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|
- Sat Oct 7 16:21:56 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
- -subjid 0051492 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Caltech/0051492/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
- subjid 0051492
- 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-582 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
- cputime unlimited
- filesize unlimited
- datasize unlimited
- stacksize 10240 kbytes
- coredumpsize 0 kbytes
- memoryuse 10485760 kbytes
- vmemoryuse unlimited
- descriptors 65536
- memorylocked 64 kbytes
- maxproc 1024
- total used free shared buffers cached
- Mem: 65993848 56857196 9136652 1762780 0 54162492
- -/+ buffers/cache: 2694704 63299144
- 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: 2017/10/07-14:21:56-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-582 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: 2017/10/07-14:21:56-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-582 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: 2017/10/07-14:21:56-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-582 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: 2017/10/07-14:21:56-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-582 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: 2017/10/07-14:21:56-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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: 2017/10/07-14:21:57-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-582 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-6.0.0/0051492
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Caltech/0051492/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/orig/001.mgz
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Caltech/0051492/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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/Caltech/0051492/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-6.0.0/0051492/mri/orig/001.mgz...
- #--------------------------------------------
- #@# MotionCor Sat Oct 7 16:22:00 CEST 2017
- Found 1 runs
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/rawavg.mgz
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/orig.mgz --conform
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/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-6.0.0/0051492/mri/orig.mgz...
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Sat Oct 7 16:22:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/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-582 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 16:22:11 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.29877
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29877/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.29877/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.29877/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 16:22:13 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.29877/nu0.mnc ./tmp.mri_nu_correct.mni.29877/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.29877/0/ -iterations 1000 -distance 50
- [ntraut@tars-582:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/] [2017-10-07 16:22:13] running:
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.29877/0/ ./tmp.mri_nu_correct.mni.29877/nu0.mnc ./tmp.mri_nu_correct.mni.29877/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 41
- CV of field change: 0.000923302
-
-
-
- mri_convert ./tmp.mri_nu_correct.mni.29877/nu1.mnc orig_nu.mgz --like orig.mgz --conform
- mri_convert.bin ./tmp.mri_nu_correct.mni.29877/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.29877/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 16:23:17 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 16:23:17 CEST 2017
- Ended at Sat Oct 7 16:23:49 CEST 2017
- talairach_avi done
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Sat Oct 7 16:23:51 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7010, pval=0.4932 >= threshold=0.0050)
- awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/transforms/talairach_avi.log
- tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/transforms/talairach_avi.log
- TalAviQA: 0.97048
- z-score: -1
- #--------------------------------------------
- #@# Nu Intensity Correction Sat Oct 7 16:23:51 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-6.0.0/0051492/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-582 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 16:23:51 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.30659
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30659/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.30659/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.30659/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 16:23:53 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.30659/nu0.mnc ./tmp.mri_nu_correct.mni.30659/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30659/0/
- [ntraut@tars-582:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/] [2017-10-07 16:23:54] running:
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.30659/0/ ./tmp.mri_nu_correct.mni.30659/nu0.mnc ./tmp.mri_nu_correct.mni.30659/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
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- Processing:.................................................................Done
- Number of iterations: 36
- CV of field change: 0.000997007
-
-
- --------------------------------------------------------
- Iteration 2 Sat Oct 7 16:24:40 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.30659/nu1.mnc ./tmp.mri_nu_correct.mni.30659/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.30659/1/
- [ntraut@tars-582:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/] [2017-10-07 16:24:41] 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.30659/1/ ./tmp.mri_nu_correct.mni.30659/nu1.mnc ./tmp.mri_nu_correct.mni.30659/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 8
- CV of field change: 0.000930375
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.30659/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.30659/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-6.0.0/0051492/mri
- cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.30659/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.30659/ones.mgz
- sysname Linux
- hostname tars-582
- machine x86_64
- user ntraut
- input ./tmp.mri_nu_correct.mni.30659/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.30659/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.30659/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.30659/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30659/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.30659/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.30659/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30659/input.mean.dat
- sysname Linux
- hostname tars-582
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.30659/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.30659/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.30659/ones.mgz --i ./tmp.mri_nu_correct.mni.30659/nu2.mnc --sum ./tmp.mri_nu_correct.mni.30659/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30659/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.30659/ones.mgz --i ./tmp.mri_nu_correct.mni.30659/nu2.mnc --sum ./tmp.mri_nu_correct.mni.30659/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30659/output.mean.dat
- sysname Linux
- hostname tars-582
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.30659/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.30659/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.30659/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.30659/nu2.mnc ./tmp.mri_nu_correct.mni.30659/nu2.mnc mul .95708798224477583988
- Saving result to './tmp.mri_nu_correct.mni.30659/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.30659/nu2.mnc nu.mgz --like orig.mgz
- mri_convert.bin ./tmp.mri_nu_correct.mni.30659/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.30659/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, 170) to ( 3, 110)
-
-
- Sat Oct 7 16:25:46 CEST 2017
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Sat Oct 7 16:25:47 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri
- mri_normalize -g 1 -mprage nu.mgz T1.mgz
- using max gradient = 1.000
- assuming input volume is MGH (Van der Kouwe) MP-RAGE
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 0.99809 -0.04121 -0.02359 0.46310;
- 0.04900 0.94045 0.13609 -65.07710;
- -0.00176 -0.17632 1.07962 -13.90986;
- 0.00000 0.00000 0.00000 1.00000;
- processing without aseg, no1d=0
- MRInormInit():
- INFO: Modifying talairach volume c_(r,a,s) based on average_305
- MRInormalize():
- MRIsplineNormalize(): npeaks = 15
- Starting OpenSpline(): npoints = 15
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 110
- white matter peak found at 110
- gm peak at 88 (88), valley at 27 (27)
- csf peak at 46, setting threshold to 74
- 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 88 (88), valley at 25 (25)
- csf peak at 45, setting threshold to 73
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 1 minutes and 57 seconds.
- #--------------------------------------------
- #@# Skull Stripping Sat Oct 7 16:27:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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=9.0
- skull bounding box = (44, 15, 13) --> (209, 170, 227)
- using (99, 67, 120) as brain centroid...
