0, invalid=762
- 0106: dt=129.472000, rms=0.650 (0.043%), neg=0, invalid=762
- 0107: dt=129.472000, rms=0.650 (0.077%), neg=0, invalid=762
- 0108: dt=129.472000, rms=0.649 (0.120%), neg=0, invalid=762
- 0109: dt=129.472000, rms=0.648 (0.163%), neg=0, invalid=762
- 0110: dt=129.472000, rms=0.647 (0.167%), neg=0, invalid=762
- 0111: dt=129.472000, rms=0.645 (0.211%), neg=0, invalid=762
- 0112: dt=129.472000, rms=0.644 (0.185%), neg=0, invalid=762
- 0113: dt=129.472000, rms=0.643 (0.163%), neg=0, invalid=762
- 0114: dt=129.472000, rms=0.642 (0.128%), neg=0, invalid=762
- 0115: dt=129.472000, rms=0.642 (0.108%), neg=0, invalid=762
- 0116: dt=129.472000, rms=0.641 (0.104%), neg=0, invalid=762
- 0117: dt=129.472000, rms=0.640 (0.105%), neg=0, invalid=762
- 0118: dt=129.472000, rms=0.640 (0.099%), neg=0, invalid=762
- 0119: dt=129.472000, rms=0.639 (0.103%), neg=0, invalid=762
- 0120: dt=129.472000, rms=0.638 (0.114%), neg=0, invalid=762
- 0121: dt=129.472000, rms=0.638 (0.120%), neg=0, invalid=762
- 0122: dt=129.472000, rms=0.637 (0.115%), neg=0, invalid=762
- 0123: dt=129.472000, rms=0.636 (0.109%), neg=0, invalid=762
- 0124: dt=129.472000, rms=0.635 (0.109%), neg=0, invalid=762
- 0125: dt=129.472000, rms=0.635 (0.118%), neg=0, invalid=762
- 0126: dt=129.472000, rms=0.634 (0.113%), neg=0, invalid=762
- 0127: dt=129.472000, rms=0.633 (0.106%), neg=0, invalid=762
- 0128: dt=129.472000, rms=0.633 (0.101%), neg=0, invalid=762
- 0129: dt=129.472000, rms=0.632 (0.103%), neg=0, invalid=762
- 0130: dt=129.472000, rms=0.631 (0.102%), neg=0, invalid=762
- 0131: dt=129.472000, rms=0.631 (0.095%), neg=0, invalid=762
- 0132: dt=129.472000, rms=0.630 (0.089%), neg=0, invalid=762
- 0133: dt=129.472000, rms=0.630 (0.078%), neg=0, invalid=762
- 0134: dt=129.472000, rms=0.629 (0.077%), neg=0, invalid=762
- 0135: dt=129.472000, rms=0.629 (0.068%), neg=0, invalid=762
- 0136: dt=129.472000, rms=0.628 (0.066%), neg=0, invalid=762
- 0137: dt=129.472000, rms=0.628 (0.045%), neg=0, invalid=762
- 0138: dt=129.472000, rms=0.628 (0.052%), neg=0, invalid=762
- 0139: dt=129.472000, rms=0.627 (0.054%), neg=0, invalid=762
- 0140: dt=129.472000, rms=0.627 (0.054%), neg=0, invalid=762
- 0141: dt=129.472000, rms=0.627 (0.048%), neg=0, invalid=762
- 0142: dt=129.472000, rms=0.627 (0.045%), neg=0, invalid=762
- 0143: dt=129.472000, rms=0.626 (0.039%), neg=0, invalid=762
- 0144: dt=129.472000, rms=0.626 (0.037%), neg=0, invalid=762
- 0145: dt=129.472000, rms=0.626 (0.038%), neg=0, invalid=762
- 0146: dt=129.472000, rms=0.626 (0.040%), neg=0, invalid=762
- 0147: dt=129.472000, rms=0.625 (0.040%), neg=0, invalid=762
- 0148: dt=129.472000, rms=0.625 (0.032%), neg=0, invalid=762
- 0149: dt=129.472000, rms=0.625 (0.032%), neg=0, invalid=762
- 0150: dt=129.472000, rms=0.625 (0.031%), neg=0, invalid=762
- 0151: dt=129.472000, rms=0.624 (0.042%), neg=0, invalid=762
- 0152: dt=129.472000, rms=0.624 (0.033%), neg=0, invalid=762
- 0153: dt=129.472000, rms=0.624 (0.026%), neg=0, invalid=762
- 0154: dt=129.472000, rms=0.624 (0.023%), neg=0, invalid=762
- 0155: dt=129.472000, rms=0.624 (0.025%), neg=0, invalid=762
- 0156: dt=129.472000, rms=0.624 (0.033%), neg=0, invalid=762
- 0157: dt=129.472000, rms=0.623 (0.034%), neg=0, invalid=762
- 0158: dt=129.472000, rms=0.623 (0.024%), neg=0, invalid=762
- 0159: dt=129.472000, rms=0.623 (0.024%), neg=0, invalid=762
- 0160: dt=517.888000, rms=0.623 (0.011%), neg=0, invalid=762
- 0161: dt=517.888000, rms=0.623 (-0.052%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.623, neg=0, invalid=762
- 0162: dt=517.888000, rms=0.621 (0.376%), neg=0, invalid=762
- 0163: dt=110.976000, rms=0.621 (0.048%), neg=0, invalid=762
- 0164: dt=110.976000, rms=0.621 (0.003%), neg=0, invalid=762
- 0165: dt=110.976000, rms=0.621 (-0.003%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.623, neg=0, invalid=762
- 0166: dt=145.152000, rms=0.619 (0.580%), neg=0, invalid=762
- 0167: dt=209.185185, rms=0.610 (1.372%), neg=0, invalid=762
- 0168: dt=50.701299, rms=0.608 (0.461%), neg=0, invalid=762
- 0169: dt=331.776000, rms=0.605 (0.480%), neg=0, invalid=762
- 0170: dt=131.072000, rms=0.599 (0.993%), neg=0, invalid=762
- 0171: dt=36.288000, rms=0.598 (0.132%), neg=0, invalid=762
- 0172: dt=82.944000, rms=0.597 (0.075%), neg=0, invalid=762
- 0173: dt=580.608000, rms=0.592 (0.900%), neg=0, invalid=762
- 0174: dt=53.538462, rms=0.590 (0.332%), neg=0, invalid=762
- 0175: dt=414.720000, rms=0.588 (0.328%), neg=0, invalid=762
- 0176: dt=71.578947, rms=0.586 (0.294%), neg=0, invalid=762
- 0177: dt=145.152000, rms=0.586 (0.143%), neg=0, invalid=762
- 0178: dt=62.208000, rms=0.585 (0.079%), neg=0, invalid=762
- 0179: dt=497.664000, rms=0.583 (0.358%), neg=0, invalid=762
- 0180: dt=36.288000, rms=0.582 (0.177%), neg=0, invalid=762
- 0181: dt=62.208000, rms=0.582 (0.037%), neg=0, invalid=762
- 0182: dt=62.208000, rms=0.581 (0.061%), neg=0, invalid=762
- 0183: dt=62.208000, rms=0.581 (0.100%), neg=0, invalid=762
- 0184: dt=62.208000, rms=0.580 (0.124%), neg=0, invalid=762
- 0185: dt=62.208000, rms=0.579 (0.148%), neg=0, invalid=762
- 0186: dt=62.208000, rms=0.578 (0.180%), neg=0, invalid=762
- 0187: dt=62.208000, rms=0.577 (0.199%), neg=0, invalid=762
- 0188: dt=62.208000, rms=0.576 (0.196%), neg=0, invalid=762
- 0189: dt=62.208000, rms=0.575 (0.195%), neg=0, invalid=762
- 0190: dt=62.208000, rms=0.574 (0.188%), neg=0, invalid=762
- 0191: dt=62.208000, rms=0.573 (0.196%), neg=0, invalid=762
- 0192: dt=62.208000, rms=0.572 (0.192%), neg=0, invalid=762
- 0193: dt=62.208000, rms=0.571 (0.179%), neg=0, invalid=762
- 0194: dt=62.208000, rms=0.570 (0.171%), neg=0, invalid=762
- 0195: dt=62.208000, rms=0.569 (0.158%), neg=0, invalid=762
- 0196: dt=62.208000, rms=0.568 (0.146%), neg=0, invalid=762
- 0197: dt=62.208000, rms=0.567 (0.140%), neg=0, invalid=762
- 0198: dt=62.208000, rms=0.566 (0.132%), neg=0, invalid=762
- 0199: dt=62.208000, rms=0.566 (0.129%), neg=0, invalid=762
- 0200: dt=62.208000, rms=0.565 (0.123%), neg=0, invalid=762
- 0201: dt=62.208000, rms=0.565 (0.012%), neg=0, invalid=762
- 0202: dt=62.208000, rms=0.565 (0.027%), neg=0, invalid=762
- 0203: dt=62.208000, rms=0.564 (0.034%), neg=0, invalid=762
- 0204: dt=62.208000, rms=0.564 (0.043%), neg=0, invalid=762
- 0205: dt=62.208000, rms=0.564 (0.014%), neg=0, invalid=762
- 0206: dt=7.776000, rms=0.564 (0.001%), neg=0, invalid=762
- 0207: dt=1.944000, rms=0.564 (0.000%), neg=0, invalid=762
- 0208: dt=0.243000, rms=0.564 (0.000%), neg=0, invalid=762
- 0209: dt=0.030375, rms=0.564 (0.000%), neg=0, invalid=762
- 0210: dt=0.015187, rms=0.564 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.565, neg=0, invalid=762
- 0211: dt=0.000000, rms=0.564 (0.121%), neg=0, invalid=762
- 0212: dt=0.000000, rms=0.564 (0.000%), neg=0, invalid=762
- 0213: dt=0.000220, rms=0.564 (0.000%), neg=0, invalid=762
- 0214: dt=0.000110, rms=0.564 (0.000%), neg=0, invalid=762
- 0215: dt=0.000027, rms=0.564 (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=0.574, neg=0, invalid=762
- 0216: dt=137.788635, rms=0.557 (2.927%), neg=0, invalid=762
- 0217: dt=11.200000, rms=0.554 (0.545%), neg=0, invalid=762
- 0218: dt=32.000000, rms=0.549 (0.884%), neg=0, invalid=762
- 0219: dt=128.000000, rms=0.541 (1.428%), neg=0, invalid=762
- 0220: dt=11.200000, rms=0.540 (0.206%), neg=0, invalid=762
- 0221: dt=32.000000, rms=0.539 (0.275%), neg=0, invalid=762
- 0222: dt=128.000000, rms=0.537 (0.393%), neg=0, invalid=762
- 0223: dt=9.600000, rms=0.536 (0.198%), neg=0, invalid=762
- 0224: dt=0.700000, rms=0.535 (0.018%), neg=0, invalid=762
- 0225: dt=0.700000, rms=0.535 (0.010%), neg=0, invalid=762
- 0226: dt=0.087500, rms=0.535 (0.002%), neg=0, invalid=762
- 0227: dt=0.043750, rms=0.535 (0.000%), neg=0, invalid=762
- 0228: dt=0.002734, rms=0.535 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.536, neg=0, invalid=762
- 0229: dt=11.200000, rms=0.534 (0.416%), neg=0, invalid=762
- 0230: dt=11.200000, rms=0.533 (0.198%), neg=0, invalid=762
- 0231: dt=2.800000, rms=0.533 (0.040%), neg=0, invalid=762
- 0232: dt=0.175000, rms=0.533 (0.003%), neg=0, invalid=762
- 0233: dt=0.010937, rms=0.533 (0.000%), neg=0, invalid=762
- 0234: dt=0.005469, rms=0.533 (0.000%), neg=0, invalid=762
- 0235: dt=0.001367, rms=0.533 (0.000%), neg=0, invalid=762
- 0236: dt=0.000000, rms=0.533 (0.000%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.556, neg=0, invalid=762
- 0237: dt=6.333333, rms=0.554 (0.339%), neg=0, invalid=762
- 0238: dt=8.879581, rms=0.553 (0.158%), neg=0, invalid=762
- 0239: dt=22.492754, rms=0.551 (0.364%), neg=0, invalid=762
- 0240: dt=2.880000, rms=0.551 (0.123%), neg=0, invalid=762
- 0241: dt=0.252000, rms=0.550 (0.010%), neg=0, invalid=762
- 0242: dt=0.063000, rms=0.550 (0.002%), neg=0, invalid=762
- 0243: dt=0.007875, rms=0.550 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.551, neg=0, invalid=762
- 0244: dt=0.011250, rms=0.550 (0.100%), neg=0, invalid=762
- 0245: dt=0.000984, rms=0.550 (0.000%), neg=0, invalid=762
- 0246: dt=0.000492, rms=0.550 (0.000%), neg=0, invalid=762
- 0247: dt=0.000246, rms=0.550 (0.000%), neg=0, invalid=762
- 0248: dt=0.000015, rms=0.550 (0.000%), neg=0, invalid=762
- 0249: dt=0.000000, rms=0.550 (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=0.579, neg=0, invalid=762
- 0250: dt=0.000000, rms=0.578 (0.091%), neg=0, invalid=762
- 0251: dt=0.000000, rms=0.578 (0.000%), neg=0, invalid=762
- 0252: dt=0.100000, rms=0.578 (-0.024%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.579, neg=0, invalid=762
- 0253: dt=0.192000, rms=0.578 (0.095%), neg=0, invalid=762
- 0254: dt=0.112000, rms=0.578 (0.001%), neg=0, invalid=762
- 0255: dt=0.112000, rms=0.578 (-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=0.533, neg=0, invalid=762
- 0256: dt=0.448000, rms=0.519 (2.762%), neg=0, invalid=762
- 0257: dt=0.448000, rms=0.515 (0.674%), neg=0, invalid=762
- 0258: dt=0.448000, rms=0.513 (0.377%), neg=0, invalid=762
- 0259: dt=0.448000, rms=0.512 (0.231%), neg=0, invalid=762
- 0260: dt=0.500000, rms=0.511 (0.186%), neg=0, invalid=762
- 0261: dt=0.448000, rms=0.510 (0.125%), neg=0, invalid=762
- 0262: dt=0.448000, rms=0.510 (0.099%), neg=0, invalid=762
- 0263: dt=0.448000, rms=0.510 (0.080%), neg=0, invalid=762
- 0264: dt=0.448000, rms=0.509 (0.067%), neg=0, invalid=762
- 0265: dt=0.448000, rms=0.509 (0.057%), neg=0, invalid=762
- 0266: dt=0.448000, rms=0.509 (0.047%), neg=0, invalid=762
- 0267: dt=0.448000, rms=0.508 (0.042%), neg=0, invalid=762
- 0268: dt=0.448000, rms=0.508 (0.073%), neg=0, invalid=762
- 0269: dt=0.448000, rms=0.508 (0.030%), neg=0, invalid=762
- 0270: dt=0.448000, rms=0.508 (0.024%), neg=0, invalid=762
- 0271: dt=0.448000, rms=0.508 (0.043%), neg=0, invalid=762
- 0272: dt=0.224000, rms=0.508 (0.012%), neg=0, invalid=762
- 0273: dt=0.224000, rms=0.507 (0.022%), neg=0, invalid=762
- 0274: dt=0.224000, rms=0.507 (0.025%), neg=0, invalid=762
- 0275: dt=0.224000, rms=0.507 (0.004%), neg=0, invalid=762
- 0276: dt=0.224000, rms=0.507 (0.008%), neg=0, invalid=762
- 0277: dt=0.224000, rms=0.507 (0.019%), neg=0, invalid=762
- 0278: dt=0.224000, rms=0.507 (0.025%), neg=0, invalid=762
- 0279: dt=0.224000, rms=0.507 (0.022%), neg=0, invalid=762
- 0280: dt=0.112000, rms=0.507 (0.001%), neg=0, invalid=762
- 0281: dt=0.112000, rms=0.507 (0.001%), neg=0, invalid=762
- 0282: dt=0.112000, rms=0.507 (0.003%), neg=0, invalid=762
- 0283: dt=0.112000, rms=0.507 (0.004%), neg=0, invalid=762
- 0284: dt=0.112000, rms=0.507 (0.006%), neg=0, invalid=762
- 0285: dt=0.112000, rms=0.507 (0.006%), neg=0, invalid=762
- 0286: dt=0.112000, rms=0.507 (0.007%), neg=0, invalid=762
- 0287: dt=0.112000, rms=0.507 (0.006%), neg=0, invalid=762
- 0288: dt=0.112000, rms=0.507 (0.008%), neg=0, invalid=762
- 0289: dt=0.112000, rms=0.507 (0.007%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.507, neg=0, invalid=762
- 0290: dt=0.448000, rms=0.502 (1.035%), neg=0, invalid=762
- 0291: dt=0.320000, rms=0.501 (0.102%), neg=0, invalid=762
- 0292: dt=0.384000, rms=0.501 (0.072%), neg=0, invalid=762
- 0293: dt=0.384000, rms=0.501 (0.023%), neg=0, invalid=762
- 0294: dt=0.384000, rms=0.501 (0.016%), neg=0, invalid=762
- 0295: dt=0.384000, rms=0.501 (0.013%), neg=0, invalid=762
- 0296: dt=0.384000, rms=0.501 (-0.001%), neg=0, invalid=762
- label assignment complete, 0 changed (0.00%)
- ********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
- **************** pass 1 of 1 ************************
- enabling zero nodes
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.499, neg=0, invalid=762
- 0297: dt=0.000000, rms=0.498 (0.119%), neg=0, invalid=762
- 0298: dt=0.000000, rms=0.498 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.499, neg=0, invalid=762
- 0299: dt=110.976000, rms=0.498 (0.154%), neg=0, invalid=762
- 0300: dt=295.936000, rms=0.498 (0.064%), neg=0, invalid=762
- 0301: dt=295.936000, rms=0.498 (-0.324%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.499, neg=0, invalid=762
- 0302: dt=36.288000, rms=0.498 (0.199%), neg=0, invalid=762
- 0303: dt=36.288000, rms=0.497 (0.047%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0304: dt=36.288000, rms=0.497 (0.055%), neg=0, invalid=762
- 0305: dt=36.288000, rms=0.497 (0.060%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0306: dt=36.288000, rms=0.497 (0.028%), neg=0, invalid=762
- 0307: dt=36.288000, rms=0.497 (-0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.497, neg=0, invalid=762
- 0308: dt=124.416000, rms=0.493 (0.755%), neg=0, invalid=762
- 0309: dt=36.288000, rms=0.493 (0.129%), neg=0, invalid=762
- 0310: dt=36.288000, rms=0.493 (0.054%), neg=0, invalid=762
- 0311: dt=36.288000, rms=0.492 (0.082%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0312: dt=36.288000, rms=0.492 (0.101%), neg=0, invalid=762
- 0313: dt=36.288000, rms=0.491 (0.124%), neg=0, invalid=762
- 0314: dt=36.288000, rms=0.490 (0.134%), neg=0, invalid=762
- 0315: dt=36.288000, rms=0.490 (0.130%), neg=0, invalid=762
- 0316: dt=36.288000, rms=0.489 (0.114%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0317: dt=36.288000, rms=0.489 (0.106%), neg=0, invalid=762
- 0318: dt=145.152000, rms=0.489 (0.029%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 7 iterations, nbhd size=1, neg = 0
- 0319: dt=145.152000, rms=0.488 (0.018%), neg=0, invalid=762
- 0320: dt=145.152000, rms=0.488 (-0.010%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.490, neg=0, invalid=762
- 0321: dt=32.000000, rms=0.487 (0.560%), neg=0, invalid=762
- iter 0, gcam->neg = 14
- after 10 iterations, nbhd size=1, neg = 0
- 0322: dt=82.400000, rms=0.483 (0.700%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0323: dt=28.465116, rms=0.482 (0.344%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0324: dt=38.400000, rms=0.480 (0.325%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 2 iterations, nbhd size=0, neg = 0
- 0325: dt=25.600000, rms=0.479 (0.157%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0326: dt=25.600000, rms=0.479 (0.129%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 2 iterations, nbhd size=0, neg = 0
- 0327: dt=25.600000, rms=0.478 (0.207%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 2 iterations, nbhd size=0, neg = 0
- 0328: dt=25.600000, rms=0.477 (0.239%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0329: dt=25.600000, rms=0.476 (0.216%), neg=0, invalid=762
- iter 0, gcam->neg = 14
- after 4 iterations, nbhd size=0, neg = 0
- 0330: dt=25.600000, rms=0.475 (0.196%), neg=0, invalid=762
- iter 0, gcam->neg = 8
- after 5 iterations, nbhd size=0, neg = 0
- 0331: dt=25.600000, rms=0.474 (0.195%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 4 iterations, nbhd size=0, neg = 0
- 0332: dt=25.600000, rms=0.473 (0.186%), neg=0, invalid=762
- iter 0, gcam->neg = 23
- after 4 iterations, nbhd size=0, neg = 0
- 0333: dt=25.600000, rms=0.472 (0.149%), neg=0, invalid=762
- iter 0, gcam->neg = 27
- after 6 iterations, nbhd size=0, neg = 0
- 0334: dt=25.600000, rms=0.472 (0.140%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 2 iterations, nbhd size=0, neg = 0
- 0335: dt=25.600000, rms=0.471 (0.151%), neg=0, invalid=762
- iter 0, gcam->neg = 6
- after 2 iterations, nbhd size=0, neg = 0
- 0336: dt=25.600000, rms=0.470 (0.142%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 15 iterations, nbhd size=1, neg = 0
- 0337: dt=25.600000, rms=0.470 (0.090%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 9 iterations, nbhd size=1, neg = 0
- 0338: dt=25.600000, rms=0.469 (0.051%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0339: dt=44.800000, rms=0.469 (0.081%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0340: dt=11.200000, rms=0.469 (0.008%), neg=0, invalid=762
- 0341: dt=11.200000, rms=0.469 (0.008%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0342: dt=11.200000, rms=0.469 (0.010%), neg=0, invalid=762
- 0343: dt=11.200000, rms=0.469 (0.010%), neg=0, invalid=762
- 0344: dt=11.200000, rms=0.469 (0.013%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0345: dt=11.200000, rms=0.469 (0.016%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 2 iterations, nbhd size=0, neg = 0
- 0346: dt=11.200000, rms=0.469 (0.012%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.469, neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0347: dt=69.723577, rms=0.465 (0.954%), neg=0, invalid=762
- 0348: dt=24.782979, rms=0.464 (0.218%), neg=0, invalid=762
- 0349: dt=24.782979, rms=0.463 (0.091%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0350: dt=24.782979, rms=0.463 (0.106%), neg=0, invalid=762
- 0351: dt=24.782979, rms=0.462 (0.120%), neg=0, invalid=762
- 0352: dt=24.782979, rms=0.462 (0.095%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 5 iterations, nbhd size=0, neg = 0
- 0353: dt=24.782979, rms=0.462 (0.096%), neg=0, invalid=762
- 0354: dt=24.782979, rms=0.461 (0.089%), neg=0, invalid=762
- 0355: dt=44.800000, rms=0.461 (0.042%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.469, neg=0, invalid=762
- 0356: dt=0.000000, rms=0.468 (0.121%), neg=0, invalid=762
- 0357: dt=0.000000, rms=0.468 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.469, neg=0, invalid=762
- 0358: dt=2.304000, rms=0.468 (0.143%), neg=0, invalid=762
- 0359: dt=1.008000, rms=0.468 (0.006%), neg=0, invalid=762
- 0360: dt=1.008000, rms=0.468 (0.001%), neg=0, invalid=762
- 0361: dt=1.008000, rms=0.468 (-0.012%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.481, neg=0, invalid=762
- 0362: dt=1.024000, rms=0.479 (0.299%), neg=0, invalid=762
- 0363: dt=0.384000, rms=0.479 (0.013%), neg=0, invalid=762
- 0364: dt=0.384000, rms=0.479 (-0.006%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.480, neg=0, invalid=762
- 0365: dt=1.792000, rms=0.478 (0.339%), neg=0, invalid=762
- 0366: dt=0.768000, rms=0.478 (0.025%), neg=0, invalid=762
- 0367: dt=0.768000, rms=0.478 (-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=0.469, neg=0, invalid=762
- iter 0, gcam->neg = 715
- after 16 iterations, nbhd size=1, neg = 0
- 0368: dt=2.239688, rms=0.437 (6.722%), neg=0, invalid=762
- 0369: dt=0.096000, rms=0.437 (0.075%), neg=0, invalid=762
- 0370: dt=0.096000, rms=0.437 (-0.076%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.437, neg=0, invalid=762
- 0371: dt=0.064000, rms=0.437 (0.191%), neg=0, invalid=762
- 0372: dt=0.007000, rms=0.437 (0.002%), neg=0, invalid=762
- 0373: dt=0.007000, rms=0.437 (-0.000%), neg=0, invalid=762
- label assignment complete, 0 changed (0.00%)
- label assignment complete, 0 changed (0.00%)
- ***************** morphing with label term set to 0 *******************************
- **************** pass 1 of 1 ************************
- enabling zero nodes
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.421, neg=0, invalid=762
- 0374: 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
- 0375: dt=0.000000, rms=0.421 (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=0.422, neg=0, invalid=762
- 0376: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.422, neg=0, invalid=762
- 0377: dt=36.288000, rms=0.421 (0.034%), neg=0, invalid=762
- 0378: dt=124.416000, rms=0.421 (0.044%), neg=0, invalid=762
- 0379: dt=331.776000, rms=0.421 (0.139%), neg=0, invalid=762
- 0380: dt=31.104000, rms=0.421 (0.023%), neg=0, invalid=762
- 0381: dt=31.104000, rms=0.421 (-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=0.421, neg=0, invalid=762
- 0382: dt=11.200000, rms=0.421 (0.066%), neg=0, invalid=762
- 0383: dt=11.200000, rms=0.421 (0.029%), neg=0, invalid=762
- 0384: dt=11.200000, rms=0.421 (0.023%), neg=0, invalid=762
- 0385: dt=11.200000, rms=0.421 (-0.006%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.421, neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0386: dt=68.403670, rms=0.418 (0.775%), neg=0, invalid=762
- 0387: dt=24.131148, rms=0.416 (0.293%), neg=0, invalid=762
- 0388: dt=44.800000, rms=0.416 (0.175%), neg=0, invalid=762
- 0389: dt=44.800000, rms=0.415 (0.099%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 0 iterations, nbhd size=0, neg = 0
- 0390: dt=44.800000, rms=0.414 (0.296%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 8 iterations, nbhd size=1, neg = 0
- 0391: dt=44.800000, rms=0.413 (0.242%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 6 iterations, nbhd size=0, neg = 0
- 0392: dt=44.800000, rms=0.412 (0.218%), neg=0, invalid=762
- iter 0, gcam->neg = 12
- after 3 iterations, nbhd size=0, neg = 0
- 0393: dt=44.800000, rms=0.411 (0.235%), neg=0, invalid=762
- iter 0, gcam->neg = 15
- after 3 iterations, nbhd size=0, neg = 0
- 0394: dt=44.800000, rms=0.410 (0.190%), neg=0, invalid=762
- iter 0, gcam->neg = 30
- after 15 iterations, nbhd size=1, neg = 0
- 0395: dt=44.800000, rms=0.410 (0.138%), neg=0, invalid=762
- iter 0, gcam->neg = 30
- after 7 iterations, nbhd size=0, neg = 0
- 0396: dt=44.800000, rms=0.409 (0.106%), neg=0, invalid=762
- iter 0, gcam->neg = 45
- after 7 iterations, nbhd size=0, neg = 0
- 0397: dt=44.800000, rms=0.409 (0.091%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0398: dt=11.200000, rms=0.409 (0.019%), neg=0, invalid=762
- 0399: dt=11.200000, rms=0.409 (0.005%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0400: dt=11.200000, rms=0.409 (0.005%), neg=0, invalid=762
- 0401: dt=11.200000, rms=0.409 (0.007%), neg=0, invalid=762
- 0402: dt=11.200000, rms=0.409 (0.012%), neg=0, invalid=762
- 0403: dt=11.200000, rms=0.409 (0.012%), neg=0, invalid=762
- 0404: dt=11.200000, rms=0.409 (0.008%), neg=0, invalid=762
- 0405: dt=11.200000, rms=0.409 (0.003%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.414, neg=0, invalid=762
- 0406: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.414, neg=0, invalid=762
- 0407: dt=1.008000, rms=0.414 (0.005%), neg=0, invalid=762
- 0408: dt=1.008000, rms=0.414 (0.002%), neg=0, invalid=762
- 0409: dt=1.008000, rms=0.414 (0.000%), neg=0, invalid=762
- 0410: dt=1.008000, rms=0.414 (-0.007%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.423, neg=0, invalid=762
- 0411: dt=0.000000, rms=0.423 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.423, neg=0, invalid=762
- 0412: dt=0.000000, rms=0.423 (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=0.407, neg=0, invalid=762
- iter 0, gcam->neg = 492
- after 16 iterations, nbhd size=1, neg = 0
- 0413: dt=1.159858, rms=0.398 (2.117%), neg=0, invalid=762
- 0414: dt=0.000023, rms=0.398 (0.000%), neg=0, invalid=762
- 0415: dt=0.000023, rms=0.398 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.398, neg=0, invalid=762
- 0416: dt=0.112000, rms=0.398 (0.072%), neg=0, invalid=762
- 0417: dt=0.112000, rms=0.398 (0.031%), neg=0, invalid=762
- 0418: dt=0.112000, rms=0.398 (0.027%), neg=0, invalid=762
- 0419: dt=0.112000, rms=0.398 (-0.005%), neg=0, invalid=762
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- mri_ca_register took 1 hours, 52 minutes and 55 seconds.