- mean wm in atlas = 108, using box (79,48,94) --> (119, 86,146) to find MRI wm
- before smoothing, mri peak at 106
- robust fit to distribution - 107 +- 4.9
- after smoothing, mri peak at 107, scaling input intensities by 1.009
- scaling channel 0 by 1.00935
- initial log_p = -4.736
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.483180 @ (9.091, 27.273, -9.091)
- max log p = -4.431979 @ (-4.545, 4.545, 4.545)
- max log p = -4.392216 @ (-6.818, -6.818, -2.273)
- max log p = -4.367235 @ (1.136, 1.136, 1.136)
- max log p = -4.367235 @ (0.000, 0.000, 0.000)
- max log p = -4.367181 @ (0.852, -0.284, -0.284)
- Found translation: (-0.3, 25.9, -6.0): log p = -4.367
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.324, old_max_log_p =-4.367 (thresh=-4.4)
- 1.00000 0.00000 0.00000 -0.28409;
- 0.00000 1.15000 0.00000 15.90399;
- 0.00000 0.00000 1.00000 -5.96591;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.311, old_max_log_p =-4.324 (thresh=-4.3)
- 1.00000 0.00000 0.00000 -0.28409;
- 0.00000 1.22567 0.14032 -8.80637;
- 0.00000 -0.15011 0.99144 11.51566;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.311, old_max_log_p =-4.311 (thresh=-4.3)
- 1.00000 0.00000 0.00000 -0.28409;
- 0.00000 1.22567 0.14032 -8.80637;
- 0.00000 -0.15011 0.99144 11.51566;
- 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=-4.245, old_max_log_p =-4.311 (thresh=-4.3)
- 1.01556 0.08074 0.01394 -10.85138;
- -0.06164 1.15572 0.12823 6.12662;
- 0.00475 -0.13908 0.95520 12.07297;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.239, old_max_log_p =-4.245 (thresh=-4.2)
- 1.01556 0.08074 0.01394 -10.85138;
- -0.06030 1.12898 0.15643 3.70035;
- 0.00689 -0.18014 0.96831 14.80827;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.239, old_max_log_p =-4.239 (thresh=-4.2)
- 1.01556 0.08074 0.01394 -10.85138;
- -0.06030 1.12898 0.15643 3.70035;
- 0.00689 -0.18014 0.96831 14.80827;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.232, old_max_log_p =-4.239 (thresh=-4.2)
- 1.01008 0.10362 0.04143 -16.50439;
- -0.08508 1.12542 0.15540 8.67816;
- -0.01805 -0.18285 0.97106 16.91629;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.228, old_max_log_p =-4.232 (thresh=-4.2)
- 1.00936 0.09293 0.04819 -16.50575;
- -0.07651 1.12906 0.13989 9.07550;
- -0.02770 -0.16526 0.97310 15.43577;
- 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
- 1.00936 0.09293 0.04819 -16.50575;
- -0.07651 1.12906 0.13989 9.07550;
- -0.02770 -0.16526 0.97310 15.43577;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3243
- Quasinewton: input matrix
- 1.00936 0.09293 0.04819 -16.50575;
- -0.07651 1.12906 0.13989 9.07550;
- -0.02770 -0.16526 0.97310 15.43577;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.00936 0.09293 0.04819 -16.50575;
- -0.07651 1.12906 0.13989 9.07550;
- -0.02770 -0.16526 0.97310 15.43577;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -4.228 (old=-4.736)
- transform before final EM align:
- 1.00936 0.09293 0.04819 -16.50575;
- -0.07651 1.12906 0.13989 9.07550;
- -0.02770 -0.16526 0.97310 15.43577;
- 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
- 1.00936 0.09293 0.04819 -16.50575;
- -0.07651 1.12906 0.13989 9.07550;
- -0.02770 -0.16526 0.97310 15.43577;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 364799
- Quasinewton: input matrix
- 1.00936 0.09293 0.04819 -16.50575;
- -0.07651 1.12906 0.13989 9.07550;
- -0.02770 -0.16526 0.97310 15.43577;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 012: -log(p) = 4.6 tol 0.000000
- final transform:
- 1.00936 0.09293 0.04819 -16.50575;
- -0.07651 1.12906 0.13989 9.07550;
- -0.02770 -0.16526 0.97310 15.43577;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach_with_skull.lta...
- mri_em_register utimesec 1535.026640
- mri_em_register stimesec 1.929706
- 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 157059
- mri_em_register ru_majflt 0
- mri_em_register ru_nswap 0
- mri_em_register ru_inblock 148912
- 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 387
- mri_em_register ru_nivcsw 5493
- registration took 13 minutes and 14 seconds.
- mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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=128 y=89 z=119 r=71
- first estimation of the main basin volume: 1519076 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 18 found in the rest of the brain
- global maximum in x=151, y=72, z=85, Imax=255
- CSF=13, 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=9826798218 voxels, voxel volume =1.000
- = 9826798218 mmm3 = 9826798.592 cm3
- done.
- PostAnalyze...Basin Prior
- 94 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=126,y=93, z=111, r=10256 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=10 , nb = 44468
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=7 , nb = -1039136139
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = 1109931855
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=10 , nb = 1074210856
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 1075101840
- OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=11 , nb = 1073614420
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 10, 26, 64, 83
- after analyzing : 10, 51, 64, 59
- RIGHT_CER
- before analyzing : 7, 16, 61, 85
- after analyzing : 7, 46, 61, 55
- LEFT_CER
- before analyzing : 12, 27, 66, 90
- after analyzing : 12, 53, 66, 62
- RIGHT_BRAIN
- before analyzing : 10, 24, 62, 83
- after analyzing : 10, 49, 62, 57
- LEFT_BRAIN
- before analyzing : 9, 22, 63, 84
- after analyzing : 9, 49, 63, 57
- OTHER
- before analyzing : 11, 15, 22, 36
- after analyzing : 11, 21, 25, 24
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...61 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.009
- curvature mean = 74.119, std = 7.817
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 2.13, sigma = 3.59
- after rotation: sse = 2.13, sigma = 3.59
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 2.19, its var is 3.09
- before Erosion-Dilatation 0.08% of inacurate vertices
- after Erosion-Dilatation 0.00% of inacurate vertices
- Validation of the shape of the surface done.
- Scaling of atlas fields onto current surface fields
- ********FINAL ITERATIVE TEMPLATE DEFORMATION********
- Compute Local values csf/gray
- Fine Segmentation...40 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1929920 voxels, voxel volume = 1.000 mm3
- = 1929920 mmm3 = 1929.920 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- mri_watershed utimesec 24.085338
- mri_watershed stimesec 0.551916
- mri_watershed ru_maxrss 821284
- mri_watershed ru_ixrss 0
- mri_watershed ru_idrss 0
- mri_watershed ru_isrss 0
- mri_watershed ru_minflt 212657
- mri_watershed ru_majflt 0
- mri_watershed ru_nswap 0
- mri_watershed ru_inblock 7552
- mri_watershed ru_oublock 2928
- mri_watershed ru_msgsnd 0
- mri_watershed ru_msgrcv 0
- mri_watershed ru_nsignals 0
- mri_watershed ru_nvcsw 3033
- mri_watershed ru_nivcsw 943
- mri_watershed done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Sat Oct 7 16:41:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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=16.0
- skull bounding box = (55, 28, 26) --> (198, 154, 208)
- using (103, 70, 117) as brain centroid...
- mean wm in atlas = 107, using box (85,55,95) --> (120, 85,139) to find MRI wm
- before smoothing, mri peak at 106
- robust fit to distribution - 106 +- 4.7
- after smoothing, mri peak at 106, scaling input intensities by 1.009
- scaling channel 0 by 1.00943
- initial log_p = -4.497
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.063543 @ (-9.091, 27.273, -9.091)
- max log p = -3.971119 @ (4.545, 4.545, 4.545)
- max log p = -3.852837 @ (2.273, -6.818, -2.273)
- max log p = -3.818614 @ (1.136, 1.136, -1.136)
- max log p = -3.818614 @ (0.000, 0.000, 0.000)
- max log p = -3.792928 @ (0.852, -0.284, -0.284)
- Found translation: (-0.3, 25.9, -8.2): log p = -3.793
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.753, old_max_log_p =-3.793 (thresh=-3.8)
- 1.00000 0.00000 0.00000 -0.28409;
- 0.00000 1.06580 0.11927 6.14498;
- 0.00000 -0.14032 0.90593 15.56598;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.753, old_max_log_p =-3.753 (thresh=-3.7)
- 1.00000 0.00000 0.00000 -0.28409;
- 0.00000 1.06580 0.11927 6.14498;
- 0.00000 -0.14032 0.90593 15.56598;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.686, old_max_log_p =-3.753 (thresh=-3.7)
- 0.97436 0.09859 0.06497 -13.62575;
- -0.09999 1.06503 0.08447 22.87436;
- -0.06568 -0.10778 0.94163 16.81106;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.686, old_max_log_p =-3.686 (thresh=-3.7)
- 0.97436 0.09859 0.06497 -13.62575;
- -0.09999 1.06503 0.08447 22.87436;
- -0.06568 -0.10778 0.94163 16.81106;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.668, old_max_log_p =-3.686 (thresh=-3.7)
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09264 1.06614 0.09274 21.36420;
- -0.05694 -0.11581 0.94251 16.81920;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.667, old_max_log_p =-3.668 (thresh=-3.7)
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09242 1.06364 0.09253 21.59371;
- -0.05707 -0.11609 0.94472 16.61148;
- 0.00000 0.00000 0.00000 1.00000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 2830 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09242 1.06364 0.09253 21.59371;
- -0.05707 -0.11609 0.94472 16.61148;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2830
- Quasinewton: input matrix
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09242 1.06364 0.09253 21.59371;
- -0.05707 -0.11609 0.94472 16.61148;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09242 1.06364 0.09253 21.59371;
- -0.05707 -0.11609 0.94472 16.61148;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.667 (old=-4.497)
- transform before final EM align:
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09242 1.06364 0.09253 21.59371;
- -0.05707 -0.11609 0.94472 16.61148;
- 0.00000 0.00000 0.00000 1.00000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 315557 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09242 1.06364 0.09253 21.59371;
- -0.05707 -0.11609 0.94472 16.61148;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 315557
- Quasinewton: input matrix
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09242 1.06364 0.09253 21.59371;
- -0.05707 -0.11609 0.94472 16.61148;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 010: -log(p) = 4.1 tol 0.000000
- final transform:
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09242 1.06364 0.09253 21.59371;
- -0.05707 -0.11609 0.94472 16.61148;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach.lta...
- mri_em_register utimesec 960.872925
- mri_em_register stimesec 2.834569
- 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 158986
- 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 185
- mri_em_register ru_nivcsw 8963
- registration took 8 minutes and 18 seconds.
- #--------------------------------------
- #@# CA Normalize Sat Oct 7 16:49:41 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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=15.0
- skull bounding box = (55, 28, 26) --> (198, 154, 209)
- using (103, 70, 118) as brain centroid...
- mean wm in atlas = 107, using box (85,55,95) --> (120, 85,140) to find MRI wm
- before smoothing, mri peak at 106
- robust fit to distribution - 106 +- 4.8
- after smoothing, mri peak at 106, scaling input intensities by 1.009
- scaling channel 0 by 1.00943
- using 246344 sample points...
- INFO: compute sample coordinates transform
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09242 1.06364 0.09253 21.59371;
- -0.05707 -0.11609 0.94472 16.61148;
- 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 (125, 31, 32) --> (196, 142, 208)
- Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
- 0 of 2219 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (60, 31, 29) --> (131, 137, 206)
- Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
- 1 of 1975 (0.1%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (127, 113, 59) --> (175, 156, 116)
- Left_Cerebellum_White_Matter: limiting intensities to 106.0 --> 132.0
- 4 of 21 (19.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (79, 113, 54) --> (127, 150, 115)
- Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0
- 1 of 25 (4.0%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (106, 103, 95) --> (143, 169, 127)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 0 of 11 (0.0%) samples deleted
- using 4251 total control points for intensity normalization...
- bias field = 0.942 +- 0.049
- 9 of 4245 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (125, 31, 32) --> (196, 142, 208)
- Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 0 of 2980 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (60, 31, 29) --> (131, 137, 206)
- Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 1 of 2846 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (127, 113, 59) --> (175, 156, 116)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 13 of 64 (20.3%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (79, 113, 54) --> (127, 150, 115)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 13 of 69 (18.8%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (106, 103, 95) --> (143, 169, 127)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 31 of 96 (32.3%) samples deleted
- using 6055 total control points for intensity normalization...
- bias field = 1.048 +- 0.050
- 21 of 5952 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (125, 31, 32) --> (196, 142, 208)
- Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 3 of 3007 (0.1%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (60, 31, 29) --> (131, 137, 206)
- Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 2 of 2815 (0.1%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (127, 113, 59) --> (175, 156, 116)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 62 of 109 (56.9%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (79, 113, 54) --> (127, 150, 115)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 58 of 104 (55.8%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (106, 103, 95) --> (143, 169, 127)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 52 of 119 (43.7%) samples deleted
- using 6154 total control points for intensity normalization...
- bias field = 1.047 +- 0.046
- 15 of 5877 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 1 minutes and 46 seconds.
- #--------------------------------------
- #@# CA Reg Sat Oct 7 16:51:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri
- mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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) = 1.00 (predicted orig area = 8.0)
- label assignment complete, 0 changed (0.00%)
- freeing gibbs priors...done.
- average std[0] = 5.0
- **************** pass 1 of 1 ************************
- enabling zero nodes
- setting smoothness coefficient to 0.039
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.889, neg=0, invalid=762
- 0001: dt=298.224112, rms=0.823 (7.450%), neg=0, invalid=762
- 0002: dt=211.336170, rms=0.802 (2.482%), neg=0, invalid=762
- 0003: dt=228.794425, rms=0.793 (1.138%), neg=0, invalid=762
- 0004: dt=179.532468, rms=0.788 (0.705%), neg=0, invalid=762
- 0005: dt=443.904000, rms=0.782 (0.733%), neg=0, invalid=762
- 0006: dt=129.472000, rms=0.778 (0.542%), neg=0, invalid=762
- 0007: dt=1183.744000, rms=0.770 (0.928%), neg=0, invalid=762
- 0008: dt=129.472000, rms=0.766 (0.517%), neg=0, invalid=762
- 0009: dt=443.904000, rms=0.765 (0.200%), neg=0, invalid=762
- 0010: dt=443.904000, rms=0.765 (-0.664%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.765, neg=0, invalid=762
- 0011: dt=182.634146, rms=0.759 (0.846%), neg=0, invalid=762
- 0012: dt=517.888000, rms=0.756 (0.311%), neg=0, invalid=762
- 0013: dt=129.472000, rms=0.756 (0.128%), neg=0, invalid=762
- 0014: dt=129.472000, rms=0.755 (0.070%), neg=0, invalid=762
- 0015: dt=129.472000, rms=0.754 (0.110%), neg=0, invalid=762
- 0016: dt=129.472000, rms=0.753 (0.139%), neg=0, invalid=762
- 0017: dt=129.472000, rms=0.752 (0.183%), neg=0, invalid=762
- 0018: dt=129.472000, rms=0.750 (0.206%), neg=0, invalid=762
- 0019: dt=129.472000, rms=0.749 (0.212%), neg=0, invalid=762
- 0020: dt=129.472000, rms=0.747 (0.205%), neg=0, invalid=762
- 0021: dt=129.472000, rms=0.746 (0.200%), neg=0, invalid=762
- 0022: dt=129.472000, rms=0.744 (0.186%), neg=0, invalid=762
- 0023: dt=129.472000, rms=0.743 (0.195%), neg=0, invalid=762
- 0024: dt=129.472000, rms=0.741 (0.193%), neg=0, invalid=762
- 0025: dt=129.472000, rms=0.740 (0.177%), neg=0, invalid=762
- 0026: dt=129.472000, rms=0.739 (0.163%), neg=0, invalid=762