- mri_ca_register utimesec 7610.836976
- mri_ca_register stimesec 10.152456
- mri_ca_register ru_maxrss 1346540
- mri_ca_register ru_ixrss 0
- mri_ca_register ru_idrss 0
- mri_ca_register ru_isrss 0
- mri_ca_register ru_minflt 5243748
- mri_ca_register ru_majflt 0
- mri_ca_register ru_nswap 0
- mri_ca_register ru_inblock 0
- mri_ca_register ru_oublock 63520
- mri_ca_register ru_msgsnd 0
- mri_ca_register ru_msgrcv 0
- mri_ca_register ru_nsignals 0
- mri_ca_register ru_nvcsw 4139
- mri_ca_register ru_nivcsw 22663
- FSRUNTIME@ mri_ca_register 1.8820 hours 2 threads
- #--------------------------------------
- #@# SubCort Seg Sun Oct 8 01:51:32 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-623
- 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-6.0.0/0050319/mri
- mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz
- == Number of threads available to mri_ca_label for OpenMP = 2 ==
- relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
- using Gibbs prior factor = 0.500
- renormalizing sequences with structure alignment, equivalent to:
- -renormalize
- -renormalize_mean 0.500
- -regularize 0.500
- reading 1 input volumes
- reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
- reading input volume from norm.mgz
- average std[0] = 7.3
- reading transform from transforms/talairach.m3z
- setting orig areas to linear transform determinant scaled 6.88
- 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 = 0.10292 (26)
- Left_Lateral_Ventricle (4): linear fit = 1.25 x + 0.0 (1156 voxels, overlap=0.981)
- Left_Lateral_Ventricle (4): linear fit = 1.25 x + 0.0 (1156 voxels, peak = 25), gca=25.1
- gca peak = 0.17677 (13)
- mri peak = 0.11762 (26)
- Right_Lateral_Ventricle (43): linear fit = 1.82 x + 0.0 (2080 voxels, overlap=0.368)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2080 voxels, peak = 24), gca=19.5
- gca peak = 0.28129 (95)
- mri peak = 0.13949 (91)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (509 voxels, overlap=0.753)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (509 voxels, peak = 91), gca=90.7
- gca peak = 0.16930 (96)
- mri peak = 0.12883 (91)
- Left_Pallidum (13): linear fit = 0.95 x + 0.0 (650 voxels, overlap=0.665)
- Left_Pallidum (13): linear fit = 0.95 x + 0.0 (650 voxels, peak = 92), gca=91.7
- gca peak = 0.24553 (55)
- mri peak = 0.10697 (66)
- Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (808 voxels, overlap=0.017)
- Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (808 voxels, peak = 65), gca=64.6
- gca peak = 0.30264 (59)
- mri peak = 0.09267 (64)
- Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (797 voxels, overlap=0.433)
- Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (797 voxels, peak = 67), gca=67.0
- gca peak = 0.07580 (103)
- mri peak = 0.08653 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32723 voxels, overlap=0.737)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32723 voxels, peak = 106), gca=105.6
- gca peak = 0.07714 (104)
- mri peak = 0.10286 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32128 voxels, overlap=0.659)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32128 voxels, peak = 104), gca=104.0
- gca peak = 0.09712 (58)
- mri peak = 0.04638 (70)
- Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (38524 voxels, overlap=0.447)
- Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (38524 voxels, peak = 69), gca=68.7
- gca peak = 0.11620 (58)
- mri peak = 0.04494 (72)
- Right_Cerebral_Cortex (42): linear fit = 1.18 x + 0.0 (37521 voxels, overlap=0.432)
- Right_Cerebral_Cortex (42): linear fit = 1.18 x + 0.0 (37521 voxels, peak = 69), gca=68.7
- gca peak = 0.30970 (66)
- mri peak = 0.09861 (72)
- Right_Caudate (50): linear fit = 1.10 x + 0.0 (1227 voxels, overlap=0.379)
- Right_Caudate (50): linear fit = 1.10 x + 0.0 (1227 voxels, peak = 72), gca=72.3
- gca peak = 0.15280 (69)
- mri peak = 0.12798 (75)
- Left_Caudate (11): linear fit = 1.05 x + 0.0 (1126 voxels, overlap=0.896)
- Left_Caudate (11): linear fit = 1.05 x + 0.0 (1126 voxels, peak = 73), gca=72.8
- gca peak = 0.13902 (56)
- mri peak = 0.06206 (64)
- Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (26808 voxels, overlap=0.470)
- Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (26808 voxels, peak = 65), gca=64.7
- gca peak = 0.14777 (55)
- mri peak = 0.05653 (66)
- Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (27187 voxels, overlap=0.227)
- Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (27187 voxels, peak = 66), gca=65.7
- gca peak = 0.16765 (84)
- mri peak = 0.09063 (82)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5924 voxels, overlap=0.959)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5924 voxels, peak = 84), gca=83.6
- gca peak = 0.18739 (84)
- mri peak = 0.10772 (79)
- Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (5440 voxels, overlap=0.967)
- Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (5440 voxels, peak = 81), gca=81.1
- gca peak = 0.29869 (57)
- mri peak = 0.10463 (75)
- Left_Amygdala (18): linear fit = 1.25 x + 0.0 (584 voxels, overlap=0.057)
- Left_Amygdala (18): linear fit = 1.25 x + 0.0 (584 voxels, peak = 72), gca=71.5
- gca peak = 0.33601 (57)
- mri peak = 0.08360 (72)
- Right_Amygdala (54): linear fit = 1.23 x + 0.0 (631 voxels, overlap=0.049)
- Right_Amygdala (54): linear fit = 1.23 x + 0.0 (631 voxels, peak = 70), gca=69.8
- gca peak = 0.11131 (90)
- mri peak = 0.09163 (87)
- Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4531 voxels, overlap=0.912)
- Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4531 voxels, peak = 88), gca=87.8
- gca peak = 0.11793 (83)
- mri peak = 0.07515 (87)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4052 voxels, overlap=0.978)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4052 voxels, peak = 84), gca=84.2
- gca peak = 0.08324 (81)
- mri peak = 0.08641 (81)
- Left_Putamen (12): linear fit = 1.02 x + 0.0 (1731 voxels, overlap=0.851)
- Left_Putamen (12): linear fit = 1.02 x + 0.0 (1731 voxels, peak = 83), gca=83.0
- gca peak = 0.10360 (77)
- mri peak = 0.09314 (77)
- Right_Putamen (51): linear fit = 1.01 x + 0.0 (1855 voxels, overlap=0.844)
- Right_Putamen (51): linear fit = 1.01 x + 0.0 (1855 voxels, peak = 78), gca=78.2
- gca peak = 0.08424 (78)
- mri peak = 0.07723 (87)
- Brain_Stem (16): linear fit = 1.11 x + 0.0 (12719 voxels, overlap=0.476)
- Brain_Stem (16): linear fit = 1.11 x + 0.0 (12719 voxels, peak = 86), gca=86.2
- gca peak = 0.12631 (89)
- mri peak = 0.08489 (91)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1645 voxels, overlap=0.737)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1645 voxels, peak = 91), gca=91.2
- gca peak = 0.14500 (87)
- mri peak = 0.09283 (92)
- Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1764 voxels, overlap=0.878)
- Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1764 voxels, peak = 91), gca=90.9
- gca peak = 0.14975 (24)
- mri peak = 0.10771 (18)
- Third_Ventricle (14): linear fit = 0.67 x + 0.0 (116 voxels, overlap=0.230)
- Third_Ventricle (14): linear fit = 0.67 x + 0.0 (116 voxels, peak = 16), gca=16.0
- gca peak = 0.19357 (14)
- mri peak = 0.14311 (16)
- Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (385 voxels, overlap=0.778)
- Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (385 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 1.19 x + 0.0
- estimating mean wm scale to be 1.01 x + 0.0
- estimating mean csf scale to be 1.26 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.16113 (23)
- mri peak = 0.10292 (26)
- Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1156 voxels, overlap=0.879)
- Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1156 voxels, peak = 23), gca=23.3
- gca peak = 0.13906 (19)
- mri peak = 0.11762 (26)
- Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (2080 voxels, overlap=0.738)
- Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (2080 voxels, peak = 23), gca=22.5
- gca peak = 0.26787 (90)
- mri peak = 0.13949 (91)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (509 voxels, overlap=1.002)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (509 voxels, peak = 90), gca=90.0
- gca peak = 0.20037 (92)
- mri peak = 0.12883 (91)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (650 voxels, overlap=1.002)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (650 voxels, peak = 92), gca=92.0
- gca peak = 0.23493 (65)
- mri peak = 0.10697 (66)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (808 voxels, overlap=1.002)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (808 voxels, peak = 65), gca=65.0
- gca peak = 0.27687 (67)
- mri peak = 0.09267 (64)
- Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (797 voxels, overlap=1.004)
- Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (797 voxels, peak = 66), gca=66.0
- gca peak = 0.07612 (105)
- mri peak = 0.08653 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32723 voxels, overlap=0.829)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32723 voxels, peak = 104), gca=104.5
- gca peak = 0.07714 (104)
- mri peak = 0.10286 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32128 voxels, overlap=0.659)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32128 voxels, peak = 104), gca=104.0
- gca peak = 0.08217 (69)
- mri peak = 0.04638 (70)
- Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (38524 voxels, overlap=0.962)
- Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (38524 voxels, peak = 68), gca=68.0
- gca peak = 0.09966 (69)
- mri peak = 0.04494 (72)
- Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (37521 voxels, overlap=0.966)
- Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (37521 voxels, peak = 69), gca=69.0
- gca peak = 0.25611 (73)
- mri peak = 0.09861 (72)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (1227 voxels, overlap=1.007)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (1227 voxels, peak = 72), gca=71.9
- gca peak = 0.15187 (72)
- mri peak = 0.12798 (75)
- Left_Caudate (11): linear fit = 1.01 x + 0.0 (1126 voxels, overlap=0.730)
- Left_Caudate (11): linear fit = 1.01 x + 0.0 (1126 voxels, peak = 73), gca=73.1
- gca peak = 0.12510 (65)
- mri peak = 0.06206 (64)
- Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (26808 voxels, overlap=0.986)
- Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (26808 voxels, peak = 65), gca=65.0
- gca peak = 0.12227 (66)
- mri peak = 0.05653 (66)
- Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27187 voxels, overlap=0.988)
- Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27187 voxels, peak = 66), gca=66.0
- gca peak = 0.16673 (84)
- mri peak = 0.09063 (82)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5924 voxels, overlap=0.959)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5924 voxels, peak = 85), gca=85.3
- gca peak = 0.17629 (81)
- mri peak = 0.10772 (79)
- Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5440 voxels, overlap=0.878)
- Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5440 voxels, peak = 80), gca=79.8
- gca peak = 0.27773 (73)
- mri peak = 0.10463 (75)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (584 voxels, overlap=1.008)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (584 voxels, peak = 73), gca=73.0
- gca peak = 0.25293 (70)
- mri peak = 0.08360 (72)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (631 voxels, overlap=1.003)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (631 voxels, peak = 70), gca=70.0
- gca peak = 0.11017 (86)
- mri peak = 0.09163 (87)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4531 voxels, overlap=0.968)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4531 voxels, peak = 86), gca=86.0
- gca peak = 0.11237 (82)
- mri peak = 0.07515 (87)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4052 voxels, overlap=0.993)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4052 voxels, peak = 82), gca=82.0
- gca peak = 0.09216 (77)
- mri peak = 0.08641 (81)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1731 voxels, overlap=0.890)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1731 voxels, peak = 77), gca=77.0
- gca peak = 0.08217 (78)
- mri peak = 0.09314 (77)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1855 voxels, overlap=0.880)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1855 voxels, peak = 78), gca=78.0
- gca peak = 0.06830 (89)
- mri peak = 0.07723 (87)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (12719 voxels, overlap=0.806)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (12719 voxels, peak = 89), gca=88.6
- gca peak = 0.13630 (92)
- mri peak = 0.08489 (91)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1645 voxels, overlap=0.790)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1645 voxels, peak = 94), gca=94.3
- gca peak = 0.16203 (89)
- mri peak = 0.09283 (92)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1764 voxels, overlap=0.927)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1764 voxels, peak = 89), gca=88.6
- gca peak = 0.12659 (32)
- mri peak = 0.10771 (18)
- Third_Ventricle (14): linear fit = 0.52 x + 0.0 (116 voxels, overlap=0.039)
- Third_Ventricle (14): linear fit = 0.52 x + 0.0 (116 voxels, peak = 17), gca=16.8
- gca peak = 0.18343 (17)
- mri peak = 0.14311 (16)
- Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (385 voxels, overlap=0.774)
- Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (385 voxels, peak = 15), gca=15.4
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.15706 (38)
- gca peak Left_Thalamus = 0.36646 (102)
- gca peak Third_Ventricle = 0.12659 (32)
- gca peak CSF = 0.23862 (46)
- gca peak Left_Accumbens_area = 0.65107 (66)
- gca peak Left_undetermined = 0.96707 (29)
- gca peak Left_vessel = 0.75997 (52)
- gca peak Left_choroid_plexus = 0.11916 (35)
- gca peak Right_Inf_Lat_Vent = 0.21147 (27)
- gca peak Right_Accumbens_area = 0.31145 (71)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14507 (37)
- gca peak Fifth_Ventricle = 0.62949 (40)
- gca peak WM_hypointensities = 0.08296 (76)
- gca peak non_WM_hypointensities = 0.11922 (55)
- gca peak Optic_Chiasm = 0.70948 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.00 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 1.03 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
- 66820 voxels changed in iteration 0 of unlikely voxel relabeling
- 242 voxels changed in iteration 1 of unlikely voxel relabeling
- 103 voxels changed in iteration 2 of unlikely voxel relabeling
- 15 voxels changed in iteration 3 of unlikely voxel relabeling
- 0 voxels changed in iteration 4 of unlikely voxel relabeling
- 51525 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels)
- 585 hippocampal voxels changed.
- 0 amygdala voxels changed.
- pass 1: 73861 changed. image ll: -2.104, PF=0.500
- pass 2: 20518 changed. image ll: -2.103, PF=0.500
- pass 3: 5931 changed.
- pass 4: 2054 changed.
- 50242 voxels changed in iteration 0 of unlikely voxel relabeling
- 419 voxels changed in iteration 1 of unlikely voxel relabeling
- 26 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 7567 voxels changed in iteration 0 of unlikely voxel relabeling
- 105 voxels changed in iteration 1 of unlikely voxel relabeling
- 9 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 5692 voxels changed in iteration 0 of unlikely voxel relabeling
- 121 voxels changed in iteration 1 of unlikely voxel relabeling
- 2 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 5829 voxels changed in iteration 0 of unlikely voxel relabeling
- 51 voxels changed in iteration 1 of unlikely voxel relabeling
- 1 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- MRItoUCHAR: min=0, max=85
- MRItoUCHAR: converting to UCHAR
- writing labeled volume to aseg.auto_noCCseg.mgz
- mri_ca_label utimesec 3664.261947
- mri_ca_label stimesec 2.959550
- mri_ca_label ru_maxrss 2091920
- mri_ca_label ru_ixrss 0
- mri_ca_label ru_idrss 0
- mri_ca_label ru_isrss 0
- mri_ca_label ru_minflt 768765
- mri_ca_label ru_majflt 0
- mri_ca_label ru_nswap 0
- mri_ca_label ru_inblock 63512
- mri_ca_label ru_oublock 464
- mri_ca_label ru_msgsnd 0
- mri_ca_label ru_msgrcv 0
- mri_ca_label ru_nsignals 0
- mri_ca_label ru_nvcsw 316
- mri_ca_label ru_nivcsw 4755
- auto-labeling took 60 minutes and 19 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/transforms/cc_up.lta 0050319
- 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-6.0.0/0050319/mri/transforms/cc_up.lta
- reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/aseg.auto_noCCseg.mgz
- reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/norm.mgz
- 74286 voxels in left wm, 85567 in right wm, xrange [121, 139]
- searching rotation angles z=[-11 3], y=[-2 12]
-
searching scale 1 Z rot -11.2
searching scale 1 Z rot -10.9
searching scale 1 Z rot -10.7
searching scale 1 Z rot -10.4
searching scale 1 Z rot -10.2
searching scale 1 Z rot -9.9
searching scale 1 Z rot -9.7
searching scale 1 Z rot -9.4
searching scale 1 Z rot -9.2
searching scale 1 Z rot -8.9
searching scale 1 Z rot -8.7
searching scale 1 Z rot -8.4
searching scale 1 Z rot -8.2
searching scale 1 Z rot -7.9
searching scale 1 Z rot -7.7
searching scale 1 Z rot -7.4
searching scale 1 Z rot -7.2
searching scale 1 Z rot -6.9
searching scale 1 Z rot -6.7
searching scale 1 Z rot -6.4
searching scale 1 Z rot -6.2
searching scale 1 Z rot -5.9
searching scale 1 Z rot -5.7
searching scale 1 Z rot -5.4
searching scale 1 Z rot -5.2
searching scale 1 Z rot -4.9
searching scale 1 Z rot -4.7
searching scale 1 Z rot -4.4
searching scale 1 Z rot -4.2
searching scale 1 Z rot -3.9
searching scale 1 Z rot -3.7
searching scale 1 Z rot -3.4
searching scale 1 Z rot -3.2
searching scale 1 Z rot -2.9
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.4
searching scale 1 Z rot -2.2
searching scale 1 Z rot -1.9
searching scale 1 Z rot -1.7
searching scale 1 Z rot -1.4
searching scale 1 Z rot -1.2
searching scale 1 Z rot -0.9
searching scale 1 Z rot -0.7
searching scale 1 Z rot -0.4
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.1
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.6
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.1
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.6
searching scale 1 Z rot 1.8
searching scale 1 Z rot 2.1
searching scale 1 Z rot 2.3
searching scale 1 Z rot 2.6
searching scale 1 Z rot 2.8 global minimum found at slice 131.0, rotations (5.04, -4.18)
- final transformation (x=131.0, yr=5.038, zr=-4.178):
- 0.99349 0.07285 0.08758 -20.36370;
- -0.07257 0.99734 -0.00640 31.55184;
- -0.08781 -0.00000 0.99614 20.96280;
- 0.00000 0.00000 0.00000 1.00000;
- updating x range to be [125, 130] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 107 119
- eigenvectors:
- 0.00035 -0.00549 0.99998;
- 0.25608 -0.96664 -0.00540;
- 0.96665 0.25608 0.00107;
- writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/aseg.auto.mgz...
- corpus callosum segmentation took 2.0 minutes
- #--------------------------------------
- #@# Merge ASeg Sun Oct 8 02:53:52 CEST 2017
- cp aseg.auto.mgz aseg.presurf.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Sun Oct 8 02:53:52 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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...
- 763 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 75 (75), valley at 0 (-1)
- csf peak at 37, setting threshold to 62
- 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 73 (73), valley at 46 (46)
- csf peak at 37, setting threshold to 61
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 2 minutes and 54 seconds.
- #--------------------------------------------
- #@# Mask BFS Sun Oct 8 02:56:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1518122 voxels in mask (pct= 9.05)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Sun Oct 8 02:56:49 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 (102.0): 101.7 +- 7.0 [79.0 --> 125.0]
- GM (73.0) : 71.3 +- 10.6 [30.0 --> 95.0]
- setting bottom of white matter range to 81.8
- setting top of gray matter range to 92.4
- 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...
- 5833 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 2864 filled
- 2542 bright non-wm voxels segmented.
- 2604 diagonally connected voxels added...
- white matter segmentation took 1.7 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 0.59 minutes
- reading wm segmentation from wm.seg.mgz...
- 955 voxels added to wm to prevent paths from MTL structures to cortex
- 3405 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 47832 voxels turned on, 48162 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 103 new 103
- 115,126,128 old 103 new 103
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 14 found - 14 modified | TOTAL: 14
- pass 2 (xy+): 0 found - 14 modified | TOTAL: 14
- pass 1 (xy-): 11 found - 11 modified | TOTAL: 25
- pass 2 (xy-): 0 found - 11 modified | TOTAL: 25
- pass 1 (yz+): 33 found - 33 modified | TOTAL: 58
- pass 2 (yz+): 0 found - 33 modified | TOTAL: 58
- pass 1 (yz-): 26 found - 26 modified | TOTAL: 84
- pass 2 (yz-): 0 found - 26 modified | TOTAL: 84
- pass 1 (xz+): 22 found - 22 modified | TOTAL: 106
- pass 2 (xz+): 0 found - 22 modified | TOTAL: 106
- pass 1 (xz-): 19 found - 19 modified | TOTAL: 125
- pass 2 (xz-): 0 found - 19 modified | TOTAL: 125
- Iteration Number : 1
- pass 1 (+++): 10 found - 10 modified | TOTAL: 10
- pass 2 (+++): 0 found - 10 modified | TOTAL: 10
- pass 1 (+++): 20 found - 20 modified | TOTAL: 30
- pass 2 (+++): 0 found - 20 modified | TOTAL: 30
- pass 1 (+++): 13 found - 13 modified | TOTAL: 43
- pass 2 (+++): 0 found - 13 modified | TOTAL: 43
- pass 1 (+++): 18 found - 18 modified | TOTAL: 61
- pass 2 (+++): 0 found - 18 modified | TOTAL: 61
- Iteration Number : 1
- pass 1 (++): 74 found - 74 modified | TOTAL: 74
- pass 2 (++): 0 found - 74 modified | TOTAL: 74
- pass 1 (+-): 71 found - 71 modified | TOTAL: 145
- pass 2 (+-): 0 found - 71 modified | TOTAL: 145
- pass 1 (--): 54 found - 54 modified | TOTAL: 199
- pass 2 (--): 0 found - 54 modified | TOTAL: 199
- pass 1 (-+): 79 found - 79 modified | TOTAL: 278
- pass 2 (-+): 0 found - 79 modified | TOTAL: 278
- Iteration Number : 2
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 7 found - 7 modified | TOTAL: 10
- pass 2 (xy-): 0 found - 7 modified | TOTAL: 10
- pass 1 (yz+): 3 found - 3 modified | TOTAL: 13
- pass 2 (yz+): 0 found - 3 modified | TOTAL: 13
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 15
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 15
- pass 1 (xz+): 6 found - 6 modified | TOTAL: 21
- pass 2 (xz+): 0 found - 6 modified | TOTAL: 21
- pass 1 (xz-): 3 found - 3 modified | TOTAL: 24
- pass 2 (xz-): 0 found - 3 modified | TOTAL: 24
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 3 found - 3 modified | TOTAL: 3
- pass 2 (+++): 0 found - 3 modified | TOTAL: 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 3
- Iteration Number : 2
- pass 1 (++): 3 found - 3 modified | TOTAL: 3
- pass 2 (++): 0 found - 3 modified | TOTAL: 3
- pass 1 (+-): 3 found - 3 modified | TOTAL: 6
- pass 2 (+-): 0 found - 3 modified | TOTAL: 6
- pass 1 (--): 2 found - 2 modified | TOTAL: 8
- pass 2 (--): 0 found - 2 modified | TOTAL: 8
- pass 1 (-+): 0 found - 0 modified | TOTAL: 8
- Iteration Number : 3
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 2
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 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 (--): 1 found - 1 modified | TOTAL: 1
- pass 2 (--): 0 found - 1 modified | TOTAL: 1
- pass 1 (-+): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 4
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 502 (out of 510971: 0.098244)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Sun Oct 8 02:59:07 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05557;
- -0.13749 0.23552 0.97898 -19.11014;
- 0.00000 0.00000 0.00000 1.00000;
- voxel to talairach voxel transform
- 1.01894 0.08999 0.11980 -31.71439;
- -0.05643 1.08058 -0.25392 20.05557;
- -0.13749 0.23552 0.97898 -19.11014;
- 0.00000 0.00000 0.00000 1.00000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 783 (min = 350, max = 1400), aspect = 0.36 (min = 0.10, max = 0.75)
- no need to search
- using seed (126, 114, 92), TAL = (2.0, -36.0, 14.0)
- talairach voxel to voxel transform
- 0.96090 -0.05148 -0.13094 29.00453;
- 0.07751 0.87176 0.21662 -10.88577;
- 0.11630 -0.21695 0.95096 26.21253;
- 0.00000 0.00000 0.00000 1.00000;
- segmentation indicates cc at (126, 114, 92) --> (2.0, -36.0, 14.0)
- done.
- writing output to filled.mgz...
- filling took 0.7 minutes
- talairach cc position changed to (2.00, -36.00, 14.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, -36.00, 14.00) SRC: (114.87, 116.80, 101.53)
- search lh wm seed point around talairach space (-16.00, -36.00, 14.00), SRC: (149.46, 119.59, 105.72)
- 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 02:59:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 2 found - 2 modified | TOTAL: 5
- pass 2 (xy-): 0 found - 2 modified | TOTAL: 5
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 6
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 6
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 6
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 7
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 7
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 8
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 8
- Iteration Number : 1
- pass 1 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- pass 1 (+++): 2 found - 2 modified | TOTAL: 4
- pass 2 (+++): 0 found - 2 modified | TOTAL: 4
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 1 found - 1 modified | TOTAL: 1
- pass 2 (+-): 0 found - 1 modified | TOTAL: 1
- pass 1 (--): 0 found - 0 modified | TOTAL: 1
- pass 1 (-+): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 2
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 2
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 0 found - 0 modified | TOTAL: 1
- pass 1 (--): 0 found - 0 modified | TOTAL: 1
- pass 1 (-+): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 16 (out of 243772: 0.006564)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- slice 50: 2294 vertices, 2434 faces
- slice 60: 7748 vertices, 7976 faces
- slice 70: 15186 vertices, 15486 faces
- slice 80: 23888 vertices, 24232 faces
- slice 90: 33657 vertices, 34041 faces
- slice 100: 43753 vertices, 44120 faces
- slice 110: 55739 vertices, 56230 faces
- slice 120: 69655 vertices, 70207 faces
- slice 130: 83238 vertices, 83713 faces
- slice 140: 95196 vertices, 95676 faces
- slice 150: 104890 vertices, 105325 faces
- slice 160: 113208 vertices, 113650 faces
- slice 170: 121772 vertices, 122196 faces
- slice 180: 128814 vertices, 129176 faces
- slice 190: 134220 vertices, 134547 faces
- slice 200: 136360 vertices, 136535 faces
- slice 210: 136380 vertices, 136544 faces
- slice 220: 136380 vertices, 136544 faces
- slice 230: 136380 vertices, 136544 faces
- slice 240: 136380 vertices, 136544 faces
- slice 250: 136380 vertices, 136544 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...
- 136380 voxel in cpt #1: X=-164 [v=136380,e=409632,f=273088] located at (-29.520817, -9.794530, 6.748886)
- For the whole surface: X=-164 [v=136380,e=409632,f=273088]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Tessellate rh Sun Oct 8 02:59:53 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 2 found - 2 modified | TOTAL: 2
- pass 2 (xy+): 0 found - 2 modified | TOTAL: 2
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 3
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 3
- pass 1 (yz+): 3 found - 3 modified | TOTAL: 6
- pass 2 (yz+): 0 found - 3 modified | TOTAL: 6
- pass 1 (yz-): 8 found - 8 modified | TOTAL: 14
- pass 2 (yz-): 0 found - 8 modified | TOTAL: 14
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 16
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 16
- pass 1 (xz-): 2 found - 2 modified | TOTAL: 18
- pass 2 (xz-): 0 found - 2 modified | TOTAL: 18
- 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 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 0 found - 0 modified | TOTAL: 1
- pass 1 (--): 3 found - 3 modified | TOTAL: 4
- pass 2 (--): 0 found - 3 modified | TOTAL: 4
- pass 1 (-+): 1 found - 1 modified | TOTAL: 5
- pass 2 (-+): 0 found - 1 modified | TOTAL: 5
- 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 = 23 (out of 245990: 0.009350)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
- $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- slice 40: 44 vertices, 60 faces
- slice 50: 3051 vertices, 3213 faces
- slice 60: 8581 vertices, 8817 faces
- slice 70: 16511 vertices, 16802 faces
- slice 80: 26159 vertices, 26585 faces
- slice 90: 38033 vertices, 38456 faces
- slice 100: 48785 vertices, 49212 faces
- slice 110: 61966 vertices, 62454 faces
- slice 120: 75973 vertices, 76500 faces
- slice 130: 88734 vertices, 89229 faces
- slice 140: 99941 vertices, 100397 faces
- slice 150: 108369 vertices, 108799 faces
- slice 160: 117278 vertices, 117692 faces
- slice 170: 124675 vertices, 125039 faces
- slice 180: 130587 vertices, 130896 faces
- slice 190: 134777 vertices, 135007 faces
- slice 200: 135656 vertices, 135792 faces
- slice 210: 135656 vertices, 135792 faces
- slice 220: 135656 vertices, 135792 faces
- slice 230: 135656 vertices, 135792 faces
- slice 240: 135656 vertices, 135792 faces
- slice 250: 135656 vertices, 135792 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...
- 135656 voxel in cpt #1: X=-136 [v=135656,e=407376,f=271584] located at (25.255447, -13.861001, 10.617274)
- For the whole surface: X=-136 [v=135656,e=407376,f=271584]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Sun Oct 8 02:59:59 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- #--------------------------------------------
- #@# Smooth1 rh Sun Oct 8 02:59:59 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- Waiting for PID 20680 of (20680 20683) to complete...
- Waiting for PID 20683 of (20680 20683) 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 (20680 20683) completed and logs appended.
- #--------------------------------------------
- #@# Inflation1 lh Sun Oct 8 03:00:05 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- #--------------------------------------------
- #@# Inflation1 rh Sun Oct 8 03:00:05 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Waiting for PID 20743 of (20743 20746) to complete...
- Waiting for PID 20746 of (20743 20746) 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 = 45.5 mm, total surface area = 71604 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.7 minutes
-
step 000: RMS=0.167 (target=0.015)
step 005: RMS=0.132 (target=0.015)
step 010: RMS=0.105 (target=0.015)
step 015: RMS=0.092 (target=0.015)
step 020: RMS=0.084 (target=0.015)
step 025: RMS=0.079 (target=0.015)
step 030: RMS=0.074 (target=0.015)
step 035: RMS=0.070 (target=0.015)
step 040: RMS=0.068 (target=0.015)
step 045: RMS=0.068 (target=0.015)
step 050: RMS=0.068 (target=0.015)
step 055: RMS=0.068 (target=0.015)
step 060: RMS=0.068 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 43.695357
- mris_inflate stimesec 0.115982
- mris_inflate ru_maxrss 199852
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 28948
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 9600
- mris_inflate ru_oublock 9616
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2021
- mris_inflate ru_nivcsw 3316
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Not saving sulc
- Reading ../surf/rh.smoothwm.nofix
- avg radius = 45.3 mm, total surface area = 71062 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.7 minutes
-
step 000: RMS=0.167 (target=0.015)
step 005: RMS=0.131 (target=0.015)
step 010: RMS=0.104 (target=0.015)
step 015: RMS=0.092 (target=0.015)
step 020: RMS=0.084 (target=0.015)
step 025: RMS=0.077 (target=0.015)
step 030: RMS=0.073 (target=0.015)
step 035: RMS=0.070 (target=0.015)
step 040: RMS=0.067 (target=0.015)
step 045: RMS=0.065 (target=0.015)
step 050: RMS=0.063 (target=0.015)
step 055: RMS=0.062 (target=0.015)
step 060: RMS=0.062 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 43.766346
- mris_inflate stimesec 0.095985
- mris_inflate ru_maxrss 198980
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 28729
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 9552
- mris_inflate ru_oublock 9568
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2061
- mris_inflate ru_nivcsw 3393
- PIDs (20743 20746) completed and logs appended.