- 0027: dt=129.472000, rms=0.738 (0.154%), neg=0, invalid=762
- 0028: dt=129.472000, rms=0.736 (0.156%), neg=0, invalid=762
- 0029: dt=129.472000, rms=0.735 (0.153%), neg=0, invalid=762
- 0030: dt=129.472000, rms=0.734 (0.137%), neg=0, invalid=762
- 0031: dt=129.472000, rms=0.733 (0.133%), neg=0, invalid=762
- 0032: dt=129.472000, rms=0.732 (0.127%), neg=0, invalid=762
- 0033: dt=129.472000, rms=0.732 (0.122%), neg=0, invalid=762
- 0034: dt=129.472000, rms=0.731 (0.105%), neg=0, invalid=762
- 0035: dt=369.920000, rms=0.731 (0.017%), neg=0, invalid=762
- 0036: dt=369.920000, rms=0.730 (0.062%), neg=0, invalid=762
- 0037: dt=369.920000, rms=0.730 (0.043%), neg=0, invalid=762
- 0038: dt=369.920000, rms=0.729 (0.064%), neg=0, invalid=762
- 0039: dt=369.920000, rms=0.729 (0.118%), neg=0, invalid=762
- 0040: dt=369.920000, rms=0.728 (0.097%), neg=0, invalid=762
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.737, neg=0, invalid=762
- 0041: dt=30.523077, rms=0.735 (0.209%), neg=0, invalid=762
- 0042: dt=36.288000, rms=0.734 (0.135%), neg=0, invalid=762
- 0043: dt=36.288000, rms=0.732 (0.217%), neg=0, invalid=762
- 0044: dt=36.288000, rms=0.730 (0.389%), neg=0, invalid=762
- 0045: dt=36.288000, rms=0.725 (0.567%), neg=0, invalid=762
- 0046: dt=36.288000, rms=0.720 (0.770%), neg=0, invalid=762
- 0047: dt=36.288000, rms=0.713 (0.900%), neg=0, invalid=762
- 0048: dt=36.288000, rms=0.707 (0.915%), neg=0, invalid=762
- 0049: dt=36.288000, rms=0.702 (0.682%), neg=0, invalid=762
- 0050: dt=36.288000, rms=0.702 (-0.081%), neg=0, invalid=762
- 0051: dt=0.000000, rms=0.702 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.703, neg=0, invalid=762
- 0052: dt=88.630015, rms=0.697 (0.831%), neg=0, invalid=762
- 0053: dt=36.288000, rms=0.695 (0.309%), neg=0, invalid=762
- 0054: dt=145.152000, rms=0.693 (0.298%), neg=0, invalid=762
- 0055: dt=145.152000, rms=0.691 (0.287%), neg=0, invalid=762
- 0056: dt=31.104000, rms=0.690 (0.081%), neg=0, invalid=762
- 0057: dt=31.104000, rms=0.690 (0.042%), neg=0, invalid=762
- 0058: dt=31.104000, rms=0.689 (0.056%), neg=0, invalid=762
- 0059: dt=31.104000, rms=0.689 (0.069%), neg=0, invalid=762
- 0060: dt=31.104000, rms=0.688 (0.111%), neg=0, invalid=762
- 0061: dt=31.104000, rms=0.687 (0.129%), neg=0, invalid=762
- 0062: dt=31.104000, rms=0.686 (0.139%), neg=0, invalid=762
- 0063: dt=31.104000, rms=0.685 (0.133%), neg=0, invalid=762
- 0064: dt=31.104000, rms=0.685 (0.118%), neg=0, invalid=762
- 0065: dt=31.104000, rms=0.684 (0.120%), neg=0, invalid=762
- 0066: dt=31.104000, rms=0.683 (0.123%), neg=0, invalid=762
- 0067: dt=31.104000, rms=0.682 (0.139%), neg=0, invalid=762
- 0068: dt=31.104000, rms=0.681 (0.154%), neg=0, invalid=762
- 0069: dt=31.104000, rms=0.680 (0.162%), neg=0, invalid=762
- 0070: dt=31.104000, rms=0.679 (0.155%), neg=0, invalid=762
- 0071: dt=31.104000, rms=0.678 (0.151%), neg=0, invalid=762
- 0072: dt=31.104000, rms=0.677 (0.137%), neg=0, invalid=762
- 0073: dt=31.104000, rms=0.676 (0.145%), neg=0, invalid=762
- 0074: dt=31.104000, rms=0.675 (0.144%), neg=0, invalid=762
- 0075: dt=31.104000, rms=0.674 (0.136%), neg=0, invalid=762
- 0076: dt=31.104000, rms=0.673 (0.126%), neg=0, invalid=762
- 0077: dt=31.104000, rms=0.672 (0.103%), neg=0, invalid=762
- 0078: dt=31.104000, rms=0.672 (0.106%), neg=0, invalid=762
- 0079: dt=31.104000, rms=0.671 (0.108%), neg=0, invalid=762
- 0080: dt=31.104000, rms=0.670 (0.107%), neg=0, invalid=762
- 0081: dt=82.944000, rms=0.670 (0.004%), neg=0, invalid=762
- 0082: dt=82.944000, rms=0.670 (0.021%), neg=0, invalid=762
- 0083: dt=82.944000, rms=0.670 (0.037%), neg=0, invalid=762
- 0084: dt=82.944000, rms=0.669 (0.049%), neg=0, invalid=762
- 0085: dt=82.944000, rms=0.669 (0.036%), neg=0, invalid=762
- 0086: dt=82.944000, rms=0.669 (0.044%), neg=0, invalid=762
- 0087: dt=82.944000, rms=0.668 (0.088%), neg=0, invalid=762
- 0088: dt=82.944000, rms=0.668 (0.094%), neg=0, invalid=762
- 0089: dt=82.944000, rms=0.667 (0.069%), neg=0, invalid=762
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.699, neg=0, invalid=762
- 0090: dt=2.800000, rms=0.699 (0.099%), neg=0, invalid=762
- 0091: dt=2.800000, rms=0.699 (0.016%), neg=0, invalid=762
- 0092: dt=2.800000, rms=0.699 (0.005%), neg=0, invalid=762
- 0093: dt=2.800000, rms=0.699 (-0.018%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.699, neg=0, invalid=762
- 0094: dt=0.700000, rms=0.699 (0.077%), neg=0, invalid=762
- 0095: dt=0.400000, rms=0.699 (-0.001%), neg=0, invalid=762
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.786, neg=0, invalid=762
- 0096: dt=6.397260, rms=0.762 (3.011%), neg=0, invalid=762
- 0097: dt=9.380153, rms=0.755 (0.928%), neg=0, invalid=762
- 0098: dt=2.304000, rms=0.755 (0.027%), neg=0, invalid=762
- 0099: dt=2.304000, rms=0.755 (0.029%), neg=0, invalid=762
- 0100: dt=2.304000, rms=0.755 (0.025%), neg=0, invalid=762
- 0101: dt=2.304000, rms=0.755 (0.005%), neg=0, invalid=762
- 0102: dt=16.128000, rms=0.753 (0.171%), neg=0, invalid=762
- 0103: dt=0.000000, rms=0.753 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.754, neg=0, invalid=762
- 0104: dt=0.000000, rms=0.753 (0.070%), neg=0, invalid=762
- 0105: dt=0.000000, rms=0.753 (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=0.798, neg=0, invalid=762
- 0106: dt=0.000000, rms=0.798 (0.062%), neg=0, invalid=762
- 0107: dt=0.000000, rms=0.798 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.798, neg=0, invalid=762
- 0108: dt=0.000000, rms=0.798 (0.062%), neg=0, invalid=762
- 0109: dt=0.000000, rms=0.798 (0.000%), 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=0.723, neg=0, invalid=762
- 0110: dt=0.833069, rms=0.706 (2.317%), neg=0, invalid=762
- 0111: dt=0.080000, rms=0.705 (0.136%), neg=0, invalid=762
- 0112: dt=0.080000, rms=0.705 (-0.057%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.705, neg=0, invalid=762
- 0113: dt=0.028000, rms=0.705 (0.102%), neg=0, invalid=762
- 0114: dt=0.016000, rms=0.705 (-0.001%), neg=0, invalid=762
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.10027 (20)
- mri peak = 0.09850 (30)
- Left_Lateral_Ventricle (4): linear fit = 1.59 x + 0.0 (1851 voxels, overlap=0.292)
- Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1851 voxels, peak = 32), gca=30.0
- gca peak = 0.15565 (16)
- mri peak = 0.10230 (32)
- Right_Lateral_Ventricle (43): linear fit = 1.92 x + 0.0 (1182 voxels, overlap=0.099)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1182 voxels, peak = 31), gca=24.0
- gca peak = 0.26829 (96)
- mri peak = 0.07496 (94)
- Right_Pallidum (52): linear fit = 0.96 x + 0.0 (1174 voxels, overlap=1.011)
- Right_Pallidum (52): linear fit = 0.96 x + 0.0 (1174 voxels, peak = 93), gca=92.6
- gca peak = 0.20183 (93)
- mri peak = 0.06058 (95)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (1054 voxels, overlap=1.018)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (1054 voxels, peak = 93), gca=92.5
- gca peak = 0.21683 (55)
- mri peak = 0.08111 (75)
- Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1182 voxels, overlap=0.013)
- Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1182 voxels, peak = 70), gca=70.1
- gca peak = 0.30730 (58)
- mri peak = 0.09806 (72)
- Left_Hippocampus (17): linear fit = 1.24 x + 0.0 (1262 voxels, overlap=0.014)
- Left_Hippocampus (17): linear fit = 1.24 x + 0.0 (1262 voxels, peak = 72), gca=71.6
- gca peak = 0.11430 (101)
- mri peak = 0.10987 (103)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (87589 voxels, overlap=0.808)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (87589 voxels, peak = 103), gca=102.5
- gca peak = 0.12076 (102)
- mri peak = 0.10013 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (91282 voxels, overlap=0.827)
- Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (91282 voxels, peak = 104), gca=103.5
- gca peak = 0.14995 (59)
- mri peak = 0.04785 (84)
- Left_Cerebral_Cortex (3): linear fit = 1.47 x + 0.0 (39004 voxels, overlap=0.000)
- Left_Cerebral_Cortex (3): linear fit = 1.47 x + 0.0 (39004 voxels, peak = 86), gca=86.4
- gca peak = 0.15082 (58)
- mri peak = 0.04127 (84)
- Right_Cerebral_Cortex (42): linear fit = 1.47 x + 0.0 (41498 voxels, overlap=0.000)
- Right_Cerebral_Cortex (42): linear fit = 1.47 x + 0.0 (41498 voxels, peak = 85), gca=85.0
- gca peak = 0.14161 (67)
- mri peak = 0.11031 (83)
- Right_Caudate (50): linear fit = 1.23 x + 0.0 (1209 voxels, overlap=0.013)
- Right_Caudate (50): linear fit = 1.23 x + 0.0 (1209 voxels, peak = 82), gca=82.1
- gca peak = 0.15243 (71)
- mri peak = 0.08092 (87)
- Left_Caudate (11): linear fit = 1.17 x + 0.0 (1286 voxels, overlap=0.050)
- Left_Caudate (11): linear fit = 1.17 x + 0.0 (1286 voxels, peak = 83), gca=83.4
- gca peak = 0.13336 (57)
- mri peak = 0.05910 (78)
- Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (26936 voxels, overlap=0.001)
- Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (26936 voxels, peak = 78), gca=78.4
- gca peak = 0.13252 (56)
- mri peak = 0.05575 (72)
- Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (32810 voxels, overlap=0.005)
- Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (32810 voxels, peak = 71), gca=70.8
- gca peak = 0.18181 (84)
- mri peak = 0.07358 (88)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (10812 voxels, overlap=0.975)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (10812 voxels, peak = 88), gca=87.8
- gca peak = 0.20573 (83)
- mri peak = 0.08103 (85)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (9541 voxels, overlap=0.939)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (9541 voxels, peak = 86), gca=85.9
- gca peak = 0.21969 (57)
- mri peak = 0.09948 (74)
- Left_Amygdala (18): linear fit = 1.29 x + 0.0 (576 voxels, overlap=0.049)
- Left_Amygdala (18): linear fit = 1.29 x + 0.0 (576 voxels, peak = 74), gca=73.8
- gca peak = 0.39313 (56)
- mri peak = 0.09422 (77)
- Right_Amygdala (54): linear fit = 1.32 x + 0.0 (700 voxels, overlap=0.035)
- Right_Amygdala (54): linear fit = 1.32 x + 0.0 (700 voxels, peak = 74), gca=73.6
- gca peak = 0.14181 (85)
- mri peak = 0.07171 (95)
- Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6806 voxels, overlap=0.486)
- Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6806 voxels, peak = 91), gca=90.5
- gca peak = 0.11978 (83)
- mri peak = 0.07348 (92)
- Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5614 voxels, overlap=0.540)
- Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5614 voxels, peak = 93), gca=92.5
- gca peak = 0.13399 (79)
- mri peak = 0.08797 (88)
- Left_Putamen (12): linear fit = 1.14 x + 0.0 (3050 voxels, overlap=0.066)
- Left_Putamen (12): linear fit = 1.14 x + 0.0 (3050 voxels, peak = 90), gca=90.5
- gca peak = 0.14159 (79)
- mri peak = 0.08414 (89)
- Right_Putamen (51): linear fit = 1.12 x + 0.0 (3185 voxels, overlap=0.453)
- Right_Putamen (51): linear fit = 1.12 x + 0.0 (3185 voxels, peak = 88), gca=88.1
- gca peak = 0.10025 (80)
- mri peak = 0.09108 (88)
- Brain_Stem (16): linear fit = 1.11 x + 0.0 (11503 voxels, overlap=0.402)
- Brain_Stem (16): linear fit = 1.11 x + 0.0 (11503 voxels, peak = 88), gca=88.4
- gca peak = 0.13281 (86)
- mri peak = 0.07298 (99)
- Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1645 voxels, overlap=0.329)
- Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1645 voxels, peak = 97), gca=96.8
- gca peak = 0.12801 (89)
- mri peak = 0.07287 (92)
- Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1529 voxels, overlap=0.650)
- Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1529 voxels, peak = 97), gca=97.5
- gca peak = 0.20494 (23)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.15061 (21)
- mri peak = 0.15190 (32)
- Fourth_Ventricle (15): linear fit = 1.50 x + 0.0 (879 voxels, overlap=0.223)
- Fourth_Ventricle (15): linear fit = 1.50 x + 0.0 (879 voxels, peak = 31), gca=31.4
- 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 1.34 x + 0.0
- estimating mean wm scale to be 1.01 x + 0.0
- estimating mean csf scale to be 1.50 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=0.685, neg=0, invalid=762
- 0115: dt=100.000000, rms=0.646 (5.719%), neg=0, invalid=762
- 0116: dt=221.952000, rms=0.639 (1.164%), neg=0, invalid=762