- #--------------------------------------------
- #@# QSphere lh Sun Oct 8 03:00:49 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- #--------------------------------------------
- #@# QSphere rh Sun Oct 8 03:00:49 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- Waiting for PID 20812 of (20812 20816) to complete...
- Waiting for PID 20816 of (20812 20816) 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 0.98 +- 0.60 (0.00-->7.24) (max @ vno 38354 --> 39279)
- face area 0.03 +- 0.03 (-0.18-->0.71)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.315...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.710, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.454, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.904, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.181, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.353, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.464, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.543, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.606, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.662, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.716, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.769, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.824, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.883, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.946, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.013, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.085, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.161, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.243, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.329, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.420, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.516, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.617, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.723, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.833, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.949, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.069, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.194, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.324, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.458, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.597, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.741, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.890, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.044, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.202, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.364, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.532, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.704, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.880, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.061, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.247, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.437, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.631, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.831, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.034, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.242, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.455, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.672, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.893, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.119, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.349, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.583, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.822, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.065, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.312, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.563, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.819, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.079, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.343, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.611, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.883, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.160, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 15919.62
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00008
- epoch 2 (K=40.0), pass 1, starting sse = 2678.09
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00007
- epoch 3 (K=160.0), pass 1, starting sse = 309.52
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.07/11 = 0.00649
- epoch 4 (K=640.0), pass 1, starting sse = 30.75
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.06/11 = 0.00575
- final distance error %26.64
- writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.07 hours
- mris_sphere utimesec 248.440231
- mris_sphere stimesec 0.443932
- mris_sphere ru_maxrss 200060
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 29518
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 9648
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 11701
- mris_sphere ru_nivcsw 19519
- FSRUNTIME@ mris_sphere 0.0691 hours 1 threads
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.98 +- 0.59 (0.00-->7.46) (max @ vno 52396 --> 52397)
- face area 0.03 +- 0.03 (-0.16-->0.88)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.323...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.274, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.017, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.466, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.740, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.910, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.023, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.104, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.168, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.224, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.277, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.331, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.388, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.448, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.512, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.580, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.654, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.732, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.815, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.904, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.996, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.094, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.197, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.304, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.416, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.534, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.656, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.782, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.914, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.051, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.192, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.338, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.489, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.644, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.804, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.969, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.139, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.313, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.491, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.675, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.863, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.055, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.252, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.454, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.660, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.870, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.085, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.305, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.528, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.756, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.989, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.225, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.466, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.711, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.961, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.214, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.472, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.734, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.000, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.271, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.545, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.824, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 15695.03
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
- epoch 2 (K=40.0), pass 1, starting sse = 2584.73
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
- epoch 3 (K=160.0), pass 1, starting sse = 283.71
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.08/11 = 0.00708
- epoch 4 (K=640.0), pass 1, starting sse = 27.84
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.07/11 = 0.00644
- final distance error %25.19
- writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.07 hours
- mris_sphere utimesec 249.291101
- mris_sphere stimesec 0.203968
- mris_sphere ru_maxrss 199184
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 28785
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 9552
- mris_sphere ru_oublock 9592
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 10559
- mris_sphere ru_nivcsw 20667
- FSRUNTIME@ mris_sphere 0.0692 hours 1 threads
- PIDs (20812 20816) completed and logs appended.
- #--------------------------------------------
- #@# Fix Topology Copy lh Sun Oct 8 03:04:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- #--------------------------------------------
- #@# Fix Topology Copy rh Sun Oct 8 03:04:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- #@# Fix Topology lh Sun Oct 8 03:04:59 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050319 lh
- #@# Fix Topology rh Sun Oct 8 03:04:59 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050319 rh
- Waiting for PID 21131 of (21131 21134) to complete...
- Waiting for PID 21134 of (21131 21134) to complete...
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050319 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=-164 (nv=136380, nf=273088, ne=409632, g=83)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 8 iterations
- marking ambiguous vertices...
- 14861 ambiguous faces found in tessellation
- segmenting defects...
- 98 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 7 into 6
- -merging segment 48 into 36
- 96 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.0967 (-4.5484)
- -vertex loglikelihood: -6.0400 (-3.0200)
- -normal dot loglikelihood: -3.5985 (-3.5985)
- -quad curv loglikelihood: -6.2072 (-3.1036)
- Total Loglikelihood : -24.9425
- CORRECTING DEFECT 0 (vertices=61, convex hull=123, v0=45)
- After retessellation of defect 0 (v0=45), euler #=-93 (127620,379969,252256) : difference with theory (-93) = 0
- CORRECTING DEFECT 1 (vertices=39, convex hull=48, v0=81)
- After retessellation of defect 1 (v0=81), euler #=-92 (127629,380017,252296) : difference with theory (-92) = 0
- CORRECTING DEFECT 2 (vertices=659, convex hull=202, v0=105)
- After retessellation of defect 2 (v0=105), euler #=-91 (127723,380411,252597) : difference with theory (-91) = 0
- CORRECTING DEFECT 3 (vertices=36, convex hull=60, v0=947)
- After retessellation of defect 3 (v0=947), euler #=-90 (127740,380481,252651) : difference with theory (-90) = 0
- CORRECTING DEFECT 4 (vertices=48, convex hull=83, v0=1057)
- After retessellation of defect 4 (v0=1057), euler #=-89 (127757,380570,252724) : difference with theory (-89) = 0
- CORRECTING DEFECT 5 (vertices=119, convex hull=145, v0=1125)
- After retessellation of defect 5 (v0=1125), euler #=-88 (127824,380835,252923) : difference with theory (-88) = 0
- CORRECTING DEFECT 6 (vertices=119, convex hull=107, v0=1560)
- After retessellation of defect 6 (v0=1560), euler #=-86 (127849,380964,253029) : difference with theory (-87) = -1
- CORRECTING DEFECT 7 (vertices=54, convex hull=82, v0=2951)
- After retessellation of defect 7 (v0=2951), euler #=-85 (127886,381110,253139) : difference with theory (-86) = -1
- CORRECTING DEFECT 8 (vertices=114, convex hull=117, v0=3118)
- After retessellation of defect 8 (v0=3118), euler #=-84 (127917,381255,253254) : difference with theory (-85) = -1
- CORRECTING DEFECT 9 (vertices=33, convex hull=30, v0=3178)
- After retessellation of defect 9 (v0=3178), euler #=-83 (127918,381268,253267) : difference with theory (-84) = -1
- CORRECTING DEFECT 10 (vertices=41, convex hull=46, v0=6349)
- After retessellation of defect 10 (v0=6349), euler #=-82 (127924,381301,253295) : difference with theory (-83) = -1
- CORRECTING DEFECT 11 (vertices=12, convex hull=22, v0=7136)
- After retessellation of defect 11 (v0=7136), euler #=-81 (127925,381311,253305) : difference with theory (-82) = -1
- CORRECTING DEFECT 12 (vertices=83, convex hull=46, v0=7649)
- After retessellation of defect 12 (v0=7649), euler #=-80 (127934,381355,253341) : difference with theory (-81) = -1
- CORRECTING DEFECT 13 (vertices=10, convex hull=30, v0=8395)
- After retessellation of defect 13 (v0=8395), euler #=-79 (127935,381370,253356) : difference with theory (-80) = -1
- CORRECTING DEFECT 14 (vertices=26, convex hull=57, v0=9694)
- After retessellation of defect 14 (v0=9694), euler #=-78 (127945,381422,253399) : difference with theory (-79) = -1
- CORRECTING DEFECT 15 (vertices=33, convex hull=82, v0=9813)
- After retessellation of defect 15 (v0=9813), euler #=-77 (127955,381485,253453) : difference with theory (-78) = -1
- CORRECTING DEFECT 16 (vertices=527, convex hull=244, v0=10154)
- After retessellation of defect 16 (v0=10154), euler #=-76 (128075,381963,253812) : difference with theory (-77) = -1
- CORRECTING DEFECT 17 (vertices=29, convex hull=59, v0=14446)
- After retessellation of defect 17 (v0=14446), euler #=-75 (128090,382031,253866) : difference with theory (-76) = -1
- CORRECTING DEFECT 18 (vertices=140, convex hull=109, v0=19435)
- After retessellation of defect 18 (v0=19435), euler #=-74 (128119,382167,253974) : difference with theory (-75) = -1
- CORRECTING DEFECT 19 (vertices=46, convex hull=73, v0=24362)
- After retessellation of defect 19 (v0=24362), euler #=-73 (128145,382276,254058) : difference with theory (-74) = -1
- CORRECTING DEFECT 20 (vertices=39, convex hull=60, v0=26926)
- After retessellation of defect 20 (v0=26926), euler #=-72 (128154,382326,254100) : difference with theory (-73) = -1
- CORRECTING DEFECT 21 (vertices=19, convex hull=38, v0=36451)
- After retessellation of defect 21 (v0=36451), euler #=-71 (128164,382370,254135) : difference with theory (-72) = -1
- CORRECTING DEFECT 22 (vertices=30, convex hull=47, v0=36775)
- After retessellation of defect 22 (v0=36775), euler #=-70 (128169,382399,254160) : difference with theory (-71) = -1
- CORRECTING DEFECT 23 (vertices=21, convex hull=57, v0=40269)
- After retessellation of defect 23 (v0=40269), euler #=-69 (128178,382450,254203) : difference with theory (-70) = -1
- CORRECTING DEFECT 24 (vertices=18, convex hull=19, v0=41151)
- After retessellation of defect 24 (v0=41151), euler #=-68 (128180,382460,254212) : difference with theory (-69) = -1
- CORRECTING DEFECT 25 (vertices=39, convex hull=92, v0=41623)
- After retessellation of defect 25 (v0=41623), euler #=-67 (128194,382541,254280) : difference with theory (-68) = -1
- CORRECTING DEFECT 26 (vertices=330, convex hull=164, v0=42661)
- After retessellation of defect 26 (v0=42661), euler #=-67 (128297,382932,254568) : difference with theory (-67) = 0
- CORRECTING DEFECT 27 (vertices=37, convex hull=76, v0=43442)
- After retessellation of defect 27 (v0=43442), euler #=-66 (128310,382997,254621) : difference with theory (-66) = 0
- CORRECTING DEFECT 28 (vertices=27, convex hull=41, v0=44305)
- After retessellation of defect 28 (v0=44305), euler #=-65 (128321,383044,254658) : difference with theory (-65) = 0
- CORRECTING DEFECT 29 (vertices=510, convex hull=190, v0=45441)
- After retessellation of defect 29 (v0=45441), euler #=-64 (128375,383291,254852) : difference with theory (-64) = 0
- CORRECTING DEFECT 30 (vertices=18, convex hull=66, v0=48160)
- After retessellation of defect 30 (v0=48160), euler #=-63 (128384,383343,254896) : difference with theory (-63) = 0
- CORRECTING DEFECT 31 (vertices=11, convex hull=27, v0=50106)
- After retessellation of defect 31 (v0=50106), euler #=-62 (128387,383359,254910) : difference with theory (-62) = 0
- CORRECTING DEFECT 32 (vertices=50, convex hull=29, v0=53115)
- After retessellation of defect 32 (v0=53115), euler #=-61 (128393,383387,254933) : difference with theory (-61) = 0
- CORRECTING DEFECT 33 (vertices=73, convex hull=102, v0=57427)
- After retessellation of defect 33 (v0=57427), euler #=-60 (128436,383564,255068) : difference with theory (-60) = 0
- CORRECTING DEFECT 34 (vertices=75, convex hull=152, v0=60454)
- After retessellation of defect 34 (v0=60454), euler #=-59 (128488,383785,255238) : difference with theory (-59) = 0
- CORRECTING DEFECT 35 (vertices=293, convex hull=200, v0=60842)
- After retessellation of defect 35 (v0=60842), euler #=-57 (128522,383999,255420) : difference with theory (-58) = -1
- CORRECTING DEFECT 36 (vertices=52, convex hull=25, v0=62063)
- After retessellation of defect 36 (v0=62063), euler #=-56 (128528,384026,255442) : difference with theory (-57) = -1
- CORRECTING DEFECT 37 (vertices=43, convex hull=25, v0=64906)
- After retessellation of defect 37 (v0=64906), euler #=-55 (128534,384050,255461) : difference with theory (-56) = -1
- CORRECTING DEFECT 38 (vertices=278, convex hull=90, v0=65209)
- After retessellation of defect 38 (v0=65209), euler #=-54 (128579,384227,255594) : difference with theory (-55) = -1
- CORRECTING DEFECT 39 (vertices=38, convex hull=67, v0=67776)
- After retessellation of defect 39 (v0=67776), euler #=-53 (128599,384316,255664) : difference with theory (-54) = -1
- CORRECTING DEFECT 40 (vertices=237, convex hull=43, v0=67828)
- After retessellation of defect 40 (v0=67828), euler #=-52 (128610,384365,255703) : difference with theory (-53) = -1
- CORRECTING DEFECT 41 (vertices=46, convex hull=89, v0=69351)
- After retessellation of defect 41 (v0=69351), euler #=-51 (128639,384486,255796) : difference with theory (-52) = -1
- CORRECTING DEFECT 42 (vertices=37, convex hull=54, v0=69522)
- After retessellation of defect 42 (v0=69522), euler #=-50 (128654,384556,255852) : difference with theory (-51) = -1
- CORRECTING DEFECT 43 (vertices=74, convex hull=97, v0=70972)
- After retessellation of defect 43 (v0=70972), euler #=-49 (128699,384733,255985) : difference with theory (-50) = -1
- CORRECTING DEFECT 44 (vertices=173, convex hull=52, v0=71038)
- After retessellation of defect 44 (v0=71038), euler #=-48 (128715,384801,256038) : difference with theory (-49) = -1
- CORRECTING DEFECT 45 (vertices=48, convex hull=69, v0=74339)
- After retessellation of defect 45 (v0=74339), euler #=-47 (128726,384864,256091) : difference with theory (-48) = -1
- CORRECTING DEFECT 46 (vertices=14, convex hull=25, v0=74492)
- After retessellation of defect 46 (v0=74492), euler #=-46 (128728,384879,256105) : difference with theory (-47) = -1
- CORRECTING DEFECT 47 (vertices=40, convex hull=63, v0=76171)
- After retessellation of defect 47 (v0=76171), euler #=-45 (128748,384965,256172) : difference with theory (-46) = -1
- CORRECTING DEFECT 48 (vertices=25, convex hull=37, v0=76291)
- After retessellation of defect 48 (v0=76291), euler #=-44 (128751,384987,256192) : difference with theory (-45) = -1
- CORRECTING DEFECT 49 (vertices=52, convex hull=97, v0=77719)
- After retessellation of defect 49 (v0=77719), euler #=-43 (128784,385131,256304) : difference with theory (-44) = -1
- CORRECTING DEFECT 50 (vertices=19, convex hull=26, v0=79165)
- After retessellation of defect 50 (v0=79165), euler #=-42 (128786,385148,256320) : difference with theory (-43) = -1
- CORRECTING DEFECT 51 (vertices=116, convex hull=44, v0=80667)
- After retessellation of defect 51 (v0=80667), euler #=-41 (128804,385218,256373) : difference with theory (-42) = -1
- CORRECTING DEFECT 52 (vertices=33, convex hull=61, v0=80812)
- After retessellation of defect 52 (v0=80812), euler #=-40 (128817,385282,256425) : difference with theory (-41) = -1
- CORRECTING DEFECT 53 (vertices=228, convex hull=93, v0=81788)
- After retessellation of defect 53 (v0=81788), euler #=-39 (128847,385414,256528) : difference with theory (-40) = -1
- CORRECTING DEFECT 54 (vertices=5, convex hull=29, v0=81828)
- After retessellation of defect 54 (v0=81828), euler #=-38 (128848,385424,256538) : difference with theory (-39) = -1
- CORRECTING DEFECT 55 (vertices=31, convex hull=66, v0=82058)
- After retessellation of defect 55 (v0=82058), euler #=-37 (128861,385486,256588) : difference with theory (-38) = -1
- CORRECTING DEFECT 56 (vertices=622, convex hull=341, v0=83992)
- After retessellation of defect 56 (v0=83992), euler #=-37 (129032,386205,257136) : difference with theory (-37) = 0
- CORRECTING DEFECT 57 (vertices=190, convex hull=78, v0=84081)
- After retessellation of defect 57 (v0=84081), euler #=-36 (129050,386294,257208) : difference with theory (-36) = 0
- CORRECTING DEFECT 58 (vertices=27, convex hull=27, v0=85158)
- After retessellation of defect 58 (v0=85158), euler #=-35 (129052,386308,257221) : difference with theory (-35) = 0
- CORRECTING DEFECT 59 (vertices=7, convex hull=36, v0=86366)
- After retessellation of defect 59 (v0=86366), euler #=-34 (129055,386328,257239) : difference with theory (-34) = 0
- CORRECTING DEFECT 60 (vertices=93, convex hull=114, v0=86780)
- After retessellation of defect 60 (v0=86780), euler #=-33 (129076,386444,257335) : difference with theory (-33) = 0
- CORRECTING DEFECT 61 (vertices=26, convex hull=42, v0=88979)
- After retessellation of defect 61 (v0=88979), euler #=-32 (129089,386498,257377) : difference with theory (-32) = 0
- CORRECTING DEFECT 62 (vertices=29, convex hull=46, v0=89242)
- After retessellation of defect 62 (v0=89242), euler #=-31 (129106,386564,257427) : difference with theory (-31) = 0
- CORRECTING DEFECT 63 (vertices=26, convex hull=57, v0=90163)
- After retessellation of defect 63 (v0=90163), euler #=-30 (129119,386622,257473) : difference with theory (-30) = 0
- CORRECTING DEFECT 64 (vertices=137, convex hull=79, v0=91713)
- After retessellation of defect 64 (v0=91713), euler #=-29 (129150,386749,257570) : difference with theory (-29) = 0
- CORRECTING DEFECT 65 (vertices=300, convex hull=149, v0=92546)
- After retessellation of defect 65 (v0=92546), euler #=-28 (129209,386995,257758) : difference with theory (-28) = 0
- CORRECTING DEFECT 66 (vertices=30, convex hull=65, v0=92582)
- After retessellation of defect 66 (v0=92582), euler #=-27 (129227,387075,257821) : difference with theory (-27) = 0
- CORRECTING DEFECT 67 (vertices=31, convex hull=42, v0=93766)
- After retessellation of defect 67 (v0=93766), euler #=-26 (129240,387130,257864) : difference with theory (-26) = 0
- CORRECTING DEFECT 68 (vertices=58, convex hull=82, v0=93843)
- After retessellation of defect 68 (v0=93843), euler #=-25 (129279,387280,257976) : difference with theory (-25) = 0
- CORRECTING DEFECT 69 (vertices=39, convex hull=83, v0=94968)
- After retessellation of defect 69 (v0=94968), euler #=-24 (129302,387379,258053) : difference with theory (-24) = 0
- CORRECTING DEFECT 70 (vertices=460, convex hull=180, v0=95155)
- After retessellation of defect 70 (v0=95155), euler #=-23 (129387,387728,258318) : difference with theory (-23) = 0
- CORRECTING DEFECT 71 (vertices=19, convex hull=53, v0=102331)
- After retessellation of defect 71 (v0=102331), euler #=-22 (129397,387777,258358) : difference with theory (-22) = 0
- CORRECTING DEFECT 72 (vertices=11, convex hull=18, v0=102957)
- After retessellation of defect 72 (v0=102957), euler #=-21 (129397,387783,258365) : difference with theory (-21) = 0
- CORRECTING DEFECT 73 (vertices=101, convex hull=45, v0=103662)
- After retessellation of defect 73 (v0=103662), euler #=-20 (129415,387852,258417) : difference with theory (-20) = 0
- CORRECTING DEFECT 74 (vertices=50, convex hull=36, v0=107151)
- After retessellation of defect 74 (v0=107151), euler #=-19 (129424,387894,258451) : difference with theory (-19) = 0
- CORRECTING DEFECT 75 (vertices=37, convex hull=31, v0=107317)
- After retessellation of defect 75 (v0=107317), euler #=-18 (129426,387910,258466) : difference with theory (-18) = 0
- CORRECTING DEFECT 76 (vertices=24, convex hull=47, v0=107739)
- After retessellation of defect 76 (v0=107739), euler #=-17 (129435,387958,258506) : difference with theory (-17) = 0
- CORRECTING DEFECT 77 (vertices=86, convex hull=99, v0=107976)
- After retessellation of defect 77 (v0=107976), euler #=-16 (129465,388090,258609) : difference with theory (-16) = 0
- CORRECTING DEFECT 78 (vertices=77, convex hull=80, v0=108126)
- After retessellation of defect 78 (v0=108126), euler #=-15 (129477,388157,258665) : difference with theory (-15) = 0
- CORRECTING DEFECT 79 (vertices=58, convex hull=41, v0=110810)
- After retessellation of defect 79 (v0=110810), euler #=-14 (129483,388190,258693) : difference with theory (-14) = 0
- CORRECTING DEFECT 80 (vertices=86, convex hull=62, v0=114912)
- After retessellation of defect 80 (v0=114912), euler #=-13 (129500,388264,258751) : difference with theory (-13) = 0
- CORRECTING DEFECT 81 (vertices=38, convex hull=27, v0=115627)
- After retessellation of defect 81 (v0=115627), euler #=-12 (129506,388291,258773) : difference with theory (-12) = 0
- CORRECTING DEFECT 82 (vertices=68, convex hull=54, v0=119450)
- After retessellation of defect 82 (v0=119450), euler #=-11 (129521,388364,258832) : difference with theory (-11) = 0
- CORRECTING DEFECT 83 (vertices=50, convex hull=37, v0=120171)
- After retessellation of defect 83 (v0=120171), euler #=-10 (129523,388382,258849) : difference with theory (-10) = 0
- CORRECTING DEFECT 84 (vertices=24, convex hull=22, v0=123770)
- After retessellation of defect 84 (v0=123770), euler #=-9 (129526,388398,258863) : difference with theory (-9) = 0
- CORRECTING DEFECT 85 (vertices=159, convex hull=38, v0=124040)
- After retessellation of defect 85 (v0=124040), euler #=-8 (129537,388447,258902) : difference with theory (-8) = 0
- CORRECTING DEFECT 86 (vertices=39, convex hull=37, v0=128197)
- After retessellation of defect 86 (v0=128197), euler #=-7 (129541,388470,258922) : difference with theory (-7) = 0
- CORRECTING DEFECT 87 (vertices=51, convex hull=52, v0=128209)
- After retessellation of defect 87 (v0=128209), euler #=-6 (129555,388531,258970) : difference with theory (-6) = 0
- CORRECTING DEFECT 88 (vertices=43, convex hull=33, v0=129964)
- After retessellation of defect 88 (v0=129964), euler #=-5 (129559,388556,258992) : difference with theory (-5) = 0
- CORRECTING DEFECT 89 (vertices=40, convex hull=86, v0=130330)
- After retessellation of defect 89 (v0=130330), euler #=-4 (129583,388661,259074) : difference with theory (-4) = 0
- CORRECTING DEFECT 90 (vertices=85, convex hull=26, v0=132717)
- After retessellation of defect 90 (v0=132717), euler #=-3 (129585,388674,259086) : difference with theory (-3) = 0
- CORRECTING DEFECT 91 (vertices=6, convex hull=24, v0=132972)
- After retessellation of defect 91 (v0=132972), euler #=-2 (129586,388683,259095) : difference with theory (-2) = 0
- CORRECTING DEFECT 92 (vertices=67, convex hull=62, v0=133476)
- After retessellation of defect 92 (v0=133476), euler #=-1 (129611,388787,259175) : difference with theory (-1) = 0
- CORRECTING DEFECT 93 (vertices=53, convex hull=43, v0=134378)
- After retessellation of defect 93 (v0=134378), euler #=0 (129617,388821,259204) : difference with theory (0) = 0
- CORRECTING DEFECT 94 (vertices=23, convex hull=57, v0=134841)
- After retessellation of defect 94 (v0=134841), euler #=1 (129629,388878,259250) : difference with theory (1) = 0
- CORRECTING DEFECT 95 (vertices=5, convex hull=13, v0=136228)
- After retessellation of defect 95 (v0=136228), euler #=2 (129630,388884,259256) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.89 +- 0.26 (0.04-->9.01) (max @ vno 58619 --> 130462)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.89 +- 0.26 (0.04-->9.01) (max @ vno 58619 --> 130462)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 308 mutations (33.7%), 607 crossovers (66.3%), 447 vertices were eliminated
- building final representation...
- 6750 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=129630, nf=259256, ne=388884, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 54.7 minutes
- 0 defective edges
- removing intersecting faces
- 000: 617 intersecting
- 001: 49 intersecting
- 002: 18 intersecting
- mris_fix_topology utimesec 3280.404302
- mris_fix_topology stimesec 0.248962
- mris_fix_topology ru_maxrss 430008
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 55194
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 19200
- mris_fix_topology ru_oublock 12800
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 569
- mris_fix_topology ru_nivcsw 6822
- FSRUNTIME@ mris_fix_topology lh 0.9109 hours 1 threads
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050319 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=-136 (nv=135656, nf=271584, ne=407376, g=69)
- 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...
- 12655 ambiguous faces found in tessellation
- segmenting defects...
- 84 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 10 into 8
- -merging segment 22 into 20
- -merging segment 23 into 21
- -merging segment 40 into 32
- -merging segment 70 into 62
- 79 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -8.9901 (-4.4950)
- -vertex loglikelihood: -5.9545 (-2.9773)
- -normal dot loglikelihood: -3.5992 (-3.5992)
- -quad curv loglikelihood: -6.0129 (-3.0064)
- Total Loglikelihood : -24.5567
- CORRECTING DEFECT 0 (vertices=44, convex hull=81, v0=222)
- After retessellation of defect 0 (v0=222), euler #=-79 (128083,381543,253381) : difference with theory (-76) = 3
- CORRECTING DEFECT 1 (vertices=98, convex hull=23, v0=484)
- After retessellation of defect 1 (v0=484), euler #=-78 (128089,381568,253401) : difference with theory (-75) = 3
- CORRECTING DEFECT 2 (vertices=42, convex hull=23, v0=524)
- After retessellation of defect 2 (v0=524), euler #=-77 (128090,381578,253411) : difference with theory (-74) = 3
- CORRECTING DEFECT 3 (vertices=68, convex hull=113, v0=835)
- After retessellation of defect 3 (v0=835), euler #=-76 (128131,381745,253538) : difference with theory (-73) = 3
- CORRECTING DEFECT 4 (vertices=12, convex hull=24, v0=1065)
- After retessellation of defect 4 (v0=1065), euler #=-75 (128133,381761,253553) : difference with theory (-72) = 3
- CORRECTING DEFECT 5 (vertices=23, convex hull=28, v0=1344)
- After retessellation of defect 5 (v0=1344), euler #=-74 (128135,381778,253569) : difference with theory (-71) = 3
- CORRECTING DEFECT 6 (vertices=43, convex hull=63, v0=1478)
- After retessellation of defect 6 (v0=1478), euler #=-73 (128157,381871,253641) : difference with theory (-70) = 3
- CORRECTING DEFECT 7 (vertices=66, convex hull=97, v0=2487)
- After retessellation of defect 7 (v0=2487), euler #=-72 (128181,381986,253733) : difference with theory (-69) = 3
- CORRECTING DEFECT 8 (vertices=443, convex hull=302, v0=3040)
- After retessellation of defect 8 (v0=3040), euler #=-70 (128328,382580,254182) : difference with theory (-68) = 2
- CORRECTING DEFECT 9 (vertices=158, convex hull=47, v0=3043)
- After retessellation of defect 9 (v0=3043), euler #=-69 (128337,382622,254216) : difference with theory (-67) = 2
- CORRECTING DEFECT 10 (vertices=981, convex hull=581, v0=5367)
- L defect detected...