- 0117: dt=517.888000, rms=0.629 (1.593%), neg=0, invalid=762
- 0118: dt=32.368000, rms=0.628 (0.030%), neg=0, invalid=762
- 0119: dt=32.368000, rms=0.628 (0.005%), neg=0, invalid=762
- 0120: dt=32.368000, rms=0.628 (-0.022%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.629, neg=0, invalid=762
- 0121: dt=369.920000, rms=0.626 (0.418%), neg=0, invalid=762
- 0122: dt=129.472000, rms=0.625 (0.209%), neg=0, invalid=762
- 0123: dt=517.888000, rms=0.623 (0.225%), neg=0, invalid=762
- 0124: dt=129.472000, rms=0.622 (0.136%), neg=0, invalid=762
- 0125: dt=295.936000, rms=0.622 (0.089%), neg=0, invalid=762
- 0126: dt=129.472000, rms=0.621 (0.077%), neg=0, invalid=762
- 0127: dt=443.904000, rms=0.621 (0.090%), neg=0, invalid=762
- 0128: dt=129.472000, rms=0.620 (0.086%), neg=0, invalid=762
- 0129: dt=295.936000, rms=0.620 (0.052%), neg=0, invalid=762
- 0130: dt=129.472000, rms=0.620 (0.060%), neg=0, invalid=762
- 0131: dt=443.904000, rms=0.619 (0.058%), neg=0, invalid=762
- 0132: dt=129.472000, rms=0.619 (0.071%), neg=0, invalid=762
- 0133: dt=221.952000, rms=0.619 (0.032%), neg=0, invalid=762
- 0134: dt=221.952000, rms=0.618 (0.046%), neg=0, invalid=762
- 0135: dt=221.952000, rms=0.618 (0.083%), neg=0, invalid=762
- 0136: dt=221.952000, rms=0.617 (0.079%), neg=0, invalid=762
- 0137: dt=221.952000, rms=0.616 (0.128%), neg=0, invalid=762
- 0138: dt=221.952000, rms=0.616 (0.105%), neg=0, invalid=762
- 0139: dt=221.952000, rms=0.615 (0.107%), neg=0, invalid=762
- 0140: dt=221.952000, rms=0.615 (0.107%), neg=0, invalid=762
- 0141: dt=221.952000, rms=0.614 (0.102%), neg=0, invalid=762
- 0142: dt=221.952000, rms=0.613 (0.091%), neg=0, invalid=762
- 0143: dt=221.952000, rms=0.613 (0.070%), neg=0, invalid=762
- 0144: dt=221.952000, rms=0.612 (0.097%), neg=0, invalid=762
- 0145: dt=221.952000, rms=0.612 (0.081%), neg=0, invalid=762
- 0146: dt=221.952000, rms=0.611 (0.078%), neg=0, invalid=762
- 0147: dt=221.952000, rms=0.611 (0.077%), neg=0, invalid=762
- 0148: dt=221.952000, rms=0.610 (0.086%), neg=0, invalid=762
- 0149: dt=221.952000, rms=0.610 (0.076%), neg=0, invalid=762
- 0150: dt=221.952000, rms=0.609 (0.067%), neg=0, invalid=762
- 0151: dt=221.952000, rms=0.609 (0.077%), neg=0, invalid=762
- 0152: dt=221.952000, rms=0.609 (0.069%), neg=0, invalid=762
- 0153: dt=221.952000, rms=0.608 (0.042%), neg=0, invalid=762
- 0154: dt=221.952000, rms=0.608 (0.046%), neg=0, invalid=762
- 0155: dt=221.952000, rms=0.608 (0.068%), neg=0, invalid=762
- 0156: dt=221.952000, rms=0.607 (0.072%), neg=0, invalid=762
- 0157: dt=221.952000, rms=0.607 (0.042%), neg=0, invalid=762
- 0158: dt=221.952000, rms=0.607 (0.039%), neg=0, invalid=762
- 0159: dt=221.952000, rms=0.606 (0.055%), neg=0, invalid=762
- 0160: dt=221.952000, rms=0.606 (0.060%), neg=0, invalid=762
- 0161: dt=221.952000, rms=0.606 (0.029%), neg=0, invalid=762
- 0162: dt=221.952000, rms=0.606 (0.023%), neg=0, invalid=762
- 0163: dt=221.952000, rms=0.605 (0.046%), neg=0, invalid=762
- 0164: dt=221.952000, rms=0.605 (0.036%), neg=0, invalid=762
- 0165: dt=221.952000, rms=0.605 (0.024%), neg=0, invalid=762
- 0166: dt=221.952000, rms=0.605 (0.032%), neg=0, invalid=762
- 0167: dt=221.952000, rms=0.605 (0.045%), neg=0, invalid=762
- 0168: dt=221.952000, rms=0.604 (0.041%), neg=0, invalid=762
- 0169: dt=221.952000, rms=0.604 (0.028%), neg=0, invalid=762
- 0170: dt=221.952000, rms=0.604 (0.028%), neg=0, invalid=762
- 0171: dt=221.952000, rms=0.604 (0.020%), neg=0, invalid=762
- 0172: dt=221.952000, rms=0.604 (0.018%), neg=0, invalid=762
- 0173: dt=129.472000, rms=0.604 (0.004%), neg=0, invalid=762
- 0174: dt=129.472000, rms=0.604 (0.000%), neg=0, invalid=762
- 0175: dt=129.472000, rms=0.604 (0.005%), neg=0, invalid=762
- 0176: dt=129.472000, rms=0.604 (0.003%), neg=0, invalid=762
- 0177: dt=129.472000, rms=0.604 (0.007%), neg=0, invalid=762
- 0178: dt=129.472000, rms=0.604 (0.010%), neg=0, invalid=762
- 0179: dt=129.472000, rms=0.604 (0.007%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.605, neg=0, invalid=762
- 0180: dt=25.920000, rms=0.604 (0.067%), neg=0, invalid=762
- 0181: dt=36.288000, rms=0.604 (0.044%), neg=0, invalid=762
- 0182: dt=36.288000, rms=0.603 (0.073%), neg=0, invalid=762
- 0183: dt=36.288000, rms=0.603 (0.113%), neg=0, invalid=762
- 0184: dt=36.288000, rms=0.602 (0.148%), neg=0, invalid=762
- 0185: dt=36.288000, rms=0.601 (0.189%), neg=0, invalid=762
- 0186: dt=36.288000, rms=0.599 (0.257%), neg=0, invalid=762
- 0187: dt=36.288000, rms=0.597 (0.308%), neg=0, invalid=762
- 0188: dt=36.288000, rms=0.595 (0.317%), neg=0, invalid=762
- 0189: dt=36.288000, rms=0.593 (0.322%), neg=0, invalid=762
- 0190: dt=36.288000, rms=0.592 (0.294%), neg=0, invalid=762
- 0191: dt=36.288000, rms=0.590 (0.252%), neg=0, invalid=762
- 0192: dt=36.288000, rms=0.589 (0.235%), neg=0, invalid=762
- 0193: dt=36.288000, rms=0.588 (0.084%), neg=0, invalid=762
- 0194: dt=36.288000, rms=0.588 (0.126%), neg=0, invalid=762
- 0195: dt=36.288000, rms=0.587 (0.142%), neg=0, invalid=762
- 0196: dt=36.288000, rms=0.586 (0.157%), neg=0, invalid=762
- 0197: dt=36.288000, rms=0.585 (0.157%), neg=0, invalid=762
- 0198: dt=36.288000, rms=0.584 (0.164%), neg=0, invalid=762
- 0199: dt=36.288000, rms=0.583 (0.189%), neg=0, invalid=762
- 0200: dt=36.288000, rms=0.582 (0.203%), neg=0, invalid=762
- 0201: dt=36.288000, rms=0.581 (0.202%), neg=0, invalid=762
- 0202: dt=36.288000, rms=0.579 (0.193%), neg=0, invalid=762
- 0203: dt=36.288000, rms=0.578 (0.160%), neg=0, invalid=762
- 0204: dt=36.288000, rms=0.578 (0.138%), neg=0, invalid=762
- 0205: dt=36.288000, rms=0.577 (0.116%), neg=0, invalid=762
- 0206: dt=36.288000, rms=0.576 (0.108%), neg=0, invalid=762
- 0207: dt=36.288000, rms=0.576 (0.028%), neg=0, invalid=762
- 0208: dt=36.288000, rms=0.576 (0.045%), neg=0, invalid=762
- 0209: dt=36.288000, rms=0.576 (0.051%), neg=0, invalid=762
- 0210: dt=36.288000, rms=0.575 (0.051%), neg=0, invalid=762
- 0211: dt=36.288000, rms=0.575 (0.049%), neg=0, invalid=762
- 0212: dt=36.288000, rms=0.575 (0.051%), neg=0, invalid=762
- 0213: dt=36.288000, rms=0.574 (0.059%), neg=0, invalid=762
- 0214: dt=36.288000, rms=0.574 (0.067%), neg=0, invalid=762
- 0215: dt=36.288000, rms=0.574 (0.085%), neg=0, invalid=762
- 0216: dt=36.288000, rms=0.573 (0.088%), neg=0, invalid=762
- 0217: dt=36.288000, rms=0.573 (0.018%), neg=0, invalid=762
- 0218: dt=36.288000, rms=0.573 (0.016%), neg=0, invalid=762
- 0219: dt=25.920000, rms=0.573 (0.011%), neg=0, invalid=762
- 0220: dt=3.240000, rms=0.573 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.573, neg=0, invalid=762
- 0221: dt=145.152000, rms=0.570 (0.562%), neg=0, invalid=762
- 0222: dt=76.967320, rms=0.569 (0.172%), neg=0, invalid=762
- 0223: dt=145.152000, rms=0.568 (0.125%), neg=0, invalid=762
- 0224: dt=82.944000, rms=0.567 (0.111%), neg=0, invalid=762
- 0225: dt=103.680000, rms=0.567 (0.062%), neg=0, invalid=762
- 0226: dt=124.416000, rms=0.567 (0.091%), neg=0, invalid=762
- 0227: dt=36.288000, rms=0.566 (0.033%), neg=0, invalid=762
- 0228: dt=36.288000, rms=0.566 (0.029%), neg=0, invalid=762
- 0229: dt=36.288000, rms=0.566 (0.039%), neg=0, invalid=762
- 0230: dt=36.288000, rms=0.566 (0.055%), neg=0, invalid=762
- 0231: dt=36.288000, rms=0.565 (0.069%), neg=0, invalid=762
- 0232: dt=36.288000, rms=0.565 (0.078%), neg=0, invalid=762
- 0233: dt=36.288000, rms=0.564 (0.073%), neg=0, invalid=762
- 0234: dt=36.288000, rms=0.564 (0.071%), neg=0, invalid=762
- 0235: dt=36.288000, rms=0.564 (0.070%), neg=0, invalid=762
- 0236: dt=36.288000, rms=0.563 (0.070%), neg=0, invalid=762
- 0237: dt=36.288000, rms=0.563 (0.068%), neg=0, invalid=762
- 0238: dt=36.288000, rms=0.562 (0.069%), neg=0, invalid=762
- 0239: dt=36.288000, rms=0.562 (0.061%), neg=0, invalid=762
- 0240: dt=36.288000, rms=0.562 (0.056%), neg=0, invalid=762
- 0241: dt=36.288000, rms=0.561 (0.061%), neg=0, invalid=762
- 0242: dt=36.288000, rms=0.561 (0.063%), neg=0, invalid=762
- 0243: dt=36.288000, rms=0.561 (0.066%), neg=0, invalid=762
- 0244: dt=36.288000, rms=0.560 (0.071%), neg=0, invalid=762
- 0245: dt=36.288000, rms=0.560 (0.068%), neg=0, invalid=762
- 0246: dt=36.288000, rms=0.560 (0.065%), neg=0, invalid=762
- 0247: dt=36.288000, rms=0.559 (0.060%), neg=0, invalid=762
- 0248: dt=36.288000, rms=0.559 (0.063%), neg=0, invalid=762
- 0249: dt=36.288000, rms=0.559 (0.061%), neg=0, invalid=762
- 0250: dt=36.288000, rms=0.558 (0.063%), neg=0, invalid=762
- 0251: dt=36.288000, rms=0.558 (0.059%), neg=0, invalid=762
- 0252: dt=36.288000, rms=0.558 (0.053%), neg=0, invalid=762
- 0253: dt=36.288000, rms=0.557 (0.048%), neg=0, invalid=762
- 0254: dt=36.288000, rms=0.557 (0.048%), neg=0, invalid=762
- 0255: dt=36.288000, rms=0.557 (0.052%), neg=0, invalid=762
- 0256: dt=36.288000, rms=0.556 (0.050%), neg=0, invalid=762
- 0257: dt=36.288000, rms=0.556 (0.056%), neg=0, invalid=762
- 0258: dt=36.288000, rms=0.556 (0.055%), neg=0, invalid=762
- 0259: dt=36.288000, rms=0.556 (0.051%), neg=0, invalid=762
- 0260: dt=36.288000, rms=0.555 (0.048%), neg=0, invalid=762
- 0261: dt=36.288000, rms=0.555 (0.047%), neg=0, invalid=762
- 0262: dt=36.288000, rms=0.555 (0.042%), neg=0, invalid=762
- 0263: dt=36.288000, rms=0.555 (0.042%), neg=0, invalid=762
- 0264: dt=36.288000, rms=0.554 (0.044%), neg=0, invalid=762
- 0265: dt=36.288000, rms=0.554 (0.047%), neg=0, invalid=762
- 0266: dt=36.288000, rms=0.554 (0.047%), neg=0, invalid=762
- 0267: dt=36.288000, rms=0.554 (0.045%), neg=0, invalid=762
- 0268: dt=36.288000, rms=0.553 (0.041%), neg=0, invalid=762
- 0269: dt=36.288000, rms=0.553 (0.035%), neg=0, invalid=762
- 0270: dt=36.288000, rms=0.553 (0.026%), neg=0, invalid=762
- 0271: dt=36.288000, rms=0.553 (0.026%), neg=0, invalid=762
- 0272: dt=36.288000, rms=0.553 (0.030%), neg=0, invalid=762
- 0273: dt=36.288000, rms=0.553 (0.023%), neg=0, invalid=762
- 0274: dt=36.288000, rms=0.552 (0.029%), neg=0, invalid=762
- 0275: dt=36.288000, rms=0.552 (0.033%), neg=0, invalid=762
- 0276: dt=36.288000, rms=0.552 (0.032%), neg=0, invalid=762
- 0277: dt=36.288000, rms=0.552 (0.028%), neg=0, invalid=762
- 0278: dt=36.288000, rms=0.552 (0.003%), neg=0, invalid=762
- 0279: dt=36.288000, rms=0.552 (0.004%), neg=0, invalid=762
- 0280: dt=36.288000, rms=0.552 (0.005%), neg=0, invalid=762
- 0281: dt=36.288000, rms=0.552 (0.011%), neg=0, invalid=762
- 0282: dt=36.288000, rms=0.552 (0.007%), neg=0, invalid=762
- 0283: dt=2.268000, rms=0.552 (0.000%), neg=0, invalid=762
- 0284: dt=0.567000, rms=0.552 (0.000%), neg=0, invalid=762
- 0285: dt=0.283500, rms=0.552 (0.000%), neg=0, invalid=762
- 0286: dt=0.141750, rms=0.552 (0.000%), neg=0, invalid=762
- 0287: dt=0.004430, rms=0.552 (-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=0.559, neg=0, invalid=762
- 0288: dt=0.000000, rms=0.558 (0.027%), neg=0, invalid=762
- 0289: dt=0.000000, rms=0.558 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.559, neg=0, invalid=762
- 0290: dt=83.606936, rms=0.554 (0.734%), neg=0, invalid=762
- 0291: dt=65.795918, rms=0.549 (1.035%), neg=0, invalid=762
- 0292: dt=11.200000, rms=0.547 (0.247%), neg=0, invalid=762
- 0293: dt=11.200000, rms=0.547 (0.073%), neg=0, invalid=762
- 0294: dt=44.800000, rms=0.546 (0.141%), neg=0, invalid=762
- 0295: dt=44.800000, rms=0.543 (0.525%), neg=0, invalid=762
- 0296: dt=11.200000, rms=0.543 (0.031%), neg=0, invalid=762
- 0297: dt=11.200000, rms=0.543 (0.044%), neg=0, invalid=762
- 0298: dt=11.200000, rms=0.542 (0.086%), neg=0, invalid=762
- 0299: dt=11.200000, rms=0.542 (0.143%), neg=0, invalid=762
- 0300: dt=11.200000, rms=0.541 (0.212%), neg=0, invalid=762
- 0301: dt=2.800000, rms=0.540 (0.020%), neg=0, invalid=762
- 0302: dt=1.400000, rms=0.540 (0.010%), neg=0, invalid=762
- 0303: dt=0.175000, rms=0.540 (0.001%), neg=0, invalid=762
- 0304: dt=0.087500, rms=0.540 (0.000%), neg=0, invalid=762
- 0305: dt=0.043750, rms=0.540 (0.000%), neg=0, invalid=762
- 0306: dt=0.002734, rms=0.540 (0.000%), neg=0, invalid=762
- 0307: dt=0.001367, rms=0.540 (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=0.554, neg=0, invalid=762
- 0308: dt=4.032000, rms=0.553 (0.295%), neg=0, invalid=762
- 0309: dt=1.008000, rms=0.552 (0.058%), neg=0, invalid=762