- After retessellation of defect 10 (v0=5367), euler #=-68 (128563,383590,254959) : difference with theory (-66) = 2
- CORRECTING DEFECT 11 (vertices=127, convex hull=119, v0=6869)
- After retessellation of defect 11 (v0=6869), euler #=-67 (128607,383777,255103) : difference with theory (-65) = 2
- CORRECTING DEFECT 12 (vertices=10, convex hull=26, v0=6964)
- After retessellation of defect 12 (v0=6964), euler #=-66 (128610,383796,255120) : difference with theory (-64) = 2
- CORRECTING DEFECT 13 (vertices=53, convex hull=75, v0=8417)
- After retessellation of defect 13 (v0=8417), euler #=-65 (128631,383891,255195) : difference with theory (-63) = 2
- CORRECTING DEFECT 14 (vertices=47, convex hull=64, v0=9905)
- After retessellation of defect 14 (v0=9905), euler #=-64 (128641,383950,255245) : difference with theory (-62) = 2
- CORRECTING DEFECT 15 (vertices=26, convex hull=60, v0=10318)
- After retessellation of defect 15 (v0=10318), euler #=-63 (128655,384013,255295) : difference with theory (-61) = 2
- CORRECTING DEFECT 16 (vertices=271, convex hull=184, v0=10779)
- After retessellation of defect 16 (v0=10779), euler #=-62 (128714,384272,255496) : difference with theory (-60) = 2
- CORRECTING DEFECT 17 (vertices=53, convex hull=104, v0=13275)
- After retessellation of defect 17 (v0=13275), euler #=-61 (128738,384385,255586) : difference with theory (-59) = 2
- CORRECTING DEFECT 18 (vertices=9, convex hull=17, v0=14882)
- After retessellation of defect 18 (v0=14882), euler #=-60 (128740,384394,255594) : difference with theory (-58) = 2
- CORRECTING DEFECT 19 (vertices=152, convex hull=155, v0=20380)
- After retessellation of defect 19 (v0=20380), euler #=-58 (128796,384631,255777) : difference with theory (-57) = 1
- CORRECTING DEFECT 20 (vertices=189, convex hull=164, v0=21736)
- After retessellation of defect 20 (v0=21736), euler #=-56 (128858,384901,255987) : difference with theory (-56) = 0
- CORRECTING DEFECT 21 (vertices=23, convex hull=59, v0=26628)
- After retessellation of defect 21 (v0=26628), euler #=-55 (128869,384954,256030) : difference with theory (-55) = 0
- CORRECTING DEFECT 22 (vertices=25, convex hull=74, v0=33121)
- After retessellation of defect 22 (v0=33121), euler #=-54 (128882,385020,256084) : difference with theory (-54) = 0
- CORRECTING DEFECT 23 (vertices=38, convex hull=58, v0=34425)
- After retessellation of defect 23 (v0=34425), euler #=-53 (128894,385081,256134) : difference with theory (-53) = 0
- CORRECTING DEFECT 24 (vertices=43, convex hull=84, v0=35383)
- After retessellation of defect 24 (v0=35383), euler #=-52 (128912,385166,256202) : difference with theory (-52) = 0
- CORRECTING DEFECT 25 (vertices=45, convex hull=86, v0=37899)
- After retessellation of defect 25 (v0=37899), euler #=-51 (128943,385295,256301) : difference with theory (-51) = 0
- CORRECTING DEFECT 26 (vertices=70, convex hull=57, v0=40228)
- After retessellation of defect 26 (v0=40228), euler #=-50 (128955,385349,256344) : difference with theory (-50) = 0
- CORRECTING DEFECT 27 (vertices=18, convex hull=42, v0=40599)
- After retessellation of defect 27 (v0=40599), euler #=-49 (128963,385388,256376) : difference with theory (-49) = 0
- CORRECTING DEFECT 28 (vertices=28, convex hull=45, v0=44578)
- After retessellation of defect 28 (v0=44578), euler #=-48 (128979,385451,256424) : difference with theory (-48) = 0
- CORRECTING DEFECT 29 (vertices=507, convex hull=171, v0=45124)
- After retessellation of defect 29 (v0=45124), euler #=-47 (129089,385861,256725) : difference with theory (-47) = 0
- CORRECTING DEFECT 30 (vertices=65, convex hull=88, v0=45681)
- After retessellation of defect 30 (v0=45681), euler #=-46 (129128,386020,256846) : difference with theory (-46) = 0
- CORRECTING DEFECT 31 (vertices=95, convex hull=106, v0=47222)
- After retessellation of defect 31 (v0=47222), euler #=-45 (129183,386235,257007) : difference with theory (-45) = 0
- CORRECTING DEFECT 32 (vertices=66, convex hull=43, v0=51277)
- After retessellation of defect 32 (v0=51277), euler #=-44 (129191,386277,257042) : difference with theory (-44) = 0
- CORRECTING DEFECT 33 (vertices=23, convex hull=63, v0=55366)
- After retessellation of defect 33 (v0=55366), euler #=-43 (129200,386328,257085) : difference with theory (-43) = 0
- CORRECTING DEFECT 34 (vertices=64, convex hull=38, v0=55407)
- After retessellation of defect 34 (v0=55407), euler #=-42 (129205,386356,257109) : difference with theory (-42) = 0
- CORRECTING DEFECT 35 (vertices=15, convex hull=27, v0=55697)
- After retessellation of defect 35 (v0=55697), euler #=-41 (129206,386369,257122) : difference with theory (-41) = 0
- CORRECTING DEFECT 36 (vertices=28, convex hull=19, v0=59914)
- After retessellation of defect 36 (v0=59914), euler #=-40 (129210,386387,257137) : difference with theory (-40) = 0
- CORRECTING DEFECT 37 (vertices=199, convex hull=157, v0=60387)
- After retessellation of defect 37 (v0=60387), euler #=-39 (129245,386590,257306) : difference with theory (-39) = 0
- CORRECTING DEFECT 38 (vertices=56, convex hull=28, v0=60590)
- After retessellation of defect 38 (v0=60590), euler #=-38 (129253,386625,257334) : difference with theory (-38) = 0
- CORRECTING DEFECT 39 (vertices=6, convex hull=23, v0=65457)
- After retessellation of defect 39 (v0=65457), euler #=-37 (129255,386637,257345) : difference with theory (-37) = 0
- CORRECTING DEFECT 40 (vertices=543, convex hull=147, v0=66203)
- After retessellation of defect 40 (v0=66203), euler #=-36 (129323,386912,257553) : difference with theory (-36) = 0
- CORRECTING DEFECT 41 (vertices=314, convex hull=71, v0=67805)
- After retessellation of defect 41 (v0=67805), euler #=-35 (129365,387071,257671) : difference with theory (-35) = 0
- CORRECTING DEFECT 42 (vertices=74, convex hull=43, v0=72993)
- After retessellation of defect 42 (v0=72993), euler #=-34 (129372,387110,257704) : difference with theory (-34) = 0
- CORRECTING DEFECT 43 (vertices=23, convex hull=51, v0=74006)
- After retessellation of defect 43 (v0=74006), euler #=-33 (129380,387152,257739) : difference with theory (-33) = 0
- CORRECTING DEFECT 44 (vertices=32, convex hull=32, v0=74187)
- After retessellation of defect 44 (v0=74187), euler #=-32 (129381,387170,257757) : difference with theory (-32) = 0
- CORRECTING DEFECT 45 (vertices=23, convex hull=40, v0=76631)
- After retessellation of defect 45 (v0=76631), euler #=-31 (129391,387216,257794) : difference with theory (-31) = 0
- CORRECTING DEFECT 46 (vertices=88, convex hull=108, v0=77109)
- After retessellation of defect 46 (v0=77109), euler #=-30 (129442,387419,257947) : difference with theory (-30) = 0
- CORRECTING DEFECT 47 (vertices=13, convex hull=37, v0=79428)
- After retessellation of defect 47 (v0=79428), euler #=-29 (129444,387438,257965) : difference with theory (-29) = 0
- CORRECTING DEFECT 48 (vertices=83, convex hull=104, v0=79820)
- After retessellation of defect 48 (v0=79820), euler #=-28 (129470,387574,258076) : difference with theory (-28) = 0
- CORRECTING DEFECT 49 (vertices=19, convex hull=25, v0=80992)
- After retessellation of defect 49 (v0=80992), euler #=-27 (129471,387585,258087) : difference with theory (-27) = 0
- CORRECTING DEFECT 50 (vertices=6, convex hull=29, v0=83166)
- After retessellation of defect 50 (v0=83166), euler #=-26 (129472,387598,258100) : difference with theory (-26) = 0
- CORRECTING DEFECT 51 (vertices=11, convex hull=33, v0=83366)
- After retessellation of defect 51 (v0=83366), euler #=-25 (129474,387613,258114) : difference with theory (-25) = 0
- CORRECTING DEFECT 52 (vertices=120, convex hull=113, v0=84524)
- After retessellation of defect 52 (v0=84524), euler #=-24 (129533,387841,258284) : difference with theory (-24) = 0
- CORRECTING DEFECT 53 (vertices=100, convex hull=100, v0=84574)
- After retessellation of defect 53 (v0=84574), euler #=-23 (129570,387992,258399) : difference with theory (-23) = 0
- CORRECTING DEFECT 54 (vertices=40, convex hull=89, v0=86053)
- After retessellation of defect 54 (v0=86053), euler #=-22 (129590,388087,258475) : difference with theory (-22) = 0
- CORRECTING DEFECT 55 (vertices=43, convex hull=34, v0=87270)
- After retessellation of defect 55 (v0=87270), euler #=-21 (129601,388134,258512) : difference with theory (-21) = 0
- CORRECTING DEFECT 56 (vertices=29, convex hull=21, v0=87682)
- After retessellation of defect 56 (v0=87682), euler #=-20 (129603,388147,258524) : difference with theory (-20) = 0
- CORRECTING DEFECT 57 (vertices=74, convex hull=34, v0=89577)
- After retessellation of defect 57 (v0=89577), euler #=-19 (129612,388185,258554) : difference with theory (-19) = 0
- CORRECTING DEFECT 58 (vertices=400, convex hull=320, v0=89611)
- After retessellation of defect 58 (v0=89611), euler #=-18 (129753,388791,259020) : difference with theory (-18) = 0
- CORRECTING DEFECT 59 (vertices=15, convex hull=21, v0=90628)
- After retessellation of defect 59 (v0=90628), euler #=-17 (129755,388806,259034) : difference with theory (-17) = 0
- CORRECTING DEFECT 60 (vertices=23, convex hull=17, v0=90629)
- After retessellation of defect 60 (v0=90629), euler #=-16 (129758,388820,259046) : difference with theory (-16) = 0
- CORRECTING DEFECT 61 (vertices=275, convex hull=184, v0=90734)
- After retessellation of defect 61 (v0=90734), euler #=-15 (129806,389044,259223) : difference with theory (-15) = 0
- CORRECTING DEFECT 62 (vertices=12, convex hull=29, v0=95442)
- After retessellation of defect 62 (v0=95442), euler #=-14 (129809,389064,259241) : difference with theory (-14) = 0
- CORRECTING DEFECT 63 (vertices=162, convex hull=72, v0=96759)
- After retessellation of defect 63 (v0=96759), euler #=-13 (129823,389138,259302) : difference with theory (-13) = 0
- CORRECTING DEFECT 64 (vertices=57, convex hull=65, v0=97949)
- After retessellation of defect 64 (v0=97949), euler #=-12 (129848,389240,259380) : difference with theory (-12) = 0
- CORRECTING DEFECT 65 (vertices=58, convex hull=42, v0=98831)
- After retessellation of defect 65 (v0=98831), euler #=-11 (129856,389279,259412) : difference with theory (-11) = 0
- CORRECTING DEFECT 66 (vertices=5, convex hull=12, v0=102385)
- After retessellation of defect 66 (v0=102385), euler #=-10 (129857,389285,259418) : difference with theory (-10) = 0
- CORRECTING DEFECT 67 (vertices=32, convex hull=39, v0=102463)
- After retessellation of defect 67 (v0=102463), euler #=-9 (129863,389316,259444) : difference with theory (-9) = 0
- CORRECTING DEFECT 68 (vertices=34, convex hull=18, v0=104894)
- After retessellation of defect 68 (v0=104894), euler #=-8 (129865,389325,259452) : difference with theory (-8) = 0
- CORRECTING DEFECT 69 (vertices=8, convex hull=27, v0=110021)
- After retessellation of defect 69 (v0=110021), euler #=-7 (129866,389335,259462) : difference with theory (-7) = 0
- CORRECTING DEFECT 70 (vertices=70, convex hull=53, v0=110169)
- After retessellation of defect 70 (v0=110169), euler #=-6 (129869,389374,259499) : difference with theory (-6) = 0
- CORRECTING DEFECT 71 (vertices=94, convex hull=49, v0=119587)
- After retessellation of defect 71 (v0=119587), euler #=-5 (129876,389416,259535) : difference with theory (-5) = 0
- CORRECTING DEFECT 72 (vertices=11, convex hull=19, v0=127094)
- After retessellation of defect 72 (v0=127094), euler #=-4 (129877,389424,259543) : difference with theory (-4) = 0
- CORRECTING DEFECT 73 (vertices=36, convex hull=72, v0=131194)
- After retessellation of defect 73 (v0=131194), euler #=-3 (129890,389489,259596) : difference with theory (-3) = 0
- CORRECTING DEFECT 74 (vertices=15, convex hull=26, v0=133717)
- After retessellation of defect 74 (v0=133717), euler #=-2 (129892,389506,259612) : difference with theory (-2) = 0
- CORRECTING DEFECT 75 (vertices=53, convex hull=89, v0=134077)
- After retessellation of defect 75 (v0=134077), euler #=-1 (129912,389600,259687) : difference with theory (-1) = 0
- CORRECTING DEFECT 76 (vertices=100, convex hull=61, v0=134138)
- After retessellation of defect 76 (v0=134138), euler #=0 (129916,389642,259726) : difference with theory (0) = 0
- CORRECTING DEFECT 77 (vertices=130, convex hull=159, v0=134239)
- After retessellation of defect 77 (v0=134239), euler #=1 (129964,389859,259896) : difference with theory (1) = 0
- CORRECTING DEFECT 78 (vertices=24, convex hull=78, v0=134328)
- After retessellation of defect 78 (v0=134328), euler #=2 (129973,389913,259942) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.89 +- 0.25 (0.03-->9.87) (max @ vno 75496 --> 132823)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.89 +- 0.25 (0.03-->9.87) (max @ vno 75496 --> 132823)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 245 mutations (34.9%), 457 crossovers (65.1%), 295 vertices were eliminated
- building final representation...
- 5683 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=129973, nf=259942, ne=389913, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 49.4 minutes
- 0 defective edges
- removing intersecting faces
- 000: 645 intersecting
- 001: 43 intersecting
- mris_fix_topology utimesec 2962.174681
- mris_fix_topology stimesec 0.575912
- mris_fix_topology ru_maxrss 452104
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 64772
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 19104
- mris_fix_topology ru_oublock 12712
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 364
- mris_fix_topology ru_nivcsw 7607
- FSRUNTIME@ mris_fix_topology rh 0.8226 hours 1 threads
- PIDs (21131 21134) completed and logs appended.
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 129630 - 388884 + 259256 = 2 --> 0 holes
- F =2V-4: 259256 = 259260-4 (0)
- 2E=3F: 777768 = 777768 (0)
- total defect index = 0
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 129973 - 389913 + 259942 = 2 --> 0 holes
- F =2V-4: 259942 = 259946-4 (0)
- 2E=3F: 779826 = 779826 (0)
- total defect index = 0
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 84 intersecting
- 001: 19 intersecting
- 002: 8 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 97 intersecting
- 001: 11 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Sun Oct 8 03:59:49 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050319 lh
- #--------------------------------------------
- #@# Make White Surf rh Sun Oct 8 03:59:49 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050319 rh
- Waiting for PID 23447 of (23447 23450) to complete...
- Waiting for PID 23450 of (23447 23450) to complete...
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050319 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-6.0.0/0050319/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- 15995 bright wm thresholded.
- 2713 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.orig...
- computing class statistics...
- border white: 245529 voxels (1.46%)
- border gray 293505 voxels (1.75%)
- WM (97.0): 97.4 +- 7.6 [70.0 --> 110.0]
- GM (76.0) : 75.0 +- 10.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 61.7 (was 70)
- setting MAX_BORDER_WHITE to 108.6 (was 105)
- setting MIN_BORDER_WHITE to 72.0 (was 85)
- setting MAX_CSF to 51.4 (was 40)
- setting MAX_GRAY to 93.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 61.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 41.1 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.23 (0.03-->5.70) (max @ vno 128344 --> 128358)
- face area 0.28 +- 0.13 (0.00-->5.66)
- mean absolute distance = 0.74 +- 0.89
- 4179 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+-6.1, GM=72+-7.8
- mean inside = 93.6, mean outside = 78.6
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=82.0, 195 (195) missing vertices, mean dist 0.4 [0.6 (%31.5)->0.8 (%68.5))]
- %64 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.04-->6.48) (max @ vno 128344 --> 45364)
- face area 0.28 +- 0.14 (0.00-->4.41)
- mean absolute distance = 0.41 +- 0.60
- 4160 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2464459.2, rms=8.742
- 001: dt: 0.5000, sse=1468699.9, rms=6.165 (29.479%)
- 002: dt: 0.5000, sse=1027102.4, rms=4.513 (26.792%)
- 003: dt: 0.5000, sse=826357.4, rms=3.522 (21.967%)
- 004: dt: 0.5000, sse=739905.2, rms=2.976 (15.498%)
- 005: dt: 0.5000, sse=706133.2, rms=2.733 (8.149%)
- 006: dt: 0.5000, sse=690845.2, rms=2.626 (3.918%)
- rms = 2.58, time step reduction 1 of 3 to 0.250...
- 007: dt: 0.5000, sse=689138.6, rms=2.581 (1.723%)
- 008: dt: 0.2500, sse=607075.1, rms=1.745 (32.388%)
- 009: dt: 0.2500, sse=595718.2, rms=1.600 (8.316%)
- rms = 1.56, time step reduction 2 of 3 to 0.125...
- 010: dt: 0.2500, sse=593049.8, rms=1.562 (2.395%)
- rms = 1.52, time step reduction 3 of 3 to 0.062...
- 011: dt: 0.1250, sse=590158.0, rms=1.522 (2.516%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=85.1, 139 (46) missing vertices, mean dist -0.3 [0.5 (%74.0)->0.3 (%26.0))]
- %74 local maxima, %21 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-->7.34) (max @ vno 128344 --> 45364)
- face area 0.35 +- 0.17 (0.00-->6.61)
- mean absolute distance = 0.29 +- 0.43
- 3525 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1182027.6, rms=4.585
- 012: dt: 0.5000, sse=868216.0, rms=2.830 (38.268%)
- 013: dt: 0.5000, sse=791180.7, rms=2.288 (19.148%)
- 014: dt: 0.5000, sse=772944.9, rms=2.163 (5.478%)
- rms = 2.21, time step reduction 1 of 3 to 0.250...
- 015: dt: 0.2500, sse=729555.8, rms=1.679 (22.389%)
- 016: dt: 0.2500, sse=711650.6, rms=1.425 (15.117%)
- 017: dt: 0.2500, sse=706327.3, rms=1.353 (5.066%)
- rms = 1.32, time step reduction 2 of 3 to 0.125...
- 018: dt: 0.2500, sse=705744.5, rms=1.325 (2.070%)
- rms = 1.28, time step reduction 3 of 3 to 0.062...
- 019: dt: 0.1250, sse=704484.4, rms=1.283 (3.184%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=87.0, 146 (22) missing vertices, mean dist -0.1 [0.3 (%67.4)->0.2 (%32.6))]
- %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.11-->8.17) (max @ vno 128344 --> 45364)
- face area 0.34 +- 0.17 (0.00-->6.94)
- mean absolute distance = 0.26 +- 0.37
- 3337 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=836830.6, rms=2.781
- 020: dt: 0.5000, sse=735722.0, rms=1.890 (32.047%)
- 021: dt: 0.5000, sse=742670.1, rms=1.829 (3.213%)
- rms = 1.92, time step reduction 1 of 3 to 0.250...
- 022: dt: 0.2500, sse=709869.4, rms=1.391 (23.978%)
- 023: dt: 0.2500, sse=681109.2, rms=1.197 (13.914%)
- rms = 1.19, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.2500, sse=679647.1, rms=1.193 (0.339%)
- 025: dt: 0.1250, sse=675067.9, rms=1.142 (4.317%)
- rms = 1.14, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=674818.4, rms=1.137 (0.429%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=87.7, 173 (15) missing vertices, mean dist -0.1 [0.3 (%56.6)->0.2 (%43.4))]
- %85 local maxima, %10 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-6.0.0/0050319/surf/lh.white.preaparc...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=693372.9, rms=1.536
- 027: dt: 0.5000, sse=678465.9, rms=1.297 (15.586%)
- rms = 1.53, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=659641.0, rms=1.017 (21.606%)
- rms = 1.00, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.2500, sse=667619.5, rms=0.997 (1.962%)
- 030: dt: 0.1250, sse=654954.2, rms=0.923 (7.436%)
- rms = 0.90, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=652900.8, rms=0.903 (2.145%)
- positioning took 0.6 minutes
- generating cortex label...
- 15 non-cortical segments detected
- only using segment with 6589 vertices
- erasing segment 1 (vno[0] = 48740)
- erasing segment 2 (vno[0] = 58663)
- erasing segment 3 (vno[0] = 78877)
- erasing segment 4 (vno[0] = 79891)
- erasing segment 5 (vno[0] = 82361)
- erasing segment 6 (vno[0] = 82482)
- erasing segment 7 (vno[0] = 83597)
- erasing segment 8 (vno[0] = 83641)
- erasing segment 9 (vno[0] = 86712)
- erasing segment 10 (vno[0] = 86788)
- erasing segment 11 (vno[0] = 89532)
- erasing segment 12 (vno[0] = 89556)
- erasing segment 13 (vno[0] = 89585)
- erasing segment 14 (vno[0] = 93149)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.area
- vertex spacing 0.90 +- 0.26 (0.03-->8.37) (max @ vno 45364 --> 128344)
- face area 0.34 +- 0.16 (0.00-->6.92)
- refinement took 4.8 minutes
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050319 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-6.0.0/0050319/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- 15995 bright wm thresholded.
- 2713 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.orig...
- computing class statistics...
- border white: 245529 voxels (1.46%)
- border gray 293505 voxels (1.75%)
- WM (97.0): 97.4 +- 7.6 [70.0 --> 110.0]
- GM (76.0) : 75.0 +- 10.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 62.7 (was 70)
- setting MAX_BORDER_WHITE to 108.6 (was 105)
- setting MIN_BORDER_WHITE to 73.0 (was 85)
- setting MAX_CSF to 52.4 (was 40)
- setting MAX_GRAY to 93.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 62.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 42.1 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.23 (0.03-->4.81) (max @ vno 9585 --> 128665)
- face area 0.28 +- 0.13 (0.00-->4.02)
- mean absolute distance = 0.75 +- 0.88
- 4195 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+-5.2, GM=73+-7.0
- mean inside = 93.7, mean outside = 79.1
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=82.5, 190 (190) missing vertices, mean dist 0.3 [0.6 (%32.6)->0.8 (%67.4))]
- %62 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.10-->5.27) (max @ vno 92287 --> 90233)
- face area 0.28 +- 0.14 (0.00-->4.01)
- mean absolute distance = 0.42 +- 0.63
- 4373 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2282454.5, rms=8.281
- 001: dt: 0.5000, sse=1371444.4, rms=5.829 (29.614%)
- 002: dt: 0.5000, sse=986636.9, rms=4.323 (25.834%)
- 003: dt: 0.5000, sse=817271.9, rms=3.461 (19.932%)
- 004: dt: 0.5000, sse=741447.0, rms=2.968 (14.260%)
- 005: dt: 0.5000, sse=714326.1, rms=2.736 (7.814%)
- 006: dt: 0.5000, sse=701813.6, rms=2.605 (4.790%)
- 007: dt: 0.5000, sse=686359.0, rms=2.548 (2.191%)
- rms = 2.50, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=679874.0, rms=2.504 (1.721%)
- 009: dt: 0.2500, sse=604685.6, rms=1.690 (32.495%)
- 010: dt: 0.2500, sse=592431.8, rms=1.550 (8.273%)
- rms = 1.52, time step reduction 2 of 3 to 0.125...
- 011: dt: 0.2500, sse=594089.8, rms=1.523 (1.760%)
- rms = 1.50, time step reduction 3 of 3 to 0.062...
- 012: dt: 0.1250, sse=587789.1, rms=1.498 (1.682%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- mean border=85.5, 166 (58) missing vertices, mean dist -0.3 [0.5 (%72.7)->0.3 (%27.3))]
- %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.07-->5.05) (max @ vno 9585 --> 128665)
- face area 0.35 +- 0.17 (0.00-->5.77)
- mean absolute distance = 0.31 +- 0.45
- 3751 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1144181.4, rms=4.381
- 013: dt: 0.5000, sse=857458.6, rms=2.776 (36.632%)
- 014: dt: 0.5000, sse=792609.0, rms=2.272 (18.174%)
- 015: dt: 0.5000, sse=770478.5, rms=2.114 (6.922%)
- rms = 2.14, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.2500, sse=738968.6, rms=1.693 (19.941%)
- 017: dt: 0.2500, sse=719215.3, rms=1.444 (14.677%)
- 018: dt: 0.2500, sse=711541.6, rms=1.351 (6.427%)
- rms = 1.30, time step reduction 2 of 3 to 0.125...
- 019: dt: 0.2500, sse=707647.3, rms=1.304 (3.543%)
- rms = 1.27, time step reduction 3 of 3 to 0.062...
- 020: dt: 0.1250, sse=705260.8, rms=1.272 (2.442%)
- positioning took 0.8 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
- mean border=87.5, 160 (30) missing vertices, mean dist -0.1 [0.3 (%67.2)->0.2 (%32.8))]
- %81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.26 (0.07-->4.91) (max @ vno 92287 --> 90233)
- face area 0.34 +- 0.17 (0.00-->5.83)
- mean absolute distance = 0.26 +- 0.38
- 3388 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=846094.9, rms=2.840
- 021: dt: 0.5000, sse=733312.8, rms=1.842 (35.135%)
- 022: dt: 0.5000, sse=729788.1, rms=1.757 (4.612%)
- rms = 1.81, time step reduction 1 of 3 to 0.250...
- 023: dt: 0.2500, sse=694792.3, rms=1.362 (22.502%)
- 024: dt: 0.2500, sse=692287.8, rms=1.170 (14.095%)
- rms = 1.16, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.2500, sse=681905.9, rms=1.155 (1.232%)
- rms = 1.13, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=677991.6, rms=1.132 (2.058%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=88.2, 170 (25) missing vertices, mean dist -0.0 [0.3 (%56.1)->0.2 (%43.9))]
- %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.white.preaparc...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=691855.5, rms=1.497
- 027: dt: 0.5000, sse=681868.0, rms=1.213 (18.976%)
- rms = 1.47, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=661240.8, rms=0.976 (19.472%)
- rms = 0.95, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.2500, sse=659810.6, rms=0.945 (3.175%)
- rms = 0.91, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=660109.1, rms=0.906 (4.209%)
- positioning took 0.5 minutes
- generating cortex label...
- 15 non-cortical segments detected
- only using segment with 6688 vertices
- erasing segment 1 (vno[0] = 52575)
- erasing segment 2 (vno[0] = 52631)
- erasing segment 3 (vno[0] = 66957)
- erasing segment 4 (vno[0] = 83747)
- erasing segment 5 (vno[0] = 84844)
- erasing segment 6 (vno[0] = 84856)
- erasing segment 7 (vno[0] = 85849)
- erasing segment 8 (vno[0] = 85879)
- erasing segment 9 (vno[0] = 88060)
- erasing segment 10 (vno[0] = 89053)
- erasing segment 11 (vno[0] = 89129)
- erasing segment 12 (vno[0] = 93112)
- erasing segment 13 (vno[0] = 94747)
- erasing segment 14 (vno[0] = 94761)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.area
- vertex spacing 0.89 +- 0.26 (0.03-->5.03) (max @ vno 90233 --> 92287)
- face area 0.34 +- 0.17 (0.00-->5.96)
- refinement took 4.7 minutes
- PIDs (23447 23450) completed and logs appended.
- #--------------------------------------------
- #@# Smooth2 lh Sun Oct 8 04:04:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
- #--------------------------------------------
- #@# Smooth2 rh Sun Oct 8 04:04:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
- Waiting for PID 23732 of (23732 23735) to complete...
- Waiting for PID 23735 of (23732 23735) 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 (23732 23735) completed and logs appended.
- #--------------------------------------------
- #@# Inflation2 lh Sun Oct 8 04:04:42 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- #--------------------------------------------
- #@# Inflation2 rh Sun Oct 8 04:04:42 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Waiting for PID 23780 of (23780 23783) to complete...
- Waiting for PID 23783 of (23780 23783) to complete...
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- Reading ../surf/lh.smoothwm
- avg radius = 45.3 mm, total surface area = 79192 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.179 (target=0.015)
step 005: RMS=0.130 (target=0.015)
step 010: RMS=0.099 (target=0.015)
step 015: RMS=0.082 (target=0.015)
step 020: RMS=0.070 (target=0.015)
step 025: RMS=0.059 (target=0.015)
step 030: RMS=0.051 (target=0.015)
step 035: RMS=0.043 (target=0.015)
step 040: RMS=0.038 (target=0.015)
step 045: RMS=0.035 (target=0.015)
step 050: RMS=0.032 (target=0.015)
step 055: RMS=0.030 (target=0.015)
step 060: RMS=0.028 (target=0.015)
- inflation complete.
- inflation took 0.7 minutes
- mris_inflate utimesec 41.436700
- mris_inflate stimesec 0.118981
- mris_inflate ru_maxrss 190456
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 28261
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 10152
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 4370
- mris_inflate ru_nivcsw 3272
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Reading ../surf/rh.smoothwm
- avg radius = 45.2 mm, total surface area = 78947 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.182 (target=0.015)
step 005: RMS=0.131 (target=0.015)
step 010: RMS=0.102 (target=0.015)
step 015: RMS=0.085 (target=0.015)
step 020: RMS=0.072 (target=0.015)
step 025: RMS=0.062 (target=0.015)
step 030: RMS=0.054 (target=0.015)
step 035: RMS=0.046 (target=0.015)
step 040: RMS=0.041 (target=0.015)
step 045: RMS=0.036 (target=0.015)
step 050: RMS=0.034 (target=0.015)
step 055: RMS=0.032 (target=0.015)
step 060: RMS=0.031 (target=0.015)
- inflation complete.
- inflation took 0.7 minutes
- mris_inflate utimesec 41.788647
- mris_inflate stimesec 0.103984
- mris_inflate ru_maxrss 190948
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 27872
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 9144
- mris_inflate ru_oublock 10176
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2478
- mris_inflate ru_nivcsw 4657
- PIDs (23780 23783) completed and logs appended.
- #--------------------------------------------
- #@# Curv .H and .K lh Sun Oct 8 04:05:24 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf
- mris_curvature -w lh.white.preaparc
- rm -f lh.white.H
- ln -s lh.white.preaparc.H lh.white.H
- rm -f lh.white.K
- ln -s lh.white.preaparc.K lh.white.K
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
- #--------------------------------------------
- #@# Curv .H and .K rh Sun Oct 8 04:05:24 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/surf
- reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 23875 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- Waiting for PID 23878 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- Waiting for PID 23881 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- Waiting for PID 23884 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- Waiting for PID 23887 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- Waiting for PID 23890 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- Waiting for PID 23893 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- Waiting for PID 23896 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- Waiting for PID 23899 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- Waiting for PID 23902 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- Waiting for PID 23906 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- Waiting for PID 23909 of (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) to complete...
- mris_curvature -w lh.white.preaparc
- total integrated curvature = 14.853*4pi (186.644) --> -14 handles
- ICI = 186.9, FI = 1687.9, variation=27302.398
- 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
- 155 vertices thresholded to be in k1 ~ [-0.29 0.37], k2 ~ [-0.13 0.12]
- total integrated curvature = 0.317*4pi (3.981) --> 1 handles
- ICI = 1.3, FI = 8.3, variation=146.771
- 133 vertices thresholded to be in [-0.03 0.02]
- writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 126 vertices thresholded to be in [-0.17 0.17]
- done.
- writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.023
- done.
- mris_curvature -w rh.white.preaparc
- total integrated curvature = 12.771*4pi (160.482) --> -12 handles
- ICI = 195.5, FI = 1704.2, variation=27859.674
- 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
- 160 vertices thresholded to be in k1 ~ [-0.28 1.52], k2 ~ [-0.13 0.25]
- total integrated curvature = 0.339*4pi (4.254) --> 1 handles
- ICI = 1.3, FI = 8.6, variation=149.338
- 127 vertices thresholded to be in [-0.06 0.02]
- writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.002
- 119 vertices thresholded to be in [-0.14 0.49]
- done.
- writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.023
- done.
- PIDs (23875 23878 23881 23884 23887 23890 23893 23896 23899 23902 23906 23909) completed and logs appended.
- #-----------------------------------------
- #@# Curvature Stats lh Sun Oct 8 04:06:43 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050319 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 [ 0050319/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 [ 230 ]
- Gb_filter = 0
- WARN: S lookup min: -0.901666
- WARN: S explicit min: 0.000000 vertex = 561
- #-----------------------------------------
- #@# Curvature Stats rh Sun Oct 8 04:06:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050319 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 [ 0050319/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 [ 272 ]
- Gb_filter = 0
- WARN: S lookup min: -0.043818
- WARN: S explicit min: 0.000000 vertex = 128
- #--------------------------------------------
- #@# Sphere lh Sun Oct 8 04:06:52 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- #--------------------------------------------
- #@# Sphere rh Sun Oct 8 04:06:52 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- Waiting for PID 24053 of (24053 24056) to complete...
- Waiting for PID 24056 of (24053 24056) to complete...
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0.300...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %22.18
- pass 1: epoch 2 of 3 starting distance error %22.04
- unfolding complete - removing small folds...
- starting distance error %21.87
- removing remaining folds...
- final distance error %21.89
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 212 negative triangles
- 199: dt=0.9900, 212 negative triangles
- 200: dt=0.9900, 83 negative triangles
- 201: dt=0.9900, 66 negative triangles
- 202: dt=0.9900, 56 negative triangles
- 203: dt=0.9900, 51 negative triangles
- 204: dt=0.9900, 37 negative triangles
- 205: dt=0.9900, 38 negative triangles
- 206: dt=0.9900, 31 negative triangles
- 207: dt=0.9900, 30 negative triangles
- 208: dt=0.9900, 33 negative triangles
- 209: dt=0.9900, 31 negative triangles
- 210: dt=0.9900, 23 negative triangles
- 211: dt=0.9900, 16 negative triangles
- 212: dt=0.9900, 20 negative triangles
- 213: dt=0.9900, 16 negative triangles
- 214: dt=0.9900, 18 negative triangles
- 215: dt=0.9900, 13 negative triangles
- 216: dt=0.9900, 14 negative triangles
- 217: dt=0.9900, 16 negative triangles
- 218: dt=0.9900, 13 negative triangles
- 219: dt=0.9900, 10 negative triangles
- 220: dt=0.9900, 10 negative triangles
- 221: dt=0.9900, 9 negative triangles
- 222: dt=0.9900, 10 negative triangles
- 223: dt=0.9900, 10 negative triangles
- 224: dt=0.9900, 11 negative triangles
- 225: dt=0.9900, 11 negative triangles
- 226: dt=0.9900, 9 negative triangles
- 227: dt=0.9900, 8 negative triangles
- 228: dt=0.9900, 5 negative triangles
- 229: dt=0.9900, 6 negative triangles
- 230: dt=0.9900, 2 negative triangles
- 231: dt=0.9900, 4 negative triangles
- 232: dt=0.9900, 1 negative triangles
- 233: dt=0.9900, 3 negative triangles
- 234: dt=0.9900, 1 negative triangles
- 235: dt=0.9900, 1 negative triangles
- 236: dt=0.9900, 1 negative triangles
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.70 hours
- mris_sphere utimesec 2938.803234
- mris_sphere stimesec 1.366792
- mris_sphere ru_maxrss 267320
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 47091
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 9152
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 97569
- mris_sphere ru_nivcsw 164240
- FSRUNTIME@ mris_sphere 0.6957 hours 1 threads
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0.306...
- 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 %40.51
- pass 1: epoch 2 of 3 starting distance error %20.78
- unfolding complete - removing small folds...
- starting distance error %20.65
- removing remaining folds...
- final distance error %20.69
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 274 negative triangles
- 142: dt=0.9900, 274 negative triangles
- 143: dt=0.9900, 128 negative triangles
- 144: dt=0.9900, 97 negative triangles
- 145: dt=0.9900, 72 negative triangles
- 146: dt=0.9900, 66 negative triangles
- 147: dt=0.9900, 51 negative triangles
- 148: dt=0.9900, 54 negative triangles
- 149: dt=0.9900, 37 negative triangles
- 150: dt=0.9900, 40 negative triangles
- 151: dt=0.9900, 30 negative triangles
- 152: dt=0.9900, 29 negative triangles
- 153: dt=0.9900, 23 negative triangles
- 154: dt=0.9900, 16 negative triangles
- 155: dt=0.9900, 21 negative triangles
- 156: dt=0.9900, 18 negative triangles
- 157: dt=0.9900, 15 negative triangles
- 158: dt=0.9900, 18 negative triangles
- 159: dt=0.9900, 14 negative triangles
- 160: dt=0.9900, 15 negative triangles
- 161: dt=0.9900, 17 negative triangles
- 162: dt=0.9900, 15 negative triangles
- 163: dt=0.9900, 18 negative triangles
- 164: dt=0.9900, 15 negative triangles
- 165: dt=0.9900, 16 negative triangles
- 166: dt=0.9900, 15 negative triangles
- 167: dt=0.9900, 15 negative triangles
- 168: dt=0.9900, 19 negative triangles
- 169: dt=0.9405, 16 negative triangles
- 170: dt=0.9405, 15 negative triangles
- 171: dt=0.9405, 16 negative triangles
- 172: dt=0.9405, 16 negative triangles
- 173: dt=0.9405, 16 negative triangles
- 174: dt=0.9405, 16 negative triangles
- 175: dt=0.9405, 13 negative triangles
- 176: dt=0.9405, 17 negative triangles
- 177: dt=0.9405, 16 negative triangles
- 178: dt=0.9405, 15 negative triangles
- 179: dt=0.9405, 16 negative triangles
- 180: dt=0.9405, 15 negative triangles
- 181: dt=0.9405, 14 negative triangles
- 182: dt=0.9405, 15 negative triangles
- 183: dt=0.9405, 15 negative triangles
- 184: dt=0.9405, 15 negative triangles
- 185: dt=0.9405, 11 negative triangles
- 186: dt=0.9405, 12 negative triangles
- 187: dt=0.9405, 11 negative triangles
- 188: dt=0.9405, 12 negative triangles
- 189: dt=0.9405, 12 negative triangles
- 190: dt=0.9405, 12 negative triangles
- 191: dt=0.9405, 11 negative triangles
- 192: dt=0.9405, 10 negative triangles
- 193: dt=0.9405, 10 negative triangles
- 194: dt=0.9405, 8 negative triangles
- 195: dt=0.9405, 10 negative triangles
- 196: dt=0.9405, 8 negative triangles
- 197: dt=0.9405, 13 negative triangles
- 198: dt=0.9405, 10 negative triangles
- 199: dt=0.9405, 6 negative triangles
- 200: dt=0.9405, 12 negative triangles
- 201: dt=0.9405, 7 negative triangles
- 202: dt=0.9405, 6 negative triangles
- 203: dt=0.9405, 7 negative triangles
- 204: dt=0.9405, 4 negative triangles
- 205: dt=0.9405, 5 negative triangles
- 206: dt=0.9405, 1 negative triangles
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.55 hours
- mris_sphere utimesec 1983.046531
- mris_sphere stimesec 0.906862
- mris_sphere ru_maxrss 267792
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 47214
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 9208
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 76046
- mris_sphere ru_nivcsw 165265
- FSRUNTIME@ mris_sphere 0.5507 hours 1 threads
- PIDs (24053 24056) completed and logs appended.
- #--------------------------------------------
- #@# Surf Reg lh Sun Oct 8 04:48:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 04:48:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 26004 of (26004 26007) to complete...
- Waiting for PID 26007 of (26004 26007) to complete...
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 = 5.576
- curvature mean = 0.046, std = 0.808
- curvature mean = 0.018, std = 0.862
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, 0.00, 16.00) sse = 316894.8, tmin=0.9987
- d=32.00 min @ (-8.00, -8.00, 8.00) sse = 247896.1, tmin=2.0153
- d=16.00 min @ (4.00, 0.00, -4.00) sse = 205028.8, tmin=3.0497
- d=4.00 min @ (1.00, 1.00, 1.00) sse = 202306.0, tmin=5.1538
- d=2.00 min @ (-0.50, -0.50, 0.00) sse = 202016.2, tmin=6.2064
- d=1.00 min @ (0.00, 0.25, 0.00) sse = 201900.6, tmin=7.2562
- d=0.50 min @ (0.12, 0.00, -0.12) sse = 201849.8, tmin=8.3149
- tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 8.31 min
- curvature mean = 0.005, std = 0.829
- curvature mean = 0.006, std = 0.949
- curvature mean = 0.002, std = 0.840
- curvature mean = 0.002, std = 0.979
- curvature mean = 0.001, std = 0.843
- curvature mean = 0.000, std = 0.992
- 2 Reading smoothwm
- curvature mean = -0.040, std = 0.315
- curvature mean = 0.038, std = 0.247
- curvature mean = 0.067, std = 0.344
- curvature mean = 0.030, std = 0.310
- curvature mean = 0.046, std = 0.508
- curvature mean = 0.028, std = 0.338
- curvature mean = 0.026, std = 0.638
- curvature mean = 0.028, std = 0.349
- curvature mean = 0.010, std = 0.743
- MRISregister() return, current seed 0
- -01: dt=0.0000, 93 negative triangles
- 113: dt=0.9900, 93 negative triangles
- expanding nbhd size to 1
- 114: dt=0.9900, 135 negative triangles
- 115: dt=0.9900, 95 negative triangles
- 116: dt=0.9900, 91 negative triangles
- 117: dt=0.9900, 91 negative triangles
- 118: dt=0.9900, 91 negative triangles
- 119: dt=0.9900, 80 negative triangles
- 120: dt=0.9900, 85 negative triangles
- 121: dt=0.9900, 68 negative triangles
- 122: dt=0.9900, 67 negative triangles
- 123: dt=0.9900, 62 negative triangles
- 124: dt=0.9900, 57 negative triangles
- 125: dt=0.9900, 47 negative triangles
- 126: dt=0.9900, 48 negative triangles
- 127: dt=0.9900, 42 negative triangles
- 128: dt=0.9900, 39 negative triangles
- 129: dt=0.9900, 36 negative triangles
- 130: dt=0.9900, 34 negative triangles
- 131: dt=0.9900, 33 negative triangles
- 132: dt=0.9900, 29 negative triangles
- 133: dt=0.9900, 26 negative triangles
- 134: dt=0.9900, 23 negative triangles
- 135: dt=0.9900, 24 negative triangles
- 136: dt=0.9900, 19 negative triangles
- 137: dt=0.9900, 16 negative triangles
- 138: dt=0.9900, 15 negative triangles
- 139: dt=0.9900, 15 negative triangles
- 140: dt=0.9900, 10 negative triangles
- 141: dt=0.9900, 9 negative triangles
- 142: dt=0.9900, 8 negative triangles
- 143: dt=0.9900, 8 negative triangles
- 144: dt=0.9900, 8 negative triangles
- 145: dt=0.9900, 9 negative triangles
- 146: dt=0.9900, 8 negative triangles
- 147: dt=0.9900, 8 negative triangles
- 148: dt=0.9900, 7 negative triangles
- 149: dt=0.9900, 6 negative triangles
- 150: dt=0.9900, 7 negative triangles
- 151: dt=0.9900, 6 negative triangles
- 152: dt=0.9900, 4 negative triangles
- 153: dt=0.9900, 4 negative triangles
- 154: dt=0.9900, 4 negative triangles
- 155: dt=0.9900, 4 negative triangles
- 156: dt=0.9900, 4 negative triangles
- 157: dt=0.9900, 2 negative triangles
- 158: dt=0.9900, 1 negative triangles
- 159: dt=0.9900, 1 negative triangles
- 160: dt=0.9900, 2 negative triangles
- 161: dt=0.9900, 1 negative triangles
- 162: dt=0.9900, 1 negative triangles
- 163: dt=0.9900, 1 negative triangles
- 164: dt=0.9900, 1 negative triangles
- 165: dt=0.9900, 1 negative triangles
- 166: dt=0.9900, 1 negative triangles
- writing registered surface to ../surf/lh.sphere.reg...
- registration took 1.13 hours
- mris_register utimesec 4077.922061
- mris_register stimesec 3.299498
- mris_register ru_maxrss 244852
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 33280
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 9224
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 338164
- mris_register ru_nivcsw 211416
- FSRUNTIME@ mris_register 1.1322 hours 1 threads
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 = 5.564
- curvature mean = 0.031, std = 0.814
- curvature mean = 0.020, std = 0.864
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 16.00) sse = 321352.8, tmin=1.0012
- d=32.00 min @ (0.00, 8.00, 8.00) sse = 232844.3, tmin=2.0284
- d=16.00 min @ (0.00, -4.00, 0.00) sse = 212746.8, tmin=3.0701
- d=8.00 min @ (2.00, 2.00, 0.00) sse = 210298.1, tmin=4.1167
- d=4.00 min @ (-1.00, -1.00, -1.00) sse = 207762.6, tmin=5.1726
- d=2.00 min @ (0.00, 0.00, 0.50) sse = 207443.8, tmin=6.2316
- d=1.00 min @ (0.25, 0.25, 0.00) sse = 207327.3, tmin=7.2887
- d=0.50 min @ (-0.12, -0.12, -0.12) sse = 207317.1, tmin=8.3590
- tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 8.36 min
- curvature mean = -0.017, std = 0.828
- curvature mean = 0.007, std = 0.949
- curvature mean = -0.023, std = 0.837
- curvature mean = 0.002, std = 0.979
- curvature mean = -0.025, std = 0.839
- curvature mean = 0.000, std = 0.991
- 2 Reading smoothwm
- curvature mean = -0.043, std = 0.323
- curvature mean = 0.031, std = 0.242
- curvature mean = 0.082, std = 0.331
- curvature mean = 0.024, std = 0.304
- curvature mean = 0.057, std = 0.490
- curvature mean = 0.023, std = 0.332
- curvature mean = 0.034, std = 0.623
- curvature mean = 0.022, std = 0.344
- curvature mean = 0.013, std = 0.739
- MRISregister() return, current seed 0
- -01: dt=0.0000, 93 negative triangles
- 112: dt=0.9900, 93 negative triangles
- expanding nbhd size to 1
- 113: dt=0.9900, 125 negative triangles
- 114: dt=0.9900, 76 negative triangles
- 115: dt=0.9900, 85 negative triangles
- 116: dt=0.9900, 71 negative triangles
- 117: dt=0.9900, 72 negative triangles
- 118: dt=0.9900, 67 negative triangles
- 119: dt=0.9900, 63 negative triangles
- 120: dt=0.9900, 59 negative triangles
- 121: dt=0.9900, 49 negative triangles
- 122: dt=0.9900, 42 negative triangles
- 123: dt=0.9900, 37 negative triangles
- 124: dt=0.9900, 28 negative triangles
- 125: dt=0.9900, 20 negative triangles
- 126: dt=0.9900, 19 negative triangles
- 127: dt=0.9900, 17 negative triangles
- 128: dt=0.9900, 16 negative triangles
- 129: dt=0.9900, 13 negative triangles
- 130: dt=0.9900, 10 negative triangles
- 131: dt=0.9900, 9 negative triangles
- 132: dt=0.9900, 7 negative triangles
- 133: dt=0.9900, 3 negative triangles
- 134: dt=0.9900, 2 negative triangles
- 135: dt=0.9900, 3 negative triangles
- 136: dt=0.9900, 2 negative triangles
- 137: dt=0.9900, 1 negative triangles
- 138: dt=0.9900, 2 negative triangles
- 139: dt=0.9900, 1 negative triangles
- 140: dt=0.9900, 1 negative triangles
- 141: dt=0.9900, 1 negative triangles
- writing registered surface to ../surf/rh.sphere.reg...
- registration took 1.13 hours
- mris_register utimesec 4068.110553
- mris_register stimesec 3.546460
- mris_register ru_maxrss 247872
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 34559
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 9248
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 338087
- mris_register ru_nivcsw 214127
- FSRUNTIME@ mris_register 1.1309 hours 1 threads
- PIDs (26004 26007) completed and logs appended.
- #--------------------------------------------
- #@# Jacobian white lh Sun Oct 8 05:56:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# Jacobian white rh Sun Oct 8 05:56:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- Waiting for PID 29330 of (29330 29333) to complete...
- Waiting for PID 29333 of (29330 29333) 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 (29330 29333) completed and logs appended.
- #--------------------------------------------
- #@# AvgCurv lh Sun Oct 8 05:56:34 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 05:56:35 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 29374 of (29374 29377) to complete...
- Waiting for PID 29377 of (29374 29377) 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 (29374 29377) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc lh Sun Oct 8 05:56:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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 05:56:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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 29420 of (29420 29423) to complete...
- Waiting for PID 29423 of (29420 29423) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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...
- 1205 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3077 changed, 129630 examined...
- 001: 720 changed, 12784 examined...
- 002: 168 changed, 3967 examined...
- 003: 73 changed, 1000 examined...
- 004: 29 changed, 426 examined...
- 005: 11 changed, 179 examined...
- 006: 2 changed, 60 examined...
- 007: 3 changed, 11 examined...
- 008: 0 changed, 15 examined...
- 231 labels changed using aseg
- 000: 112 total segments, 72 labels (206 vertices) changed
- 001: 40 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 8 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 2259 vertices marked for relabeling...
- 2259 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 14 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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...
- 1004 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2584 changed, 129973 examined...
- 001: 611 changed, 11304 examined...
- 002: 147 changed, 3367 examined...
- 003: 38 changed, 878 examined...
- 004: 11 changed, 227 examined...
- 005: 2 changed, 73 examined...
- 006: 0 changed, 12 examined...
- 132 labels changed using aseg
- 000: 83 total segments, 42 labels (162 vertices) changed
- 001: 41 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 16 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 2038 vertices marked for relabeling...
- 2038 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 13 seconds.
- PIDs (29420 29423) completed and logs appended.
- #--------------------------------------------
- #@# Make Pial Surf lh Sun Oct 8 05:56:50 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050319 lh
- #--------------------------------------------
- #@# Make Pial Surf rh Sun Oct 8 05:56:50 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050319 rh
- Waiting for PID 29475 of (29475 29478) to complete...
- Waiting for PID 29478 of (29475 29478) to complete...
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050319 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-6.0.0/0050319/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- 15995 bright wm thresholded.
- 2713 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.orig...
- computing class statistics...
- border white: 245529 voxels (1.46%)
- border gray 293505 voxels (1.75%)
- WM (97.0): 97.4 +- 7.6 [70.0 --> 110.0]
- GM (76.0) : 75.0 +- 10.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 61.7 (was 70)
- setting MAX_BORDER_WHITE to 108.6 (was 105)
- setting MIN_BORDER_WHITE to 72.0 (was 85)
- setting MAX_CSF to 51.4 (was 40)
- setting MAX_GRAY to 93.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 61.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 41.1 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=101+-6.1, GM=72+-7.8
- mean inside = 93.6, mean outside = 78.6
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.26 (0.03-->8.37) (max @ vno 45364 --> 128344)
- face area 0.34 +- 0.16 (0.00-->6.87)
- mean absolute distance = 0.68 +- 0.86
- 3364 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 30 points - only 0.00% unknown
- deleting segment 3 with 190 points - only 0.00% unknown
- deleting segment 4 with 110 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- deleting segment 6 with 41 points - only 0.00% unknown
- mean border=81.7, 224 (223) missing vertices, mean dist 0.5 [0.8 (%13.2)->0.7 (%86.8))]
- %62 local maxima, %34 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 +- 0.27 (0.04-->8.38) (max @ vno 128344 --> 45364)
- face area 0.34 +- 0.17 (0.00-->6.98)
- mean absolute distance = 0.42 +- 0.61
- 4020 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2041415.4, rms=7.547
- 001: dt: 0.5000, sse=1170277.5, rms=4.672 (38.091%)
- 002: dt: 0.5000, sse=879020.7, rms=3.188 (31.768%)
- 003: dt: 0.5000, sse=797655.6, rms=2.641 (17.164%)
- 004: dt: 0.5000, sse=769666.5, rms=2.404 (8.981%)
- rms = 2.39, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.5000, sse=766911.4, rms=2.389 (0.605%)
- 006: dt: 0.2500, sse=707616.9, rms=1.691 (29.216%)
- 007: dt: 0.2500, sse=696376.1, rms=1.572 (7.063%)
- rms = 1.54, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=692669.1, rms=1.538 (2.159%)
- rms = 1.50, time step reduction 3 of 3 to 0.062...
- 009: dt: 0.1250, sse=690999.4, rms=1.500 (2.453%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 26 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 3 with 109 points - only 0.00% unknown
- deleting segment 4 with 71 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 5 with 3 points - only 0.00% unknown
- mean border=85.0, 98 (46) missing vertices, mean dist -0.3 [0.5 (%74.0)->0.3 (%26.0))]
- %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.08-->9.18) (max @ vno 128344 --> 45364)
- face area 0.36 +- 0.18 (0.00-->8.33)
- mean absolute distance = 0.30 +- 0.44
- 3416 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1196318.8, rms=4.584
- 010: dt: 0.5000, sse=877970.2, rms=2.829 (38.276%)
- 011: dt: 0.5000, sse=797352.1, rms=2.246 (20.623%)
- 012: dt: 0.5000, sse=782488.2, rms=2.099 (6.535%)
- rms = 2.13, time step reduction 1 of 3 to 0.250...
- 013: dt: 0.2500, sse=738892.9, rms=1.624 (22.623%)
- 014: dt: 0.2500, sse=721081.1, rms=1.368 (15.758%)
- 015: dt: 0.2500, sse=716717.4, rms=1.293 (5.471%)
- rms = 1.28, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=715426.4, rms=1.280 (1.017%)
- rms = 1.24, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=712660.4, rms=1.242 (2.978%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 26 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 3 with 4 points - only 0.00% unknown
- deleting segment 4 with 36 points - only 0.00% unknown
- deleting segment 6 with 113 points - only 0.00% unknown
- deleting segment 7 with 22 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 points - only 0.00% unknown
- mean border=86.9, 106 (32) missing vertices, mean dist -0.1 [0.3 (%67.7)->0.2 (%32.3))]
- %82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.26 (0.07-->9.46) (max @ vno 128344 --> 45364)
- face area 0.34 +- 0.17 (0.00-->8.30)
- mean absolute distance = 0.26 +- 0.38
- 3349 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=841328.8, rms=2.775
- 018: dt: 0.5000, sse=740630.8, rms=1.851 (33.298%)
- 019: dt: 0.5000, sse=731806.9, rms=1.798 (2.886%)
- rms = 1.88, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=698493.1, rms=1.361 (24.302%)
- 021: dt: 0.2500, sse=686123.7, rms=1.166 (14.332%)
- rms = 1.16, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=686797.3, rms=1.160 (0.494%)
- rms = 1.12, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=685618.4, rms=1.119 (3.535%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 26 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 2 with 7 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 3 with 4 points - only 0.00% unknown
- deleting segment 4 with 75 points - only 0.00% unknown
- deleting segment 5 with 105 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- deleting segment 7 with 7 points - only 0.00% unknown
- deleting segment 8 with 11 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- mean border=87.7, 135 (26) missing vertices, mean dist -0.1 [0.3 (%56.7)->0.2 (%43.3))]
- %85 local maxima, %10 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-6.0.0/0050319/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=703463.1, rms=1.522
- 024: dt: 0.5000, sse=686897.8, rms=1.294 (14.966%)
- rms = 1.51, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=672721.2, rms=1.011 (21.894%)
- rms = 0.98, time step reduction 2 of 3 to 0.125...
- 026: dt: 0.2500, sse=666681.2, rms=0.980 (3.066%)
- 027: dt: 0.1250, sse=666185.4, rms=0.911 (7.030%)
- rms = 0.89, time step reduction 3 of 3 to 0.062...
- 028: dt: 0.1250, sse=660058.2, rms=0.888 (2.527%)
- positioning took 0.6 minutes
- generating cortex label...
- 14 non-cortical segments detected
- only using segment with 6554 vertices
- erasing segment 1 (vno[0] = 38016)
- erasing segment 2 (vno[0] = 48740)
- erasing segment 3 (vno[0] = 58663)
- erasing segment 4 (vno[0] = 78877)
- erasing segment 5 (vno[0] = 79891)
- erasing segment 6 (vno[0] = 82361)
- erasing segment 7 (vno[0] = 82486)
- erasing segment 8 (vno[0] = 83597)
- erasing segment 9 (vno[0] = 86712)
- erasing segment 10 (vno[0] = 86788)
- erasing segment 11 (vno[0] = 89532)
- erasing segment 12 (vno[0] = 89556)
- erasing segment 13 (vno[0] = 89585)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.area
- vertex spacing 0.90 +- 0.27 (0.03-->9.61) (max @ vno 45364 --> 128344)
- face area 0.34 +- 0.17 (0.00-->8.36)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 10 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 4 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=60.0, 197 (197) missing vertices, mean dist 1.8 [0.0 (%0.0)->2.9 (%100.0))]
- %14 local maxima, %45 large gradients and %36 min vals, 405 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=20752014.0, rms=28.492
- 001: dt: 0.0500, sse=18668634.0, rms=26.977 (5.318%)
- 002: dt: 0.0500, sse=17164344.0, rms=25.827 (4.261%)
- 003: dt: 0.0500, sse=15997981.0, rms=24.899 (3.592%)
- 004: dt: 0.0500, sse=15043530.0, rms=24.113 (3.156%)
- 005: dt: 0.0500, sse=14229028.0, rms=23.422 (2.868%)
- 006: dt: 0.0500, sse=13516206.0, rms=22.799 (2.658%)
- 007: dt: 0.0500, sse=12878713.0, rms=22.228 (2.507%)
- 008: dt: 0.0500, sse=12300436.0, rms=21.696 (2.391%)
- 009: dt: 0.0500, sse=11769033.0, rms=21.196 (2.306%)
- 010: dt: 0.0500, sse=11277303.0, rms=20.722 (2.235%)
- positioning took 0.9 minutes
- mean border=59.8, 165 (111) missing vertices, mean dist 1.5 [0.1 (%0.0)->2.4 (%100.0))]
- %15 local maxima, %45 large gradients and %35 min vals, 374 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=12018514.0, rms=21.428
- 011: dt: 0.0500, sse=11555887.0, rms=20.987 (2.055%)
- 012: dt: 0.0500, sse=11123322.0, rms=20.567 (2.002%)
- 013: dt: 0.0500, sse=10717452.0, rms=20.165 (1.956%)
- 014: dt: 0.0500, sse=10335957.0, rms=19.779 (1.913%)
- 015: dt: 0.0500, sse=9977588.0, rms=19.410 (1.868%)
- 016: dt: 0.0500, sse=9641039.0, rms=19.056 (1.821%)
- 017: dt: 0.0500, sse=9323872.0, rms=18.717 (1.781%)
- 018: dt: 0.0500, sse=9025576.0, rms=18.392 (1.736%)
- 019: dt: 0.0500, sse=8744686.0, rms=18.081 (1.693%)
- 020: dt: 0.0500, sse=8480045.0, rms=17.782 (1.651%)
- positioning took 0.9 minutes
- mean border=59.6, 209 (97) missing vertices, mean dist 1.3 [0.1 (%1.0)->2.1 (%99.0))]
- %16 local maxima, %45 large gradients and %35 min vals, 343 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=8602577.0, rms=17.925
- 021: dt: 0.0500, sse=8345218.0, rms=17.632 (1.633%)
- 022: dt: 0.0500, sse=8104004.5, rms=17.353 (1.582%)
- 023: dt: 0.0500, sse=7875460.0, rms=17.085 (1.548%)
- 024: dt: 0.0500, sse=7660941.0, rms=16.829 (1.499%)
- 025: dt: 0.0500, sse=7459350.0, rms=16.584 (1.452%)
- 026: dt: 0.0500, sse=7269611.5, rms=16.351 (1.408%)
- 027: dt: 0.0500, sse=7089973.5, rms=16.126 (1.371%)
- 028: dt: 0.0500, sse=6918612.5, rms=15.910 (1.345%)
- 029: dt: 0.0500, sse=6754798.5, rms=15.699 (1.322%)
- 030: dt: 0.0500, sse=6598185.5, rms=15.495 (1.298%)
- positioning took 0.9 minutes
- mean border=59.5, 235 (89) missing vertices, mean dist 1.1 [0.1 (%8.7)->2.0 (%91.3))]
- %16 local maxima, %45 large gradients and %34 min vals, 331 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=6694926.0, rms=15.621
- 031: dt: 0.5000, sse=5601148.0, rms=14.129 (9.548%)
- 032: dt: 0.5000, sse=4831407.0, rms=12.970 (8.208%)
- 033: dt: 0.5000, sse=4229944.5, rms=11.986 (7.581%)
- 034: dt: 0.5000, sse=3750981.5, rms=11.136 (7.099%)
- 035: dt: 0.5000, sse=3345391.0, rms=10.363 (6.941%)
- 036: dt: 0.5000, sse=2985859.8, rms=9.622 (7.150%)
- 037: dt: 0.5000, sse=2651842.2, rms=8.884 (7.665%)
- 038: dt: 0.5000, sse=2365643.5, rms=8.196 (7.750%)
- 039: dt: 0.5000, sse=2111711.2, rms=7.537 (8.036%)
- 040: dt: 0.5000, sse=1917680.6, rms=6.989 (7.270%)
- 041: dt: 0.5000, sse=1758423.0, rms=6.510 (6.850%)
- 042: dt: 0.5000, sse=1654382.4, rms=6.172 (5.198%)
- 043: dt: 0.5000, sse=1571530.9, rms=5.894 (4.497%)
- 044: dt: 0.5000, sse=1526049.0, rms=5.732 (2.762%)
- 045: dt: 0.5000, sse=1487313.9, rms=5.596 (2.364%)
- 046: dt: 0.5000, sse=1472186.5, rms=5.536 (1.073%)
- 047: dt: 0.5000, sse=1450046.2, rms=5.458 (1.415%)
- rms = 5.43, time step reduction 1 of 3 to 0.250...
- 048: dt: 0.5000, sse=1443723.8, rms=5.429 (0.527%)
- 049: dt: 0.2500, sse=1335383.2, rms=4.967 (8.510%)
- 050: dt: 0.2500, sse=1308479.2, rms=4.853 (2.287%)
- rms = 4.85, time step reduction 2 of 3 to 0.125...
- 051: dt: 0.2500, sse=1307343.9, rms=4.846 (0.143%)
- 052: dt: 0.1250, sse=1284086.2, rms=4.743 (2.138%)
- rms = 4.72, time step reduction 3 of 3 to 0.062...
- 053: dt: 0.1250, sse=1278705.6, rms=4.719 (0.493%)
- positioning took 2.7 minutes
- mean border=58.1, 1909 (39) missing vertices, mean dist 0.2 [0.2 (%42.6)->0.6 (%57.4))]
- %31 local maxima, %33 large gradients and %30 min vals, 193 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=1628623.6, rms=5.249
- 054: dt: 0.5000, sse=1536695.4, rms=4.890 (6.840%)
- 055: dt: 0.5000, sse=1462368.1, rms=4.602 (5.896%)
- rms = 4.77, time step reduction 1 of 3 to 0.250...
- 056: dt: 0.2500, sse=1358919.2, rms=4.078 (11.376%)
- 057: dt: 0.2500, sse=1334776.0, rms=3.940 (3.395%)
- rms = 3.93, time step reduction 2 of 3 to 0.125...
- 058: dt: 0.2500, sse=1333391.0, rms=3.933 (0.180%)
- 059: dt: 0.1250, sse=1300321.9, rms=3.748 (4.697%)
- rms = 3.71, time step reduction 3 of 3 to 0.062...
- 060: dt: 0.1250, sse=1293416.6, rms=3.711 (0.986%)
- positioning took 1.1 minutes
- mean border=57.3, 2315 (33) missing vertices, mean dist 0.1 [0.2 (%43.2)->0.4 (%56.8))]
- %41 local maxima, %24 large gradients and %29 min vals, 231 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=1347598.9, rms=3.971
- rms = 4.40, time step reduction 1 of 3 to 0.250...
- 061: dt: 0.2500, sse=1313632.5, rms=3.787 (4.633%)
- 062: dt: 0.2500, sse=1302766.5, rms=3.732 (1.457%)
- rms = 3.77, time step reduction 2 of 3 to 0.125...
- rms = 3.70, time step reduction 3 of 3 to 0.062...
- 063: dt: 0.1250, sse=1296547.9, rms=3.695 (0.972%)
- positioning took 0.6 minutes
- mean border=56.8, 4722 (32) missing vertices, mean dist 0.1 [0.2 (%45.3)->0.3 (%54.7))]
- %44 local maxima, %20 large gradients and %28 min vals, 265 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-6.0.0/0050319/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1314668.4, rms=3.792
- rms = 4.14, time step reduction 1 of 3 to 0.250...
- 064: dt: 0.2500, sse=1291392.0, rms=3.663 (3.402%)
- 065: dt: 0.2500, sse=1275749.8, rms=3.593 (1.914%)
- rms = 3.62, time step reduction 2 of 3 to 0.125...
- rms = 3.55, time step reduction 3 of 3 to 0.062...
- 066: dt: 0.1250, sse=1269172.1, rms=3.553 (1.104%)
- positioning took 0.6 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.area.pial
- vertex spacing 1.05 +- 0.49 (0.05-->7.43) (max @ vno 76703 --> 75537)
- face area 0.43 +- 0.37 (0.00-->8.91)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 129630 vertices processed
- 25000 of 129630 vertices processed
- 50000 of 129630 vertices processed
- 75000 of 129630 vertices processed
- 100000 of 129630 vertices processed
- 125000 of 129630 vertices processed
- 0 of 129630 vertices processed
- 25000 of 129630 vertices processed
- 50000 of 129630 vertices processed
- 75000 of 129630 vertices processed
- 100000 of 129630 vertices processed
- 125000 of 129630 vertices processed
- thickness calculation complete, 497:2650 truncations.
- 27718 vertices at 0 distance
- 84257 vertices at 1 distance
- 77180 vertices at 2 distance
- 36940 vertices at 3 distance
- 14030 vertices at 4 distance
- 4720 vertices at 5 distance
- 1763 vertices at 6 distance
- 732 vertices at 7 distance
- 331 vertices at 8 distance
- 142 vertices at 9 distance
- 92 vertices at 10 distance
- 55 vertices at 11 distance
- 48 vertices at 12 distance
- 47 vertices at 13 distance
- 51 vertices at 14 distance
- 49 vertices at 15 distance
- 17 vertices at 16 distance
- 20 vertices at 17 distance
- 20 vertices at 18 distance
- 20 vertices at 19 distance
- 18 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.thickness
- positioning took 14.6 minutes
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050319 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-6.0.0/0050319/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- 15995 bright wm thresholded.
- 2713 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.orig...
- computing class statistics...
- border white: 245529 voxels (1.46%)
- border gray 293505 voxels (1.75%)
- WM (97.0): 97.4 +- 7.6 [70.0 --> 110.0]
- GM (76.0) : 75.0 +- 10.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 62.7 (was 70)
- setting MAX_BORDER_WHITE to 108.6 (was 105)
- setting MIN_BORDER_WHITE to 73.0 (was 85)
- setting MAX_CSF to 52.4 (was 40)
- setting MAX_GRAY to 93.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 62.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 42.1 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=101+-5.2, GM=73+-7.0
- mean inside = 93.7, mean outside = 79.1
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.26 (0.03-->5.03) (max @ vno 90233 --> 92287)
- face area 0.33 +- 0.16 (0.00-->5.92)
- mean absolute distance = 0.71 +- 0.91
- 3489 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 14 points - only 0.00% unknown
- deleting segment 3 with 226 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 115 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- mean border=82.3, 236 (235) missing vertices, mean dist 0.5 [0.9 (%13.5)->0.7 (%86.5))]
- %60 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.06-->5.18) (max @ vno 45174 --> 45162)
- face area 0.33 +- 0.17 (0.00-->5.16)
- mean absolute distance = 0.42 +- 0.64
- 4249 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1998796.2, rms=7.390
- 001: dt: 0.5000, sse=1171798.6, rms=4.638 (37.239%)
- 002: dt: 0.5000, sse=887042.1, rms=3.200 (31.008%)
- 003: dt: 0.5000, sse=802150.3, rms=2.648 (17.248%)
- 004: dt: 0.5000, sse=774749.5, rms=2.404 (9.195%)
- rms = 2.37, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.5000, sse=764637.2, rms=2.372 (1.335%)
- 006: dt: 0.2500, sse=713731.1, rms=1.722 (27.409%)
- 007: dt: 0.2500, sse=702974.9, rms=1.605 (6.822%)
- rms = 1.57, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=695184.6, rms=1.566 (2.378%)
- rms = 1.53, time step reduction 3 of 3 to 0.062...
- 009: dt: 0.1250, sse=692275.7, rms=1.532 (2.180%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 1 with 14 points - only 0.00% unknown
- deleting segment 2 with 217 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- deleting segment 5 with 44 points - only 0.00% unknown
- deleting segment 6 with 110 points - only 0.00% unknown
- mean border=85.5, 179 (62) missing vertices, mean dist -0.3 [0.5 (%73.0)->0.3 (%27.0))]
- %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.05-->5.43) (max @ vno 45174 --> 45162)
- face area 0.36 +- 0.18 (0.00-->5.89)
- mean absolute distance = 0.31 +- 0.45
- 3725 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1144686.5, rms=4.325
- 010: dt: 0.5000, sse=866281.1, rms=2.728 (36.933%)
- 011: dt: 0.5000, sse=797302.9, rms=2.197 (19.461%)
- 012: dt: 0.5000, sse=779960.9, rms=2.033 (7.460%)
- rms = 2.05, time step reduction 1 of 3 to 0.250...
- 013: dt: 0.2500, sse=742951.7, rms=1.605 (21.068%)
- 014: dt: 0.2500, sse=724300.8, rms=1.346 (16.124%)
- 015: dt: 0.2500, sse=723167.9, rms=1.264 (6.068%)
- rms = 1.24, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=720930.6, rms=1.243 (1.682%)
- rms = 1.21, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=717657.5, rms=1.214 (2.330%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 14 points - only 0.00% unknown
- deleting segment 1 with 217 points - only 0.00% unknown
- deleting segment 2 with 26 points - only 0.00% unknown
- deleting segment 3 with 8 points - only 0.00% unknown
- deleting segment 4 with 31 points - only 0.00% unknown
- deleting segment 5 with 105 points - only 0.00% unknown
- mean border=87.4, 189 (41) missing vertices, mean dist -0.2 [0.3 (%67.5)->0.2 (%32.5))]
- %81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.26 (0.09-->5.54) (max @ vno 45174 --> 45162)
- face area 0.34 +- 0.18 (0.00-->5.94)
- mean absolute distance = 0.26 +- 0.38
- 3440 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=853282.2, rms=2.820
- 018: dt: 0.5000, sse=744569.5, rms=1.812 (35.740%)
- 019: dt: 0.5000, sse=731750.6, rms=1.717 (5.229%)
- rms = 1.78, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=700146.9, rms=1.323 (22.981%)
- 021: dt: 0.2500, sse=690566.8, rms=1.141 (13.729%)
- rms = 1.13, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=687035.9, rms=1.126 (1.285%)
- rms = 1.10, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=684350.6, rms=1.101 (2.264%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 14 points - only 0.00% unknown
- deleting segment 1 with 191 points - only 0.00% unknown
- deleting segment 2 with 8 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- deleting segment 4 with 25 points - only 0.00% unknown
- deleting segment 5 with 105 points - only 0.00% unknown
- mean border=88.2, 196 (30) missing vertices, mean dist -0.0 [0.3 (%56.1)->0.2 (%43.9))]
- %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=698613.0, rms=1.487
- 024: dt: 0.5000, sse=687320.4, rms=1.209 (18.669%)
- rms = 1.45, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=667753.6, rms=0.968 (19.983%)
- rms = 0.93, time step reduction 2 of 3 to 0.125...
- 026: dt: 0.2500, sse=669621.5, rms=0.934 (3.456%)
- rms = 0.89, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=662853.5, rms=0.892 (4.533%)
- positioning took 0.5 minutes
- generating cortex label...
- 16 non-cortical segments detected
- only using segment with 6689 vertices
- erasing segment 1 (vno[0] = 52575)
- erasing segment 2 (vno[0] = 52631)
- erasing segment 3 (vno[0] = 66957)
- erasing segment 4 (vno[0] = 83747)
- erasing segment 5 (vno[0] = 84844)
- erasing segment 6 (vno[0] = 84856)
- erasing segment 7 (vno[0] = 85849)
- erasing segment 8 (vno[0] = 85899)
- erasing segment 9 (vno[0] = 88060)
- erasing segment 10 (vno[0] = 89054)
- erasing segment 11 (vno[0] = 89081)
- erasing segment 12 (vno[0] = 89129)
- erasing segment 13 (vno[0] = 93112)
- erasing segment 14 (vno[0] = 94747)
- erasing segment 15 (vno[0] = 94761)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.area
- vertex spacing 0.89 +- 0.27 (0.05-->5.60) (max @ vno 45162 --> 45174)
- face area 0.34 +- 0.17 (0.00-->6.02)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 19 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=60.8, 234 (234) missing vertices, mean dist 1.9 [3.8 (%0.0)->3.0 (%100.0))]
- %15 local maxima, %47 large gradients and %34 min vals, 435 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=20363060.0, rms=28.114
- 001: dt: 0.0500, sse=18349674.0, rms=26.641 (5.238%)
- 002: dt: 0.0500, sse=16900358.0, rms=25.528 (4.177%)
- 003: dt: 0.0500, sse=15777955.0, rms=24.632 (3.512%)
- 004: dt: 0.0500, sse=14859187.0, rms=23.873 (3.081%)
- 005: dt: 0.0500, sse=14076575.0, rms=23.207 (2.790%)
- 006: dt: 0.0500, sse=13391926.0, rms=22.608 (2.581%)
- 007: dt: 0.0500, sse=12779364.0, rms=22.058 (2.431%)
- 008: dt: 0.0500, sse=12223344.0, rms=21.547 (2.317%)
- 009: dt: 0.0500, sse=11712530.0, rms=21.066 (2.230%)
- 010: dt: 0.0500, sse=11239137.0, rms=20.611 (2.162%)
- positioning took 0.9 minutes
- mean border=60.6, 194 (131) missing vertices, mean dist 1.6 [0.7 (%0.0)->2.5 (%100.0))]
- %17 local maxima, %47 large gradients and %33 min vals, 408 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=12062802.0, rms=21.391
- 011: dt: 0.0500, sse=11616534.0, rms=20.969 (1.973%)
- 012: dt: 0.0500, sse=11198387.0, rms=20.566 (1.924%)
- 013: dt: 0.0500, sse=10805601.0, rms=20.179 (1.879%)
- 014: dt: 0.0500, sse=10436543.0, rms=19.809 (1.833%)
- 015: dt: 0.0500, sse=10089188.0, rms=19.455 (1.791%)
- 016: dt: 0.0500, sse=9761834.0, rms=19.114 (1.750%)
- 017: dt: 0.0500, sse=9453594.0, rms=18.788 (1.707%)
- 018: dt: 0.0500, sse=9163676.0, rms=18.476 (1.661%)
- 019: dt: 0.0500, sse=8890084.0, rms=18.176 (1.621%)
- 020: dt: 0.0500, sse=8631710.0, rms=17.889 (1.582%)
- positioning took 0.9 minutes
- mean border=60.4, 243 (110) missing vertices, mean dist 1.4 [0.1 (%0.9)->2.1 (%99.1))]
- %17 local maxima, %47 large gradients and %32 min vals, 383 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=8762809.0, rms=18.039
- 021: dt: 0.0500, sse=8511561.0, rms=17.758 (1.562%)
- 022: dt: 0.0500, sse=8275537.0, rms=17.489 (1.514%)
- 023: dt: 0.0500, sse=8051307.5, rms=17.229 (1.483%)
- 024: dt: 0.0500, sse=7840369.0, rms=16.982 (1.438%)
- 025: dt: 0.0500, sse=7641825.5, rms=16.745 (1.393%)
- 026: dt: 0.0500, sse=7454244.0, rms=16.518 (1.354%)
- 027: dt: 0.0500, sse=7275850.0, rms=16.300 (1.324%)
- 028: dt: 0.0500, sse=7105348.5, rms=16.088 (1.300%)
- 029: dt: 0.0500, sse=6941286.0, rms=15.881 (1.284%)
- 030: dt: 0.0500, sse=6784401.0, rms=15.681 (1.261%)
- positioning took 0.9 minutes
- mean border=60.3, 301 (102) missing vertices, mean dist 1.2 [0.1 (%8.8)->2.0 (%91.2))]
- %17 local maxima, %47 large gradients and %32 min vals, 351 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=6909570.5, rms=15.840
- 031: dt: 0.5000, sse=5789739.0, rms=14.348 (9.421%)
- 032: dt: 0.5000, sse=4977324.0, rms=13.153 (8.332%)
- 033: dt: 0.5000, sse=4326113.0, rms=12.111 (7.921%)
- 034: dt: 0.5000, sse=3811465.5, rms=11.212 (7.421%)
- 035: dt: 0.5000, sse=3368524.2, rms=10.379 (7.431%)
- 036: dt: 0.5000, sse=2994513.5, rms=9.615 (7.364%)
- 037: dt: 0.5000, sse=2647992.0, rms=8.854 (7.914%)
- 038: dt: 0.5000, sse=2360807.2, rms=8.165 (7.774%)
- 039: dt: 0.5000, sse=2113395.0, rms=7.528 (7.810%)
- 040: dt: 0.5000, sse=1922171.5, rms=6.991 (7.126%)
- 041: dt: 0.5000, sse=1772634.9, rms=6.546 (6.368%)
- 042: dt: 0.5000, sse=1667980.2, rms=6.212 (5.105%)
- 043: dt: 0.5000, sse=1589451.9, rms=5.953 (4.160%)
- 044: dt: 0.5000, sse=1539727.5, rms=5.779 (2.931%)
- 045: dt: 0.5000, sse=1499220.9, rms=5.638 (2.446%)
- 046: dt: 0.5000, sse=1472887.1, rms=5.540 (1.727%)
- 047: dt: 0.5000, sse=1447195.5, rms=5.448 (1.671%)
- rms = 5.40, time step reduction 1 of 3 to 0.250...
- 048: dt: 0.5000, sse=1435628.2, rms=5.401 (0.861%)
- 049: dt: 0.2500, sse=1325393.4, rms=4.930 (8.707%)
- 050: dt: 0.2500, sse=1296542.8, rms=4.809 (2.462%)
- rms = 4.79, time step reduction 2 of 3 to 0.125...
- 051: dt: 0.2500, sse=1293629.9, rms=4.794 (0.309%)
- 052: dt: 0.1250, sse=1273740.1, rms=4.705 (1.859%)
- rms = 4.69, time step reduction 3 of 3 to 0.062...
- 053: dt: 0.1250, sse=1269667.2, rms=4.687 (0.376%)
- positioning took 2.7 minutes
- mean border=58.9, 2027 (39) missing vertices, mean dist 0.2 [0.2 (%43.7)->0.6 (%56.3))]
- %33 local maxima, %35 large gradients and %27 min vals, 246 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=1592425.1, rms=5.124
- 054: dt: 0.5000, sse=1496038.5, rms=4.738 (7.522%)
- 055: dt: 0.5000, sse=1428920.5, rms=4.475 (5.564%)
- rms = 4.59, time step reduction 1 of 3 to 0.250...
- 056: dt: 0.2500, sse=1325394.8, rms=3.938 (11.989%)
- 057: dt: 0.2500, sse=1294328.9, rms=3.759 (4.562%)
- rms = 3.74, time step reduction 2 of 3 to 0.125...
- 058: dt: 0.2500, sse=1290203.0, rms=3.737 (0.576%)
- 059: dt: 0.1250, sse=1261435.2, rms=3.568 (4.525%)
- rms = 3.54, time step reduction 3 of 3 to 0.062...
- 060: dt: 0.1250, sse=1255868.0, rms=3.537 (0.857%)
- positioning took 1.1 minutes
- mean border=58.0, 2635 (32) missing vertices, mean dist 0.1 [0.2 (%43.6)->0.4 (%56.4))]
- %43 local maxima, %25 large gradients and %26 min vals, 283 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=1326422.4, rms=3.888
- rms = 4.21, time step reduction 1 of 3 to 0.250...
- 061: dt: 0.2500, sse=1287352.6, rms=3.673 (5.513%)
- 062: dt: 0.2500, sse=1270967.6, rms=3.586 (2.373%)
- rms = 3.58, time step reduction 2 of 3 to 0.125...
- 063: dt: 0.2500, sse=1268080.4, rms=3.580 (0.161%)
- 064: dt: 0.1250, sse=1247863.8, rms=3.459 (3.385%)
- rms = 3.43, time step reduction 3 of 3 to 0.062...
- 065: dt: 0.1250, sse=1241869.5, rms=3.427 (0.930%)
- positioning took 0.8 minutes
- mean border=57.4, 4622 (31) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.3 (%54.9))]
- %47 local maxima, %20 large gradients and %25 min vals, 265 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-6.0.0/0050319/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=1262930.1, rms=3.527
- rms = 3.83, time step reduction 1 of 3 to 0.250...
- 066: dt: 0.2500, sse=1244258.2, rms=3.416 (3.148%)
- rms = 3.37, time step reduction 2 of 3 to 0.125...
- 067: dt: 0.2500, sse=1234120.1, rms=3.371 (1.316%)
- 068: dt: 0.1250, sse=1223326.1, rms=3.302 (2.040%)
- rms = 3.27, time step reduction 3 of 3 to 0.062...
- 069: dt: 0.1250, sse=1216537.4, rms=3.266 (1.102%)
- positioning took 0.7 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.area.pial
- vertex spacing 1.04 +- 0.48 (0.08-->7.21) (max @ vno 45174 --> 45162)
- face area 0.43 +- 0.37 (0.00-->9.29)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 129973 vertices processed
- 25000 of 129973 vertices processed
- 50000 of 129973 vertices processed
- 75000 of 129973 vertices processed
- 100000 of 129973 vertices processed
- 125000 of 129973 vertices processed
- 0 of 129973 vertices processed
- 25000 of 129973 vertices processed
- 50000 of 129973 vertices processed
- 75000 of 129973 vertices processed
- 100000 of 129973 vertices processed
- 125000 of 129973 vertices processed
- thickness calculation complete, 487:2207 truncations.
- 28108 vertices at 0 distance
- 80841 vertices at 1 distance
- 77744 vertices at 2 distance
- 39550 vertices at 3 distance
- 15241 vertices at 4 distance
- 5065 vertices at 5 distance
- 1822 vertices at 6 distance
- 747 vertices at 7 distance
- 329 vertices at 8 distance
- 181 vertices at 9 distance
- 119 vertices at 10 distance
- 56 vertices at 11 distance
- 63 vertices at 12 distance
- 47 vertices at 13 distance
- 38 vertices at 14 distance
- 37 vertices at 15 distance
- 38 vertices at 16 distance
- 20 vertices at 17 distance
- 13 vertices at 18 distance
- 8 vertices at 19 distance
- 15 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.thickness
- positioning took 14.8 minutes
- PIDs (29475 29478) completed and logs appended.
- #--------------------------------------------
- #@# Surf Volume lh Sun Oct 8 06:11:41 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0050319 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/lh.cortex.label
- Total face volume 266734
- Total vertex volume 263906 (mask=0)
- #@# 0050319 lh 263906
-
- vertexvol Done
- #--------------------------------------------
- #@# Surf Volume rh Sun Oct 8 06:11:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0050319 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/rh.cortex.label
- Total face volume 266660
- Total vertex volume 263203 (mask=0)
- #@# 0050319 rh 263203
-
- vertexvol Done
- #--------------------------------------------
- #@# Cortical ribbon mask Sun Oct 8 06:11:47 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0050319
- 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 = 185
- writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/ribbon.mgz
- mris_volmask took 13.11 minutes
- writing ribbon files
- #-----------------------------------------
- #@# Parcellation Stats lh Sun Oct 8 06:24:53 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0050319 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 0050319 lh pial
- #-----------------------------------------
- #@# Parcellation Stats rh Sun Oct 8 06:24:53 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0050319 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 0050319 rh pial
- Waiting for PID 30690 of (30690 30693 30696 30699) to complete...
- Waiting for PID 30693 of (30690 30693 30696 30699) to complete...
- Waiting for PID 30696 of (30690 30693 30696 30699) to complete...
- Waiting for PID 30699 of (30690 30693 30696 30699) 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 0050319 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 266734
- Total vertex volume 263906 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 1381 978 2875 2.762 0.506 0.104 0.022 15 1.3 bankssts
- 906 570 2009 2.979 0.761 0.130 0.020 14 0.7 caudalanteriorcingulate
- 2944 2037 7060 3.022 0.698 0.121 0.024 30 2.7 caudalmiddlefrontal
- 2183 1417 2553 1.654 0.462 0.155 0.047 35 4.4 cuneus
- 668 445 1876 3.106 1.044 0.150 0.056 11 1.6 entorhinal
- 3893 2701 8572 2.680 0.726 0.135 0.033 52 5.3 fusiform
- 6628 4535 14624 2.785 0.755 0.123 0.029 81 7.3 inferiorparietal
- 5215 3541 11174 2.727 0.823 0.137 0.046 77 10.9 inferiortemporal
- 1342 861 2631 2.683 0.975 0.135 0.036 22 1.7 isthmuscingulate
- 7068 4538 11693 2.226 0.664 0.145 0.047 107 13.8 lateraloccipital
- 4557 2978 9252 2.782 0.801 0.130 0.041 79 8.2 lateralorbitofrontal
- 4334 2966 6565 2.040 0.589 0.152 0.048 65 8.9 lingual
- 3253 2263 6671 2.541 0.895 0.130 0.047 48 6.3 medialorbitofrontal
- 4441 3149 11494 2.856 0.664 0.138 0.035 69 6.8 middletemporal
- 1027 625 1737 2.389 0.785 0.087 0.024 7 1.0 parahippocampal
- 1801 1166 3663 2.841 0.794 0.109 0.022 14 1.6 paracentral
- 2092 1453 4823 2.766 0.588 0.120 0.031 29 2.5 parsopercularis
- 1221 845 3996 3.169 0.885 0.147 0.034 19 1.8 parsorbitalis
- 1668 1173 4108 2.819 0.740 0.127 0.026 21 1.8 parstriangularis
- 1817 1237 1831 1.617 0.481 0.135 0.035 19 2.7 pericalcarine
- 6816 4309 10932 2.251 0.782 0.103 0.027 63 7.6 postcentral
- 1688 1190 3641 2.892 0.784 0.151 0.034 25 2.5 posteriorcingulate
- 7296 4670 16097 3.014 0.634 0.108 0.024 64 7.3 precentral
- 5292 3640 11536 2.806 0.774 0.124 0.028 54 6.1 precuneus
- 1249 851 3050 3.074 0.770 0.140 0.045 24 2.2 rostralanteriorcingulate
- 8291 5797 21157 2.848 0.787 0.134 0.037 118 13.8 rostralmiddlefrontal
- 10006 6788 25845 3.162 0.731 0.120 0.029 107 11.7 superiorfrontal
- 7440 5107 12933 2.255 0.624 0.130 0.034 91 10.5 superiorparietal
- 5216 3685 13230 2.849 0.785 0.122 0.033 59 7.6 superiortemporal
- 5871 4061 13799 2.940 0.645 0.120 0.028 66 6.5 supramarginal
- 329 227 1426 3.687 0.586 0.195 0.080 11 1.1 frontalpole
- 585 415 2482 3.679 0.607 0.131 0.047 10 1.0 temporalpole
- 719 427 1077 2.299 0.588 0.102 0.038 8 0.9 transversetemporal
- 3245 2251 7442 3.050 0.973 0.120 0.036 31 4.9 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 0050319 lh pial
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 266734
- Total vertex volume 263906 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 1381 1110 2875 2.762 0.506 0.140 0.030 25 1.9 bankssts
- 906 782 2009 2.979 0.761 0.165 0.039 39 1.7 caudalanteriorcingulate
- 2944 2437 7060 3.022 0.698 0.135 0.030 53 3.9 caudalmiddlefrontal
- 2183 1765 2553 1.654 0.462 0.159 0.038 30 3.6 cuneus
- 668 781 1876 3.106 1.044 0.215 0.048 11 1.5 entorhinal
- 3893 3474 8572 2.680 0.726 0.163 0.041 64 7.6 fusiform
- 6628 5791 14624 2.785 0.755 0.146 0.033 82 9.8 inferiorparietal
- 5215 4544 11174 2.727 0.823 0.162 0.049 100 10.1 inferiortemporal
- 1342 1052 2631 2.683 0.975 0.164 0.052 37 3.1 isthmuscingulate
- 7068 5813 11693 2.226 0.664 0.146 0.037 121 11.7 lateraloccipital
- 4557 3619 9252 2.782 0.801 0.149 0.040 72 8.0 lateralorbitofrontal
- 4334 3627 6565 2.040 0.589 0.159 0.041 68 8.5 lingual
- 3253 2943 6671 2.541 0.895 0.160 0.040 64 5.6 medialorbitofrontal
- 4441 4737 11494 2.856 0.664 0.181 0.038 66 8.9 middletemporal
- 1027 880 1737 2.389 0.785 0.140 0.033 14 1.5 parahippocampal
- 1801 1388 3663 2.841 0.794 0.130 0.028 23 2.2 paracentral
- 2092 2014 4823 2.766 0.588 0.158 0.034 24 3.2 parsopercularis
- 1221 1536 3996 3.169 0.885 0.199 0.042 14 2.5 parsorbitalis
- 1668 1611 4108 2.819 0.740 0.162 0.036 18 2.6 parstriangularis
- 1817 1054 1831 1.617 0.481 0.119 0.035 30 2.5 pericalcarine
- 6816 5385 10932 2.251 0.782 0.122 0.027 77 8.5 postcentral
- 1688 1334 3641 2.892 0.784 0.162 0.039 38 3.0 posteriorcingulate
- 7296 5803 16097 3.014 0.634 0.117 0.025 67 7.9 precentral
- 5292 4436 11536 2.806 0.774 0.152 0.035 76 8.5 precuneus
- 1249 1106 3050 3.074 0.770 0.166 0.042 29 2.4 rostralanteriorcingulate
- 8291 8598 21157 2.848 0.787 0.181 0.040 157 16.1 rostralmiddlefrontal
- 10006 9055 25845 3.162 0.731 0.148 0.032 122 14.9 superiorfrontal
- 7440 6273 12933 2.255 0.624 0.142 0.032 95 10.7 superiorparietal
- 5216 5095 13230 2.849 0.785 0.162 0.038 68 9.3 superiortemporal
- 5871 5108 13799 2.940 0.645 0.138 0.029 64 7.3 supramarginal
- 329 526 1426 3.687 0.586 0.288 0.062 6 1.1 frontalpole
- 585 889 2482 3.679 0.607 0.246 0.054 10 1.4 temporalpole
- 719 564 1077 2.299 0.588 0.136 0.046 8 1.5 transversetemporal
- 3245 2329 7442 3.050 0.973 0.164 0.051 67 7.9 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 0050319 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 266660
- Total vertex volume 263203 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 1318 948 3096 3.114 0.594 0.119 0.021 12 1.3 bankssts
- 977 641 2088 3.192 0.623 0.131 0.020 13 0.8 caudalanteriorcingulate
- 2736 1846 5951 2.920 0.597 0.113 0.025 25 2.8 caudalmiddlefrontal
- 2086 1429 3123 1.919 0.555 0.131 0.035 25 3.1 cuneus
- 443 294 1327 3.084 0.996 0.155 0.075 10 1.5 entorhinal
- 4539 2987 8957 2.610 0.776 0.134 0.047 74 9.3 fusiform
- 8371 5752 18631 2.722 0.749 0.136 0.036 121 12.1 inferiorparietal
- 4148 2866 11021 3.098 0.767 0.140 0.045 63 7.7 inferiortemporal
- 1082 676 2315 2.923 0.952 0.127 0.032 15 1.1 isthmuscingulate
- 7578 4976 13456 2.334 0.705 0.149 0.044 129 13.4 lateraloccipital
- 4486 2961 9214 2.739 0.717 0.134 0.051 70 10.2 lateralorbitofrontal
- 4285 2808 6264 2.097 0.638 0.144 0.047 61 8.5 lingual
- 2761 1932 6445 2.727 0.809 0.123 0.037 36 4.3 medialorbitofrontal
- 4231 3080 11885 2.984 0.677 0.144 0.039 66 7.0 middletemporal
- 1016 594 1520 2.219 0.655 0.088 0.025 11 0.9 parahippocampal
- 2220 1482 4470 2.692 0.789 0.101 0.018 15 1.7 paracentral
- 1682 1138 3456 2.744 0.637 0.113 0.023 16 1.7 parsopercularis
- 1363 930 4288 3.188 0.909 0.130 0.042 22 2.3 parsorbitalis
- 2055 1376 4405 2.744 0.740 0.105 0.033 23 2.4 parstriangularis
- 2016 1465 2203 1.669 0.543 0.144 0.038 23 2.8 pericalcarine
- 6340 4018 10416 2.261 0.785 0.106 0.029 60 7.1 postcentral
- 1485 1032 3363 3.031 0.691 0.141 0.036 20 2.2 posteriorcingulate
- 7142 4643 14814 2.803 0.641 0.112 0.030 88 9.6 precentral
- 5826 3962 11535 2.625 0.728 0.122 0.028 67 6.6 precuneus
- 914 663 2576 3.122 0.762 0.162 0.048 17 1.9 rostralanteriorcingulate
- 9539 6537 24076 2.866 0.731 0.140 0.043 151 17.1 rostralmiddlefrontal
- 9244 6279 24045 3.132 0.746 0.124 0.031 108 11.3 superiorfrontal
- 7105 4490 11718 2.297 0.625 0.118 0.032 89 9.6 superiorparietal
- 5271 3515 12122 2.860 0.777 0.120 0.038 69 8.0 superiortemporal
- 5204 3589 10924 2.626 0.673 0.123 0.034 65 7.2 supramarginal
- 604 420 2024 2.855 1.006 0.192 0.084 17 2.4 frontalpole
- 640 437 2454 3.262 0.899 0.138 0.053 9 1.5 temporalpole
- 579 340 972 2.390 0.547 0.147 0.060 13 1.5 transversetemporal
- 3810 2518 8033 3.049 1.047 0.120 0.040 45 5.9 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 0050319 rh pial
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 266660
- Total vertex volume 263203 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 1318 1007 3096 3.114 0.594 0.137 0.030 15 1.8 bankssts
- 977 707 2088 3.192 0.623 0.163 0.047 68 1.6 caudalanteriorcingulate
- 2736 2164 5951 2.920 0.597 0.132 0.032 36 3.8 caudalmiddlefrontal
- 2086 1863 3123 1.919 0.555 0.158 0.035 24 3.5 cuneus
- 443 525 1327 3.084 0.996 0.211 0.074 17 1.7 entorhinal
- 4539 3618 8957 2.610 0.776 0.150 0.043 75 8.7 fusiform
- 8371 7644 18631 2.722 0.749 0.168 0.037 118 14.6 inferiorparietal
- 4148 4080 11021 3.098 0.767 0.174 0.042 57 8.0 inferiortemporal
- 1082 894 2315 2.923 0.952 0.181 0.056 43 2.2 isthmuscingulate
- 7578 6300 13456 2.334 0.705 0.148 0.037 101 13.0 lateraloccipital
- 4486 3598 9214 2.739 0.717 0.159 0.045 95 9.7 lateralorbitofrontal
- 4285 3437 6264 2.097 0.638 0.153 0.041 56 8.3 lingual
- 2761 2707 6445 2.727 0.809 0.174 0.044 52 6.1 medialorbitofrontal
- 4231 4599 11885 2.984 0.677 0.184 0.041 60 8.3 middletemporal
- 1016 788 1520 2.219 0.655 0.127 0.033 10 1.6 parahippocampal
- 2220 1741 4470 2.692 0.789 0.118 0.024 18 2.3 paracentral
- 1682 1373 3456 2.744 0.637 0.136 0.029 26 2.2 parsopercularis
- 1363 1691 4288 3.188 0.909 0.198 0.040 15 2.5 parsorbitalis
- 2055 1689 4405 2.744 0.740 0.134 0.033 24 2.6 parstriangularis
- 2016 1328 2203 1.669 0.543 0.136 0.038 34 3.1 pericalcarine
- 6340 5028 10416 2.261 0.785 0.122 0.024 62 7.0 postcentral
- 1485 1207 3363 3.031 0.691 0.170 0.047 43 3.1 posteriorcingulate
- 7142 5606 14814 2.803 0.641 0.116 0.024 69 7.5 precentral
- 5826 4716 11535 2.625 0.728 0.146 0.032 76 8.6 precuneus
- 914 974 2576 3.122 0.762 0.202 0.056 16 2.3 rostralanteriorcingulate
- 9539 9845 24076 2.866 0.731 0.184 0.043 208 21.1 rostralmiddlefrontal
- 9244 8627 24045 3.132 0.746 0.156 0.037 154 15.4 superiorfrontal
- 7105 5534 11718 2.297 0.625 0.131 0.030 91 9.4 superiorparietal
- 5271 4748 12122 2.860 0.777 0.157 0.039 72 9.7 superiortemporal
- 5204 4486 10924 2.626 0.673 0.145 0.034 59 7.6 supramarginal
- 604 896 2024 2.855 1.006 0.272 0.063 12 2.2 frontalpole
- 640 941 2454 3.262 0.899 0.230 0.049 9 1.5 temporalpole
- 579 433 972 2.390 0.547 0.137 0.041 5 1.0 transversetemporal
- 3810 2542 8033 3.049 1.047 0.147 0.046 80 7.3 insula
- PIDs (30690 30693 30696 30699) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 2 lh Sun Oct 8 06:26:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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 06:26:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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 30779 of (30779 30782) to complete...
- Waiting for PID 30782 of (30779 30782) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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...
- 17 labels changed using aseg
- relabeling using gibbs priors...
- 000: 8174 changed, 129630 examined...
- 001: 1968 changed, 32158 examined...
- 002: 553 changed, 10329 examined...
- 003: 208 changed, 3184 examined...
- 004: 100 changed, 1200 examined...
- 005: 44 changed, 574 examined...
- 006: 30 changed, 265 examined...
- 007: 13 changed, 168 examined...
- 008: 8 changed, 77 examined...
- 009: 4 changed, 46 examined...
- 010: 1 changed, 20 examined...
- 011: 1 changed, 6 examined...
- 012: 0 changed, 8 examined...
- 2 labels changed using aseg
- 000: 231 total segments, 150 labels (1931 vertices) changed
- 001: 85 total segments, 5 labels (7 vertices) changed
- 002: 80 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 41 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1517 vertices marked for relabeling...
- 1517 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 0 minutes and 18 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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...
- 2 labels changed using aseg
- relabeling using gibbs priors...
- 000: 8476 changed, 129973 examined...
- 001: 1938 changed, 33173 examined...
- 002: 571 changed, 10408 examined...
- 003: 245 changed, 3269 examined...
- 004: 118 changed, 1394 examined...
- 005: 48 changed, 623 examined...
- 006: 22 changed, 277 examined...
- 007: 14 changed, 119 examined...
- 008: 12 changed, 76 examined...
- 009: 2 changed, 63 examined...
- 010: 1 changed, 10 examined...
- 011: 0 changed, 7 examined...
- 3 labels changed using aseg
- 000: 242 total segments, 158 labels (1910 vertices) changed
- 001: 93 total segments, 10 labels (45 vertices) changed
- 002: 83 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 32 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1507 vertices marked for relabeling...
- 1507 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 0 minutes and 18 seconds.
- PIDs (30779 30782) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Sun Oct 8 06:26:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0050319 lh white
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Sun Oct 8 06:26:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0050319 rh white
- Waiting for PID 30835 of (30835 30838) to complete...
- Waiting for PID 30838 of (30835 30838) 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 0050319 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 266734
- Total vertex volume 263906 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 1168 804 3013 2.909 0.891 0.148 0.051 17 2.6 G&S_frontomargin
- 1292 865 2767 2.546 0.728 0.151 0.053 21 2.9 G&S_occipital_inf
- 1448 842 2853 2.727 0.743 0.113 0.026 13 1.6 G&S_paracentral
- 1370 926 3622 3.289 0.585 0.131 0.034 16 1.7 G&S_subcentral
- 728 569 2710 2.987 0.926 0.220 0.081 23 3.4 G&S_transv_frontopol
- 2051 1451 4627 2.876 0.766 0.117 0.033 22 2.7 G&S_cingul-Ant
- 1312 896 2743 2.976 0.681 0.115 0.020 12 1.0 G&S_cingul-Mid-Ant
- 1331 937 2900 2.908 0.618 0.129 0.030 15 1.8 G&S_cingul-Mid-Post
- 555 365 1627 3.184 0.940 0.162 0.046 12 1.0 G_cingul-Post-dorsal
- 285 172 655 2.900 0.782 0.146 0.044 5 0.4 G_cingul-Post-ventral
- 2076 1310 2514 1.675 0.472 0.161 0.055 39 4.8 G_cuneus
- 1213 803 3369 2.841 0.647 0.127 0.042 24 2.0 G_front_inf-Opercular
- 419 284 1570 3.400 0.597 0.168 0.042 10 0.8 G_front_inf-Orbital
- 953 639 2912 3.086 0.655 0.135 0.034 16 1.2 G_front_inf-Triangul
- 4600 3087 13595 3.062 0.821 0.145 0.042 82 8.3 G_front_middle
- 6631 4381 20337 3.368 0.712 0.132 0.035 95 9.2 G_front_sup
- 519 342 1255 2.941 0.944 0.137 0.056 9 1.2 G_Ins_lg&S_cent_ins
- 680 444 2540 3.813 0.898 0.121 0.044 9 1.2 G_insular_short
- 2438 1558 5832 2.619 0.699 0.156 0.050 47 5.1 G_occipital_middle
- 1398 858 2161 2.033 0.595 0.142 0.040 22 2.0 G_occipital_sup
- 1692 1112 4105 2.753 0.826 0.150 0.047 28 3.4 G_oc-temp_lat-fusifor
- 3327 2258 5108 1.938 0.591 0.165 0.058 59 8.3 G_oc-temp_med-Lingual
- 1486 947 3358 2.798 0.969 0.118 0.039 17 2.3 G_oc-temp_med-Parahip
- 2787 1822 8019 2.953 0.853 0.149 0.052 56 6.2 G_orbital
- 2380 1583 7344 3.243 0.777 0.136 0.040 40 3.4 G_pariet_inf-Angular
- 2983 2016 7961 2.984 0.634 0.139 0.037 50 4.7 G_pariet_inf-Supramar
- 2967 2000 6094 2.431 0.668 0.140 0.043 44 5.3 G_parietal_sup
- 2708 1578 4524 2.191 0.701 0.109 0.037 36 4.3 G_postcentral
- 2770 1627 7560 3.331 0.566 0.117 0.029 33 3.4 G_precentral
- 2616 1776 7027 2.880 0.782 0.148 0.042 42 4.7 G_precuneus
- 1104 797 2909 2.630 0.828 0.147 0.048 23 2.4 G_rectus
- 1220 798 2197 2.692 1.059 0.147 0.081 22 4.1 G_subcallosal
- 531 310 953 2.454 0.648 0.131 0.061 11 1.2 G_temp_sup-G_T_transv
- 1889 1331 6641 3.173 0.817 0.160 0.053 37 4.1 G_temp_sup-Lateral
- 461 388 1679 3.241 0.938 0.110 0.026 3 0.4 G_temp_sup-Plan_polar
- 823 578 1865 2.769 0.493 0.086 0.017 3 0.6 G_temp_sup-Plan_tempo
- 2615 1776 6179 2.617 0.896 0.158 0.065 54 7.8 G_temporal_inf
- 2754 1948 7801 2.845 0.710 0.157 0.042 56 5.2 G_temporal_middle
- 194 143 385 2.830 0.533 0.120 0.014 1 0.1 Lat_Fis-ant-Horizont
- 378 275 593 2.597 0.405 0.089 0.014 1 0.2 Lat_Fis-ant-Vertical
- 1128 786 1531 2.286 0.674 0.088 0.018 5 0.6 Lat_Fis-post
- 1802 1156 2728 2.001 0.644 0.157 0.056 31 4.2 Pole_occipital
- 1350 973 5077 3.264 0.826 0.151 0.044 26 2.7 Pole_temporal
- 2020 1388 2590 2.044 0.907 0.119 0.027 15 2.3 S_calcarine
- 3254 2190 4416 2.246 0.763 0.090 0.016 14 2.1 S_central
- 1025 739 1657 2.512 0.857 0.111 0.017 6 0.8 S_cingul-Marginalis
- 613 418 1136 3.342 0.787 0.092 0.018 2 0.5 S_circular_insula_ant
- 1299 897 1874 2.387 0.676 0.085 0.014 4 0.8 S_circular_insula_inf
- 1476 1060 2403 2.689 0.685 0.105 0.020 6 1.3 S_circular_insula_sup
- 897 602 1598 2.928 0.755 0.115 0.023 8 0.8 S_collat_transv_ant
- 504 357 587 2.077 0.434 0.131 0.023 4 0.6 S_collat_transv_post
- 2108 1495 4127 2.573 0.666 0.111 0.022 18 1.9 S_front_inf
- 1104 821 1931 2.666 0.479 0.110 0.017 6 0.8 S_front_middle
- 3001 2087 5870 2.890 0.621 0.096 0.016 16 1.9 S_front_sup
- 324 228 590 2.947 0.368 0.090 0.013 1 0.2 S_interm_prim-Jensen
- 2567 1823 4300 2.399 0.652 0.114 0.023 20 2.4 S_intrapariet&P_trans
- 961 638 1255 2.274 0.566 0.125 0.030 9 1.1 S_oc_middle&Lunatus
- 1396 1003 1732 1.895 0.447 0.126 0.027 14 1.7 S_oc_sup&transversal
- 707 487 960 2.260 0.542 0.113 0.023 5 0.5 S_occipital_ant
- 887 615 1274 2.488 0.500 0.104 0.014 6 0.6 S_oc-temp_lat
- 1778 1268 2697 2.318 0.542 0.117 0.026 14 1.8 S_oc-temp_med&Lingual
- 476 351 690 2.139 0.559 0.117 0.021 3 0.4 S_orbital_lateral
- 847 591 1154 2.391 0.615 0.121 0.021 7 0.7 S_orbital_med-olfact
- 1704 1126 3169 2.789 0.824 0.118 0.029 30 2.3 S_orbital-H_Shaped
- 2230 1511 3181 2.238 0.745 0.115 0.023 17 1.9 S_parieto_occipital
- 1327 840 1560 2.470 0.784 0.132 0.022 22 1.0 S_pericallosal
- 3431 2374 5444 2.450 0.639 0.096 0.016 19 2.2 S_postcentral
- 1577 1102 2815 2.840 0.521 0.093 0.016 8 0.9 S_precentral-inf-part
- 1206 876 2160 2.785 0.545 0.118 0.024 9 1.2 S_precentral-sup-part
- 648 464 1136 2.621 0.884 0.118 0.020 5 0.5 S_suborbital
- 928 656 1636 2.916 0.668 0.111 0.021 5 0.8 S_subparietal
- 1935 1359 4134 2.924 0.646 0.106 0.018 14 1.4 S_temporal_inf
- 5397 3735 9932 2.772 0.558 0.105 0.022 44 4.8 S_temporal_sup
- 447 299 658 2.524 0.521 0.105 0.017 3 0.3 S_temporal_transverse
- mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050319 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 266660
- Total vertex volume 263203 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 1225 887 2989 2.521 0.724 0.186 0.074 32 4.3 G&S_frontomargin
- 1161 775 2498 2.522 0.757 0.154 0.051 20 2.2 G&S_occipital_inf
- 1592 948 3079 2.587 0.749 0.116 0.030 17 2.1 G&S_paracentral
- 1318 892 3192 2.987 0.698 0.137 0.041 21 2.0 G&S_subcentral
- 1160 849 3818 2.971 0.756 0.174 0.065 29 3.2 G&S_transv_frontopol
- 2639 1866 5900 2.965 0.773 0.116 0.027 23 3.0 G&S_cingul-Ant
- 1193 826 2621 3.002 0.643 0.119 0.020 11 0.9 G&S_cingul-Mid-Ant
- 1291 886 2673 2.852 0.635 0.125 0.031 13 1.6 G&S_cingul-Mid-Post
- 378 242 1232 3.426 0.724 0.136 0.040 6 0.5 G_cingul-Post-dorsal
- 295 177 921 3.244 0.897 0.141 0.042 5 0.4 G_cingul-Post-ventral
- 2006 1348 3048 1.891 0.576 0.138 0.038 27 3.2 G_cuneus
- 1163 774 2872 2.633 0.731 0.129 0.035 19 1.8 G_front_inf-Opercular
- 425 264 1064 2.759 0.767 0.124 0.053 6 0.9 G_front_inf-Orbital
- 775 497 2206 3.124 0.810 0.123 0.048 12 1.3 G_front_inf-Triangul
- 4780 3077 14274 3.159 0.692 0.138 0.041 78 7.8 G_front_middle
- 6650 4427 20123 3.349 0.692 0.136 0.040 105 10.8 G_front_sup
- 475 323 1430 3.739 0.895 0.116 0.035 5 0.6 G_Ins_lg&S_cent_ins
- 718 446 2545 3.899 0.880 0.131 0.055 12 1.3 G_insular_short
- 2535 1683 6976 2.852 0.721 0.150 0.045 50 4.2 G_occipital_middle
- 1736 1040 2991 2.215 0.664 0.125 0.038 30 2.7 G_occipital_sup
- 2056 1266 4393 2.683 0.874 0.150 0.061 41 5.1 G_oc-temp_lat-fusifor
- 2792 1800 4293 2.069 0.632 0.160 0.058 50 6.8 G_oc-temp_med-Lingual
- 1165 702 2572 2.589 0.904 0.120 0.049 21 2.3 G_oc-temp_med-Parahip
- 3346 2142 9829 3.041 0.831 0.155 0.071 81 10.8 G_orbital
- 2727 1809 7110 2.827 0.870 0.151 0.051 55 5.9 G_pariet_inf-Angular
- 2833 1910 7352 2.865 0.673 0.140 0.045 51 5.2 G_pariet_inf-Supramar
- 2132 1215 4303 2.530 0.633 0.123 0.047 42 4.4 G_parietal_sup
- 2365 1321 4391 2.398 0.717 0.112 0.038 28 3.4 G_postcentral
- 2776 1619 7191 3.130 0.512 0.117 0.042 54 5.2 G_precentral
- 2565 1703 6217 2.717 0.692 0.143 0.041 46 4.2 G_precuneus
- 828 593 2248 2.540 0.632 0.148 0.056 14 1.9 G_rectus
- 649 409 990 2.406 1.009 0.112 0.040 9 1.0 G_subcallosal
- 395 229 799 2.544 0.733 0.150 0.067 11 1.1 G_temp_sup-G_T_transv
- 2061 1364 6212 3.188 0.747 0.157 0.055 47 4.5 G_temp_sup-Lateral
- 1298 850 2143 2.454 0.859 0.114 0.050 18 2.6 G_temp_sup-Plan_polar
- 624 420 1260 2.577 0.642 0.089 0.026 6 0.7 G_temp_sup-Plan_tempo
- 2421 1623 7546 3.213 0.853 0.156 0.061 49 6.1 G_temporal_inf
- 2399 1780 8504 3.191 0.682 0.161 0.050 49 4.9 G_temporal_middle
- 298 213 547 2.599 0.447 0.056 0.006 0 0.1 Lat_Fis-ant-Horizont
- 238 179 427 2.757 0.451 0.103 0.014 1 0.1 Lat_Fis-ant-Vertical
- 1310 927 1865 2.388 0.696 0.104 0.019 7 1.1 Lat_Fis-post
- 3789 2441 5077 1.948 0.596 0.152 0.045 63 7.2 Pole_occipital
- 1558 1109 5663 3.189 0.819 0.167 0.069 37 5.4 Pole_temporal
- 1877 1350 2532 2.219 0.946 0.128 0.029 17 1.9 S_calcarine
- 3262 2270 4240 2.100 0.774 0.090 0.016 13 2.1 S_central
- 1285 921 2063 2.235 0.711 0.094 0.015 6 0.7 S_cingul-Marginalis
- 746 515 1430 3.118 0.821 0.108 0.034 5 1.1 S_circular_insula_ant
- 1030 668 1405 2.532 0.711 0.083 0.016 4 0.7 S_circular_insula_inf
- 1153 807 1983 2.895 0.613 0.114 0.022 7 1.1 S_circular_insula_sup
- 802 576 1620 2.896 0.639 0.132 0.025 10 0.8 S_collat_transv_ant
- 585 399 655 1.902 0.478 0.133 0.034 5 0.8 S_collat_transv_post
- 2059 1427 3847 2.730 0.602 0.112 0.024 18 2.0 S_front_inf
- 2197 1556 3835 2.537 0.591 0.108 0.021 15 1.9 S_front_middle
- 2087 1492 3821 2.631 0.625 0.108 0.021 12 1.7 S_front_sup
- 380 275 617 2.449 0.602 0.094 0.013 1 0.3 S_interm_prim-Jensen
- 2731 1910 3944 2.240 0.583 0.111 0.019 18 2.1 S_intrapariet&P_trans
- 950 684 1318 2.317 0.444 0.147 0.035 10 1.4 S_oc_middle&Lunatus
- 1374 957 1877 2.170 0.446 0.116 0.023 10 1.2 S_oc_sup&transversal
- 703 502 1170 2.606 0.437 0.108 0.017 5 0.6 S_occipital_ant
- 1116 795 1803 2.683 0.458 0.097 0.012 5 0.7 S_oc-temp_lat
- 1904 1281 2531 2.166 0.510 0.096 0.019 12 1.5 S_oc-temp_med&Lingual
- 515 388 785 2.260 0.663 0.112 0.023 3 0.5 S_orbital_lateral
- 712 513 1003 2.300 0.674 0.099 0.015 4 0.4 S_orbital_med-olfact
- 1681 1140 2973 2.656 0.601 0.124 0.032 17 2.1 S_orbital-H_Shaped
- 2613 1773 3868 2.315 0.683 0.113 0.024 22 2.6 S_parieto_occipital
- 1257 799 1552 2.838 0.817 0.135 0.024 21 1.0 S_pericallosal
- 2384 1648 3372 2.253 0.549 0.098 0.017 13 1.6 S_postcentral
- 1488 1043 2610 2.730 0.502 0.108 0.018 11 1.2 S_precentral-inf-part
- 997 736 1627 2.581 0.522 0.096 0.013 5 0.6 S_precentral-sup-part
- 184 141 525 3.328 0.820 0.131 0.016 1 0.1 S_suborbital
- 974 658 1660 2.721 0.777 0.101 0.014 5 0.6 S_subparietal
- 962 699 1673 2.876 0.516 0.130 0.027 7 1.1 S_temporal_inf
- 6541 4602 12876 2.821 0.626 0.119 0.025 60 6.7 S_temporal_sup
- 395 250 604 2.822 0.670 0.129 0.037 4 0.6 S_temporal_transverse
- PIDs (30835 30838) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 3 lh Sun Oct 8 06:27:08 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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 06:27:08 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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 30910 of (30910 30913) to complete...
- Waiting for PID 30913 of (30910 30913) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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...
- 1288 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2031 changed, 129630 examined...
- 001: 458 changed, 9194 examined...
- 002: 145 changed, 2564 examined...
- 003: 51 changed, 848 examined...
- 004: 20 changed, 279 examined...
- 005: 13 changed, 134 examined...
- 006: 14 changed, 86 examined...
- 007: 11 changed, 78 examined...
- 008: 11 changed, 58 examined...
- 009: 12 changed, 61 examined...
- 010: 8 changed, 49 examined...
- 011: 2 changed, 44 examined...
- 012: 1 changed, 19 examined...
- 013: 1 changed, 8 examined...
- 014: 1 changed, 8 examined...
- 015: 0 changed, 6 examined...
- 190 labels changed using aseg
- 000: 52 total segments, 19 labels (219 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, 6 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1066 vertices marked for relabeling...
- 1066 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas.annot...
- classification took 0 minutes and 15 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050319 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...
- 1163 labels changed using aseg
- relabeling using gibbs priors...
- 000: 1924 changed, 129973 examined...
- 001: 449 changed, 8749 examined...
- 002: 109 changed, 2470 examined...
- 003: 42 changed, 680 examined...
- 004: 18 changed, 239 examined...
- 005: 8 changed, 97 examined...
- 006: 6 changed, 46 examined...
- 007: 2 changed, 38 examined...
- 008: 1 changed, 14 examined...
- 009: 0 changed, 9 examined...
- 147 labels changed using aseg
- 000: 52 total segments, 19 labels (118 vertices) changed
- 001: 34 total segments, 1 labels (4 vertices) changed
- 002: 33 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...
- 1197 vertices marked for relabeling...
- 1197 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas.annot...
- classification took 0 minutes and 15 seconds.
- PIDs (30910 30913) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Sun Oct 8 06:27:22 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0050319 lh white
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Sun Oct 8 06:27:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0050319 rh white
- Waiting for PID 30963 of (30963 30966) to complete...
- Waiting for PID 30966 of (30963 30966) 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 0050319 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 266734
- Total vertex volume 263906 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 1470 958 3087 2.958 0.716 0.127 0.022 19 1.3 caudalanteriorcingulate
- 3227 2218 7740 3.015 0.703 0.121 0.024 32 3.1 caudalmiddlefrontal
- 3045 1979 3770 1.760 0.542 0.146 0.044 45 5.5 cuneus
- 680 449 1764 3.043 0.958 0.146 0.056 11 1.6 entorhinal
- 3574 2469 7434 2.634 0.697 0.135 0.035 47 5.1 fusiform
- 6651 4552 14727 2.800 0.758 0.125 0.030 83 7.4 inferiorparietal
- 5143 3504 12016 2.780 0.881 0.140 0.047 82 10.8 inferiortemporal
- 1320 857 2608 2.701 0.968 0.138 0.037 22 1.7 isthmuscingulate
- 7185 4622 11879 2.226 0.666 0.145 0.046 109 13.9 lateraloccipital
- 5236 3437 11195 2.782 0.830 0.142 0.053 100 12.2 lateralorbitofrontal
- 4440 3046 6721 2.034 0.589 0.153 0.048 67 9.1 lingual
- 2473 1718 5508 2.615 0.884 0.130 0.042 39 4.4 medialorbitofrontal
- 5930 4190 14531 2.835 0.637 0.129 0.031 82 8.2 middletemporal
- 1117 679 1841 2.369 0.783 0.088 0.024 8 1.1 parahippocampal
- 2055 1332 4369 2.909 0.800 0.106 0.021 16 1.8 paracentral
- 1941 1350 4422 2.754 0.601 0.119 0.032 27 2.4 parsopercularis
- 1105 771 2972 3.061 0.780 0.138 0.028 15 1.2 parsorbitalis
- 2064 1451 4719 2.684 0.735 0.118 0.024 23 2.0 parstriangularis
- 1811 1232 1825 1.625 0.489 0.135 0.034 19 2.6 pericalcarine
- 7694 4906 12479 2.263 0.780 0.107 0.029 75 9.2 postcentral
- 1848 1301 3932 2.858 0.785 0.145 0.033 26 2.6 posteriorcingulate
- 7152 4592 15675 3.015 0.622 0.108 0.024 62 7.0 precentral
- 5148 3541 11505 2.820 0.753 0.127 0.030 56 6.6 precuneus
- 1920 1287 4306 2.984 0.868 0.135 0.042 32 3.2 rostralanteriorcingulate
- 6052 4230 15698 2.852 0.801 0.134 0.035 85 9.6 rostralmiddlefrontal
- 11048 7573 29708 3.151 0.741 0.125 0.032 131 14.4 superiorfrontal
- 5692 3946 10117 2.311 0.621 0.125 0.030 64 6.9 superiorparietal
- 6583 4688 17111 2.908 0.785 0.122 0.033 76 9.3 superiortemporal
- 5499 3782 12780 2.899 0.677 0.121 0.029 62 6.4 supramarginal
- 733 435 1087 2.292 0.579 0.102 0.037 8 0.9 transversetemporal
- 2670 1819 6379 3.108 0.979 0.107 0.031 24 3.4 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 0050319 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 266660
- Total vertex volume 263203 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 1163 757 2459 3.140 0.628 0.129 0.021 16 0.9 caudalanteriorcingulate
- 2872 1945 6243 2.921 0.602 0.116 0.026 26 3.0 caudalmiddlefrontal
- 2588 1764 3760 1.881 0.553 0.126 0.032 30 3.5 cuneus
- 475 303 1371 3.043 0.972 0.151 0.072 13 1.5 entorhinal
- 4213 2769 7746 2.545 0.751 0.131 0.042 59 7.3 fusiform
- 8390 5768 18428 2.712 0.749 0.135 0.035 119 12.2 inferiorparietal
- 4491 3104 12528 3.132 0.768 0.142 0.051 77 9.8 inferiortemporal
- 1124 698 2370 2.928 0.952 0.126 0.031 15 1.2 isthmuscingulate
- 7687 5025 13322 2.308 0.690 0.149 0.044 130 13.5 lateraloccipital
- 5484 3630 11591 2.669 0.744 0.146 0.058 102 14.1 lateralorbitofrontal
- 4205 2742 6124 2.089 0.615 0.144 0.048 61 8.5 lingual
- 2430 1696 6152 2.694 0.900 0.130 0.045 40 4.3 medialorbitofrontal
- 5126 3721 13629 2.985 0.644 0.141 0.036 75 7.9 middletemporal
- 990 595 1538 2.235 0.668 0.087 0.025 8 0.9 parahippocampal
- 2368 1571 4846 2.710 0.787 0.102 0.019 17 1.9 paracentral
- 1887 1292 3952 2.767 0.645 0.113 0.024 18 1.8 parsopercularis
- 1116 762 3051 3.107 0.863 0.125 0.038 15 1.8 parsorbitalis
- 2095 1415 4423 2.686 0.758 0.111 0.034 25 2.7 parstriangularis
- 1988 1450 2172 1.666 0.537 0.142 0.038 22 2.8 pericalcarine
- 6885 4377 11624 2.296 0.785 0.108 0.029 68 7.5 postcentral
- 1487 1031 3330 3.013 0.706 0.141 0.037 20 2.2 posteriorcingulate
- 6964 4509 14380 2.802 0.643 0.114 0.031 88 9.6 precentral
- 6075 4103 12074 2.635 0.711 0.123 0.029 71 7.1 precuneus
- 1232 872 3071 3.047 0.826 0.146 0.042 20 2.2 rostralanteriorcingulate
- 7072 4770 18294 2.943 0.725 0.135 0.041 107 12.0 rostralmiddlefrontal
- 11934 8173 30474 3.039 0.779 0.126 0.034 150 16.0 superiorfrontal
- 5682 3583 9350 2.302 0.625 0.117 0.033 73 8.0 superiorparietal
- 6862 4617 16841 2.913 0.800 0.122 0.038 88 10.5 superiortemporal
- 4888 3385 10294 2.613 0.677 0.123 0.034 60 6.8 supramarginal
- 568 338 970 2.422 0.569 0.150 0.060 13 1.5 transversetemporal
- 2743 1862 6797 3.411 0.872 0.115 0.034 25 3.7 insula
- PIDs (30963 30966) completed and logs appended.
- #-----------------------------------------
- #@# WM/GM Contrast lh Sun Oct 8 06:28:00 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- pctsurfcon --s 0050319 --lh-only
- #-----------------------------------------
- #@# WM/GM Contrast rh Sun Oct 8 06:28:00 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts
- pctsurfcon --s 0050319 --rh-only
- Waiting for PID 31027 of (31027 31039) to complete...
- Waiting for PID 31039 of (31027 31039) to complete...
- pctsurfcon --s 0050319 --lh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts/pctsurfcon.log
- Sun Oct 8 06:28:00 CEST 2017
- setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
- cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-623 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-6.0.0/0050319/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31027/lh.wm.mgh --regheader 0050319 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00003;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 = 63972
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31027/lh.wm.mgh
- Dim: 129630 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31027/lh.gm.mgh --projfrac 0.3 --regheader 0050319 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00003;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 = 77471
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31027/lh.gm.mgh
- Dim: 129630 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31027/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31027/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/surf/lh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.w-g.pct.mgh --annot 0050319 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/surf/lh.w-g.pct.mgh --annot 0050319 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-623
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/surf/lh.w-g.pct.mgh
- Vertex Area is 0.674846 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 0050319 --rh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/scripts/pctsurfcon.log
- Sun Oct 8 06:28:00 CEST 2017
- setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0
- cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-623 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-6.0.0/0050319/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31039/rh.wm.mgh --regheader 0050319 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00003;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 = 63485
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31039/rh.wm.mgh
- Dim: 129973 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31039/rh.gm.mgh --projfrac 0.3 --regheader 0050319 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 0.00000;
- 0.00000 0.00000 1.00000 0.00003;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 = 77695
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31039/rh.gm.mgh
- Dim: 129973 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31039/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/tmp.pctsurfcon.31039/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/surf/rh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.w-g.pct.mgh --annot 0050319 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/surf/rh.w-g.pct.mgh --annot 0050319 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-623
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/surf/rh.w-g.pct.mgh
- Vertex Area is 0.670553 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 (31027 31039) completed and logs appended.
- #-----------------------------------------
- #@# Relabel Hypointensities Sun Oct 8 06:28:06 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri
- mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
- reading input surface ../surf/lh.white...
- relabeling lh hypointensities...
- 1994 voxels changed to hypointensity...
- reading input surface ../surf/rh.white...
- relabeling rh hypointensities...
- 2523 voxels changed to hypointensity...
- 4315 hypointense voxels neighboring cortex changed
- #-----------------------------------------
- #@# AParc-to-ASeg aparc Sun Oct 8 06:28:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319
- mri_aparc2aseg --s 0050319 --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 06:28:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319
- mri_aparc2aseg --s 0050319 --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 06:28:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319
- mri_aparc2aseg --s 0050319 --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 31201 of (31201 31204 31207) to complete...
- Waiting for PID 31204 of (31201 31204 31207) to complete...
- Waiting for PID 31207 of (31201 31204 31207) to complete...
- mri_aparc2aseg --s 0050319 --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 0050319
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/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-6.0.0/0050319/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 6.88
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 104
- rescaling Left_Cerebral_Cortex from 61 --> 68
- rescaling Left_Lateral_Ventricle from 13 --> 23
- rescaling Left_Inf_Lat_Vent from 34 --> 37
- rescaling Left_Cerebellum_White_Matter from 86 --> 85
- rescaling Left_Cerebellum_Cortex from 60 --> 65
- rescaling Left_Thalamus from 94 --> 101
- rescaling Left_Thalamus_Proper from 84 --> 86
- rescaling Left_Caudate from 75 --> 73
- rescaling Left_Putamen from 80 --> 77
- rescaling Left_Pallidum from 98 --> 92
- rescaling Third_Ventricle from 25 --> 33
- rescaling Fourth_Ventricle from 22 --> 15
- rescaling Brain_Stem from 81 --> 89
- rescaling Left_Hippocampus from 57 --> 66
- rescaling Left_Amygdala from 56 --> 73
- rescaling CSF from 32 --> 48
- rescaling Left_Accumbens_area from 62 --> 67
- rescaling Left_VentralDC from 87 --> 89
- rescaling Right_Cerebral_White_Matter from 105 --> 104
- rescaling Right_Cerebral_Cortex from 58 --> 69
- rescaling Right_Lateral_Ventricle from 13 --> 23
- rescaling Right_Inf_Lat_Vent from 25 --> 27
- rescaling Right_Cerebellum_White_Matter from 87 --> 80
- rescaling Right_Cerebellum_Cortex from 59 --> 66
- rescaling Right_Thalamus_Proper from 85 --> 82
- rescaling Right_Caudate from 62 --> 72
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 90
- rescaling Right_Hippocampus from 53 --> 65
- rescaling Right_Amygdala from 55 --> 70
- rescaling Right_Accumbens_area from 65 --> 70
- rescaling Right_VentralDC from 86 --> 94
- rescaling Fifth_Ventricle from 40 --> 41
- rescaling WM_hypointensities from 78 --> 76
- rescaling non_WM_hypointensities from 40 --> 55
- 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 = 522936
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 187 changed.
- pass 2: 9 changed.
- pass 3: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/aparc+aseg.mgz
- mri_aparc2aseg --s 0050319 --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 0050319
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/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-6.0.0/0050319/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 6.88
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 104
- rescaling Left_Cerebral_Cortex from 61 --> 68
- rescaling Left_Lateral_Ventricle from 13 --> 23
- rescaling Left_Inf_Lat_Vent from 34 --> 37
- rescaling Left_Cerebellum_White_Matter from 86 --> 85
- rescaling Left_Cerebellum_Cortex from 60 --> 65
- rescaling Left_Thalamus from 94 --> 101
- rescaling Left_Thalamus_Proper from 84 --> 86
- rescaling Left_Caudate from 75 --> 73
- rescaling Left_Putamen from 80 --> 77
- rescaling Left_Pallidum from 98 --> 92
- rescaling Third_Ventricle from 25 --> 33
- rescaling Fourth_Ventricle from 22 --> 15
- rescaling Brain_Stem from 81 --> 89
- rescaling Left_Hippocampus from 57 --> 66
- rescaling Left_Amygdala from 56 --> 73
- rescaling CSF from 32 --> 48
- rescaling Left_Accumbens_area from 62 --> 67
- rescaling Left_VentralDC from 87 --> 89
- rescaling Right_Cerebral_White_Matter from 105 --> 104
- rescaling Right_Cerebral_Cortex from 58 --> 69
- rescaling Right_Lateral_Ventricle from 13 --> 23
- rescaling Right_Inf_Lat_Vent from 25 --> 27
- rescaling Right_Cerebellum_White_Matter from 87 --> 80
- rescaling Right_Cerebellum_Cortex from 59 --> 66
- rescaling Right_Thalamus_Proper from 85 --> 82
- rescaling Right_Caudate from 62 --> 72
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 90
- rescaling Right_Hippocampus from 53 --> 65
- rescaling Right_Amygdala from 55 --> 70
- rescaling Right_Accumbens_area from 65 --> 70
- rescaling Right_VentralDC from 86 --> 94
- rescaling Fifth_Ventricle from 40 --> 41
- rescaling WM_hypointensities from 78 --> 76
- rescaling non_WM_hypointensities from 40 --> 55
- 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 = 522981
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 187 changed.
- pass 2: 9 changed.
- pass 3: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/aparc.a2009s+aseg.mgz
- mri_aparc2aseg --s 0050319 --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 0050319
- outvol mri/aparc.DKTatlas+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/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-6.0.0/0050319/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 6.88
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 104
- rescaling Left_Cerebral_Cortex from 61 --> 68
- rescaling Left_Lateral_Ventricle from 13 --> 23
- rescaling Left_Inf_Lat_Vent from 34 --> 37
- rescaling Left_Cerebellum_White_Matter from 86 --> 85
- rescaling Left_Cerebellum_Cortex from 60 --> 65
- rescaling Left_Thalamus from 94 --> 101
- rescaling Left_Thalamus_Proper from 84 --> 86
- rescaling Left_Caudate from 75 --> 73
- rescaling Left_Putamen from 80 --> 77
- rescaling Left_Pallidum from 98 --> 92
- rescaling Third_Ventricle from 25 --> 33
- rescaling Fourth_Ventricle from 22 --> 15
- rescaling Brain_Stem from 81 --> 89
- rescaling Left_Hippocampus from 57 --> 66
- rescaling Left_Amygdala from 56 --> 73
- rescaling CSF from 32 --> 48
- rescaling Left_Accumbens_area from 62 --> 67
- rescaling Left_VentralDC from 87 --> 89
- rescaling Right_Cerebral_White_Matter from 105 --> 104
- rescaling Right_Cerebral_Cortex from 58 --> 69
- rescaling Right_Lateral_Ventricle from 13 --> 23
- rescaling Right_Inf_Lat_Vent from 25 --> 27
- rescaling Right_Cerebellum_White_Matter from 87 --> 80
- rescaling Right_Cerebellum_Cortex from 59 --> 66
- rescaling Right_Thalamus_Proper from 85 --> 82
- rescaling Right_Caudate from 62 --> 72
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 90
- rescaling Right_Hippocampus from 53 --> 65
- rescaling Right_Amygdala from 55 --> 70
- rescaling Right_Accumbens_area from 65 --> 70
- rescaling Right_VentralDC from 86 --> 94
- rescaling Fifth_Ventricle from 40 --> 41
- rescaling WM_hypointensities from 78 --> 76
- rescaling non_WM_hypointensities from 40 --> 55
- 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 = 522981
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 187 changed.
- pass 2: 9 changed.
- pass 3: 0 changed.
- nchanged = 0
- Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
- PIDs (31201 31204 31207) completed and logs appended.
- #-----------------------------------------
- #@# APas-to-ASeg Sun Oct 8 06:35:15 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri
- apas2aseg --i aparc+aseg.mgz --o aseg.mgz
- Sun Oct 8 06:35:15 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-6.0.0/0050319/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-623 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-6.0.0/0050319/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-623
- 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 06:35:15 CEST 2017
- Ended at Sun Oct 8 06:35:21 CEST 2017
- Apas2aseg-Run-Time-Sec 6
-
- apas2aseg Done
- #--------------------------------------------
- #@# ASeg Stats Sun Oct 8 06:35:21 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319
- 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 0050319
- $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 0050319
- sysname Linux
- hostname tars-623
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1542732 mm^3 (det: 1.262763 )
- Computing euler number
- orig.nofix lheno = -164, rheno = -136
- orig.nofix lhholes = 83, rhholes = 69
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 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 06:37:14 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319
- mri_aparc2aseg --s 0050319 --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 0050319
- 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-6.0.0/0050319/mri/aparc+aseg.mgz
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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-6.0.0/0050319/mri/ribbon.mgz
- Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/ribbon.mgz
- Ripping vertices labeled as unkown
- Ripped 7148 vertices from left hemi
- Ripped 6877 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-6.0.0/0050319/mri/aseg.mgz
- Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 = 930695
- Used brute-force search on 40 voxels
- Fixing Parahip LH WM
- Found 16 clusters
- 0 k 1.000000
- 1 k 2.000000
- 2 k 1.000000
- 3 k 2.000000
- 4 k 1005.000000
- 5 k 183.000000
- 6 k 2.000000
- 7 k 1.000000
- 8 k 1.000000
- 9 k 1.000000
- 10 k 2.000000
- 11 k 1.000000
- 12 k 1.000000
- 13 k 1.000000
- 14 k 1.000000
- 15 k 15.000000
- Fixing Parahip RH WM
- Found 9 clusters
- 0 k 6.000000
- 1 k 4.000000
- 2 k 1.000000
- 3 k 2.000000
- 4 k 2.000000
- 5 k 1.000000
- 6 k 8.000000
- 7 k 1062.000000
- 8 k 6.000000
- 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 0050319 --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 0050319 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname tars-623
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1542732 mm^3 (det: 1.262763 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 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-6.0.0/0050319/label
- #--------------------------------------------
- #@# BA_exvivo Labels lh Sun Oct 8 06:46:09 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 0050319 --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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 32040 of (32040 32046 32052 32057 32062) to complete...
- Waiting for PID 32046 of (32040 32046 32052 32057 32062) to complete...
- Waiting for PID 32052 of (32040 32046 32052 32057 32062) to complete...
- Waiting for PID 32057 of (32040 32046 32052 32057 32062) to complete...
- Waiting for PID 32062 of (32040 32046 32052 32057 32062) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 407
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.label 4536
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 715
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.label 8624
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 186
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.label 4263
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 472
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.label 6455
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 296
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.label 6080
- mri_label2label: Done
- PIDs (32040 32046 32052 32057 32062) 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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 32142 of (32142 32148 32154 32159) to complete...
- Waiting for PID 32148 of (32142 32148 32154 32159) to complete...
- Waiting for PID 32154 of (32142 32148 32154 32159) to complete...
- Waiting for PID 32159 of (32142 32148 32154 32159) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 190
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.label 4260
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 812
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.label 14401
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 283
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.label 4464
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 553
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.label 3975
- mri_label2label: Done
- PIDs (32142 32148 32154 32159) 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 0050319 --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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 32229 of (32229 32235 32241 32247 32253) to complete...
- Waiting for PID 32235 of (32229 32235 32241 32247 32253) to complete...
- Waiting for PID 32241 of (32229 32235 32241 32247 32253) to complete...
- Waiting for PID 32247 of (32229 32235 32241 32247 32253) to complete...
- Waiting for PID 32253 of (32229 32235 32241 32247 32253) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 1126
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.label 5767
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 2507
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.label 10621
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 286
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.label 2304
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 165
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.label 1455
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 65
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.label 1264
- mri_label2label: Done
- PIDs (32229 32235 32241 32247 32253) 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 0050319 --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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 32311 of (32311 32317 32323 32329 32335) to complete...
- Waiting for PID 32317 of (32311 32317 32323 32329 32335) to complete...
- Waiting for PID 32323 of (32311 32317 32323 32329 32335) to complete...
- Waiting for PID 32329 of (32311 32317 32323 32329 32335) to complete...
- Waiting for PID 32335 of (32311 32317 32323 32329 32335) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 126
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.thresh.label 1140
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 168
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.thresh.label 2260
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 54
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.thresh.label 1558
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 153
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.thresh.label 2149
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 111
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.thresh.label 2430
- mri_label2label: Done
- PIDs (32311 32317 32323 32329 32335) 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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 32392 of (32392 32398 32404 32409) to complete...
- Waiting for PID 32398 of (32392 32398 32404 32409) to complete...
- Waiting for PID 32404 of (32392 32398 32404 32409) to complete...
- Waiting for PID 32409 of (32392 32398 32404 32409) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 68
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.thresh.label 1617
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 390
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.thresh.label 7425
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 118
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.thresh.label 2030
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 159
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.thresh.label 1310
- mri_label2label: Done
- PIDs (32392 32398 32404 32409) 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 0050319 --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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 32457 of (32457 32463 32469 32474 32481) to complete...
- Waiting for PID 32463 of (32457 32463 32469 32474 32481) to complete...
- Waiting for PID 32469 of (32457 32463 32469 32474 32481) to complete...
- Waiting for PID 32474 of (32457 32463 32469 32474 32481) to complete...
- Waiting for PID 32481 of (32457 32463 32469 32474 32481) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 808
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.thresh.label 4213
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 1103
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.thresh.label 4437
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 68
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.thresh.label 581
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 96
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.thresh.label 566
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129630
- Number of reverse mapping hits = 32
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.thresh.label 482
- mri_label2label: Done
- PIDs (32457 32463 32469 32474 32481) completed and logs appended.
- mris_label2annot --s 0050319 --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-6.0.0/0050319/label
- cmdline mris_label2annot --s 0050319 --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-623
- machine x86_64
- user ntraut
- subject 0050319
- 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-6.0.0/0050319/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 90117 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/lh.BA_exvivo.annot
- mris_label2annot --s 0050319 --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-6.0.0/0050319/label
- cmdline mris_label2annot --s 0050319 --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-623
- machine x86_64
- user ntraut
- subject 0050319
- 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-6.0.0/0050319/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 106615 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0050319 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 266734
- Total vertex volume 263906 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 1263 699 2205 2.356 0.754 0.126 0.044 16 2.5 BA1_exvivo
- 4455 2969 7574 2.432 0.629 0.103 0.021 34 3.9 BA2_exvivo
- 1117 744 1225 2.068 0.442 0.106 0.022 7 0.9 BA3a_exvivo
- 2454 1595 3691 1.972 0.799 0.105 0.028 29 2.8 BA3b_exvivo
- 1449 817 3385 3.237 0.497 0.099 0.023 13 1.3 BA4a_exvivo
- 1296 809 2505 3.096 0.540 0.089 0.019 7 1.1 BA4p_exvivo
- 8451 5585 21955 3.175 0.734 0.119 0.027 86 9.2 BA6_exvivo
- 2074 1428 4865 2.854 0.582 0.119 0.033 30 2.5 BA44_exvivo
- 2745 1956 6623 2.707 0.745 0.124 0.027 33 3.2 BA45_exvivo
- 3233 2187 3754 1.649 0.487 0.142 0.046 41 6.6 V1_exvivo
- 7846 5111 11622 2.041 0.665 0.155 0.050 126 16.0 V2_exvivo
- 1835 1229 3808 2.562 0.658 0.132 0.033 27 2.1 MT_exvivo
- 693 453 1500 2.609 0.880 0.150 0.057 12 1.9 perirhinal_exvivo
- 602 401 1832 3.171 1.070 0.090 0.025 4 0.4 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 0050319 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 266734
- Total vertex volume 263906 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 818 433 1369 2.282 0.628 0.136 0.048 11 2.0 BA1_exvivo
- 1735 1160 2904 2.291 0.520 0.083 0.015 8 1.0 BA2_exvivo
- 937 616 958 2.009 0.399 0.111 0.022 6 0.8 BA3a_exvivo
- 1514 1023 1649 1.551 0.410 0.081 0.014 7 0.9 BA3b_exvivo
- 1479 814 3237 3.232 0.474 0.089 0.020 11 1.3 BA4a_exvivo
- 1062 695 2059 3.059 0.528 0.099 0.020 7 0.9 BA4p_exvivo
- 4705 3033 12095 3.272 0.676 0.120 0.029 50 5.6 BA6_exvivo
- 1256 892 3112 2.800 0.597 0.120 0.035 20 1.6 BA44_exvivo
- 1027 704 2715 2.914 0.760 0.125 0.025 12 1.0 BA45_exvivo
- 3414 2341 4091 1.657 0.484 0.145 0.048 45 7.5 V1_exvivo
- 3878 2505 5325 1.968 0.616 0.162 0.050 65 8.0 V2_exvivo
- 465 319 1083 2.527 0.637 0.141 0.027 7 0.5 MT_exvivo
- 384 244 752 2.429 0.885 0.129 0.048 6 0.7 perirhinal_exvivo
- 341 220 886 3.200 1.043 0.093 0.037 2 0.5 entorhinal_exvivo
- #--------------------------------------------
- #@# BA_exvivo Labels rh Sun Oct 8 06:49:14 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 0050319 --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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 32601 of (32601 32607 32613 32618 32623) to complete...
- Waiting for PID 32607 of (32601 32607 32613 32618 32623) to complete...
- Waiting for PID 32613 of (32601 32607 32613 32618 32623) to complete...
- Waiting for PID 32618 of (32601 32607 32613 32618 32623) to complete...
- Waiting for PID 32623 of (32601 32607 32613 32618 32623) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 444
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.label 4406
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 504
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.label 7191
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 186
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.label 4166
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 393
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.label 4915
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 318
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.label 6065
- mri_label2label: Done
- PIDs (32601 32607 32613 32618 32623) 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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 32676 of (32676 32682 32688 32694) to complete...
- Waiting for PID 32682 of (32676 32682 32688 32694) to complete...
- Waiting for PID 32688 of (32676 32682 32688 32694) to complete...
- Waiting for PID 32694 of (32676 32682 32688 32694) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 234
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.label 4707
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 700
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.label 12956
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 600
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.label 7512
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 903
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.label 6258
- mri_label2label: Done
- PIDs (32676 32682 32688 32694) 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 0050319 --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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 32744 of (32744 32750 32756 32761 32766) to complete...
- Waiting for PID 32750 of (32744 32750 32756 32761 32766) to complete...
- Waiting for PID 32756 of (32744 32750 32756 32761 32766) to complete...
- Waiting for PID 32761 of (32744 32750 32756 32761 32766) to complete...
- Waiting for PID 32766 of (32744 32750 32756 32761 32766) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 1361
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.label 6088
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 2575
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.label 10591
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 466
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.label 2398
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 159
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.label 1197
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 90
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.label 842
- mri_label2label: Done
- PIDs (32744 32750 32756 32761 32766) 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 0050319 --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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 378 of (378 384 390 395 401) to complete...
- Waiting for PID 384 of (378 384 390 395 401) to complete...
- Waiting for PID 390 of (378 384 390 395 401) to complete...
- Waiting for PID 395 of (378 384 390 395 401) to complete...
- Waiting for PID 401 of (378 384 390 395 401) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 114
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.thresh.label 990
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 143
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.thresh.label 2831
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 72
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.thresh.label 1770
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 129
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.thresh.label 2312
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 108
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.thresh.label 1496
- mri_label2label: Done
- PIDs (378 384 390 395 401) 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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 456 of (456 462 468 474) to complete...
- Waiting for PID 462 of (456 462 468 474) to complete...
- Waiting for PID 468 of (456 462 468 474) to complete...
- Waiting for PID 474 of (456 462 468 474) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 72
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.thresh.label 1561
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 333
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.thresh.label 7292
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 89
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.thresh.label 1101
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 136
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.thresh.label 1314
- mri_label2label: Done
- PIDs (456 462 468 474) 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 0050319 --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 0050319 --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 0050319 --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 0050319 --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 0050319 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 520 of (520 526 532 535 543) to complete...
- Waiting for PID 526 of (520 526 532 535 543) to complete...
- Waiting for PID 532 of (520 526 532 535 543) to complete...
- Waiting for PID 535 of (520 526 532 535 543) to complete...
- Waiting for PID 543 of (520 526 532 535 543) 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 917
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.thresh.label 4149
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 1243
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.thresh.label 4680
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 100
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.thresh.label 368
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 137
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.thresh.label 831
- 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 0050319 --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 = 0050319
- 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-6.0.0/0050319/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 129973
- Number of reverse mapping hits = 37
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.thresh.label 328
- mri_label2label: Done
- PIDs (520 526 532 535 543) completed and logs appended.
- mris_label2annot --s 0050319 --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-6.0.0/0050319/label
- cmdline mris_label2annot --s 0050319 --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-623
- machine x86_64
- user ntraut
- subject 0050319
- 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-6.0.0/0050319/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 90695 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/label/rh.BA_exvivo.annot
- mris_label2annot --s 0050319 --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-6.0.0/0050319/label
- cmdline mris_label2annot --s 0050319 --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-623
- machine x86_64
- user ntraut
- subject 0050319
- 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-6.0.0/0050319/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 108036 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/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 0050319 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 266660
- Total vertex volume 263203 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 1081 567 2057 2.558 0.678 0.124 0.045 15 1.9 BA1_exvivo
- 3021 1988 4931 2.317 0.592 0.098 0.020 21 2.3 BA2_exvivo
- 1195 813 1169 1.863 0.512 0.119 0.025 9 1.2 BA3a_exvivo
- 2212 1442 3007 1.780 0.650 0.096 0.031 18 2.7 BA3b_exvivo
- 1548 932 3531 3.119 0.574 0.096 0.038 24 3.3 BA4a_exvivo
- 1319 887 2505 2.828 0.588 0.096 0.018 8 1.0 BA4p_exvivo
- 7085 4614 17486 3.068 0.685 0.115 0.029 84 8.0 BA6_exvivo
- 3145 2189 6668 2.731 0.622 0.111 0.024 32 3.0 BA44_exvivo
- 4155 2759 10353 2.916 0.784 0.119 0.036 54 5.8 BA45_exvivo
- 3629 2587 4858 1.768 0.603 0.149 0.043 55 6.1 V1_exvivo
- 7801 4995 11361 2.119 0.641 0.146 0.045 120 14.4 V2_exvivo
- 2108 1492 4684 2.726 0.650 0.139 0.034 30 2.9 MT_exvivo
- 637 401 1515 2.898 1.027 0.150 0.071 16 2.1 perirhinal_exvivo
- 342 219 803 2.825 0.791 0.102 0.040 3 0.4 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 0050319 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050319/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 266660
- Total vertex volume 263203 (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) = 1542732 mm^3 (det: 1.262763 )
- lhCtxGM: 262171.511 261707.000 diff= 464.5 pctdiff= 0.177
- rhCtxGM: 261240.360 260814.000 diff= 426.4 pctdiff= 0.163
- lhCtxWM: 204631.537 205133.500 diff= -502.0 pctdiff=-0.245
- rhCtxWM: 203802.246 204828.500 diff=-1026.3 pctdiff=-0.504
- SubCortGMVol 58273.000
- SupraTentVol 1009956.655 (1007037.000) diff=2919.655 pctdiff=0.289
- SupraTentVolNotVent 993710.655 (990791.000) diff=2919.655 pctdiff=0.294
- BrainSegVol 1150047.000 (1146218.000) diff=3829.000 pctdiff=0.333
- BrainSegVolNotVent 1128892.000 (1128109.655) diff=782.345 pctdiff=0.069
- BrainSegVolNotVent 1128892.000
- CerebellumVol 137956.000
- VentChorVol 16246.000
- 3rd4th5thCSF 4909.000
- CSFVol 1080.000, OptChiasmVol 145.000
- MaskVol 1534180.000
- 767 388 1462 2.558 0.758 0.114 0.040 9 1.1 BA1_exvivo
- 1697 1094 2964 2.459 0.506 0.095 0.020 11 1.3 BA2_exvivo
- 1076 719 985 1.886 0.524 0.120 0.025 8 1.1 BA3a_exvivo
- 1640 1114 1985 1.620 0.523 0.076 0.018 8 1.0 BA3b_exvivo
- 1016 573 2042 3.059 0.606 0.097 0.031 13 1.5 BA4a_exvivo
- 1043 732 2050 2.897 0.597 0.090 0.016 5 0.7 BA4p_exvivo
- 4448 2861 11243 3.101 0.662 0.114 0.028 51 4.6 BA6_exvivo
- 695 494 1560 2.474 0.757 0.111 0.026 9 0.7 BA44_exvivo
- 936 614 2510 3.056 0.700 0.116 0.038 12 1.3 BA45_exvivo
- 3425 2422 4514 1.774 0.599 0.146 0.043 50 5.7 V1_exvivo
- 4176 2720 5730 2.001 0.635 0.156 0.051 76 9.2 V2_exvivo
- 338 209 730 2.788 0.492 0.143 0.047 7 0.6 MT_exvivo
- 424 252 961 2.785 0.977 0.154 0.082 11 1.7 perirhinal_exvivo
- 256 170 660 2.945 0.894 0.125 0.045 4 0.4 entorhinal_exvivo
- Started at Sat Oct 7 23:29:54 CEST 2017
- Ended at Sun Oct 8 06:52:19 CEST 2017
- #@#%# recon-all-run-time-hours 7.374
- recon-all -s 0050319 finished without error at Sun Oct 8 06:52:19 CEST 2017
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