- 0310: dt=0.252000, rms=0.552 (0.013%), neg=0, invalid=762
- 0311: dt=0.015750, rms=0.552 (0.001%), neg=0, invalid=762
- 0312: dt=0.007875, rms=0.552 (0.000%), neg=0, invalid=762
- 0313: dt=0.001969, rms=0.552 (0.000%), neg=0, invalid=762
- 0314: dt=0.000984, rms=0.552 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.552, neg=0, invalid=762
- 0315: dt=0.003938, rms=0.552 (0.032%), neg=0, invalid=762
- 0316: dt=0.000984, rms=0.552 (0.000%), neg=0, invalid=762
- 0317: dt=0.000492, rms=0.552 (0.000%), neg=0, invalid=762
- 0318: dt=0.000246, rms=0.552 (0.000%), neg=0, invalid=762
- 0319: dt=0.000123, rms=0.552 (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=0.578, neg=0, invalid=762
- 0320: dt=3.042857, rms=0.572 (1.113%), neg=0, invalid=762
- 0321: dt=1.792000, rms=0.571 (0.055%), neg=0, invalid=762
- 0322: dt=0.448000, rms=0.571 (0.006%), neg=0, invalid=762
- 0323: dt=0.448000, rms=0.571 (0.002%), neg=0, invalid=762
- 0324: dt=0.448000, rms=0.571 (-0.002%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.571, neg=0, invalid=762
- 0325: dt=6.144000, rms=0.566 (0.925%), neg=0, invalid=762
- 0326: dt=1.536000, rms=0.566 (0.035%), neg=0, invalid=762
- 0327: dt=1.536000, rms=0.566 (0.024%), neg=0, invalid=762
- 0328: dt=1.536000, rms=0.566 (0.021%), neg=0, invalid=762
- 0329: dt=1.536000, rms=0.566 (0.022%), neg=0, invalid=762
- 0330: dt=1.536000, rms=0.565 (0.025%), neg=0, invalid=762
- 0331: dt=1.536000, rms=0.565 (-0.007%), 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=0.551, neg=0, invalid=762
- 0332: dt=0.448000, rms=0.535 (2.784%), neg=0, invalid=762
- 0333: dt=0.448000, rms=0.531 (0.773%), neg=0, invalid=762
- 0334: dt=0.448000, rms=0.529 (0.454%), neg=0, invalid=762
- 0335: dt=0.448000, rms=0.527 (0.278%), neg=0, invalid=762
- 0336: dt=0.448000, rms=0.526 (0.216%), neg=0, invalid=762
- 0337: dt=0.500000, rms=0.525 (0.163%), neg=0, invalid=762
- 0338: dt=0.448000, rms=0.525 (0.132%), neg=0, invalid=762
- 0339: dt=0.448000, rms=0.524 (0.092%), neg=0, invalid=762
- 0340: dt=0.448000, rms=0.524 (0.090%), neg=0, invalid=762
- 0341: dt=0.448000, rms=0.523 (0.061%), neg=0, invalid=762
- 0342: dt=0.448000, rms=0.523 (0.067%), neg=0, invalid=762
- 0343: dt=0.448000, rms=0.523 (0.044%), neg=0, invalid=762
- 0344: dt=0.448000, rms=0.522 (0.053%), neg=0, invalid=762
- 0345: dt=0.448000, rms=0.522 (0.080%), neg=0, invalid=762
- 0346: dt=0.448000, rms=0.522 (0.027%), neg=0, invalid=762
- 0347: dt=0.224000, rms=0.522 (0.021%), neg=0, invalid=762
- 0348: dt=0.224000, rms=0.522 (0.034%), neg=0, invalid=762
- 0349: dt=0.224000, rms=0.522 (0.010%), neg=0, invalid=762
- 0350: dt=0.224000, rms=0.521 (0.022%), neg=0, invalid=762
- 0351: dt=0.224000, rms=0.521 (0.017%), neg=0, invalid=762
- 0352: dt=0.448000, rms=0.521 (0.022%), neg=0, invalid=762
- 0353: dt=0.448000, rms=0.521 (0.017%), neg=0, invalid=762
- 0354: dt=0.448000, rms=0.521 (0.015%), neg=0, invalid=762
- 0355: dt=0.448000, rms=0.521 (0.017%), neg=0, invalid=762
- 0356: dt=0.448000, rms=0.521 (0.011%), neg=0, invalid=762
- 0357: dt=0.448000, rms=0.521 (0.027%), neg=0, invalid=762
- 0358: dt=0.224000, rms=0.521 (0.009%), neg=0, invalid=762
- 0359: dt=0.224000, rms=0.521 (0.018%), neg=0, invalid=762
- 0360: dt=0.224000, rms=0.521 (0.005%), neg=0, invalid=762
- 0361: dt=0.320000, rms=0.521 (0.008%), neg=0, invalid=762
- 0362: dt=0.448000, rms=0.521 (0.005%), neg=0, invalid=762
- 0363: dt=0.448000, rms=0.520 (0.010%), neg=0, invalid=762
- 0364: dt=0.448000, rms=0.520 (0.005%), neg=0, invalid=762
- 0365: dt=0.448000, rms=0.520 (0.014%), neg=0, invalid=762
- 0366: dt=0.448000, rms=0.520 (0.011%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.521, neg=0, invalid=762
- 0367: dt=0.448000, rms=0.515 (0.998%), neg=0, invalid=762
- 0368: dt=0.448000, rms=0.514 (0.184%), neg=0, invalid=762
- 0369: dt=0.448000, rms=0.514 (0.059%), neg=0, invalid=762
- 0370: dt=0.448000, rms=0.514 (0.019%), neg=0, invalid=762
- 0371: dt=0.448000, rms=0.514 (0.009%), neg=0, invalid=762
- 0372: dt=0.448000, rms=0.514 (0.012%), neg=0, invalid=762
- 0373: dt=0.224000, rms=0.514 (0.003%), neg=0, invalid=762
- 0374: dt=0.224000, rms=0.514 (0.007%), neg=0, invalid=762
- 0375: dt=0.224000, rms=0.514 (0.002%), neg=0, invalid=762
- 0376: dt=0.384000, rms=0.514 (0.003%), neg=0, invalid=762
- 0377: dt=0.192000, rms=0.514 (0.003%), neg=0, invalid=762
- 0378: dt=0.384000, rms=0.514 (0.005%), neg=0, invalid=762
- 0379: dt=0.080000, rms=0.514 (0.000%), 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=0.512, neg=0, invalid=762
- 0380: dt=0.000000, rms=0.511 (0.052%), neg=0, invalid=762
- 0381: dt=0.000000, rms=0.511 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.512, neg=0, invalid=762
- 0382: dt=129.472000, rms=0.511 (0.177%), neg=0, invalid=762
- 0383: dt=32.368000, rms=0.511 (0.002%), neg=0, invalid=762
- 0384: dt=32.368000, rms=0.511 (0.006%), neg=0, invalid=762
- 0385: dt=32.368000, rms=0.511 (0.007%), neg=0, invalid=762
- 0386: dt=32.368000, rms=0.510 (0.014%), neg=0, invalid=762
- 0387: dt=32.368000, rms=0.510 (0.020%), neg=0, invalid=762
- 0388: dt=32.368000, rms=0.510 (0.024%), neg=0, invalid=762
- 0389: dt=32.368000, rms=0.510 (0.024%), neg=0, invalid=762
- 0390: dt=32.368000, rms=0.510 (0.019%), neg=0, invalid=762
- 0391: dt=32.368000, rms=0.510 (0.011%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.510, neg=0, invalid=762
- 0392: dt=7.776000, rms=0.510 (0.055%), neg=0, invalid=762
- 0393: dt=2.268000, rms=0.510 (0.001%), neg=0, invalid=762
- 0394: dt=2.268000, rms=0.510 (0.001%), neg=0, invalid=762
- 0395: dt=2.268000, rms=0.510 (-0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.510, neg=0, invalid=762
- 0396: dt=145.152000, rms=0.507 (0.561%), neg=0, invalid=762
- 0397: dt=31.104000, rms=0.507 (0.055%), neg=0, invalid=762
- 0398: dt=31.104000, rms=0.507 (0.045%), neg=0, invalid=762
- 0399: dt=31.104000, rms=0.506 (0.080%), neg=0, invalid=762
- 0400: dt=31.104000, rms=0.506 (0.110%), neg=0, invalid=762
- 0401: dt=31.104000, rms=0.505 (0.135%), neg=0, invalid=762
- 0402: dt=31.104000, rms=0.504 (0.139%), neg=0, invalid=762
- 0403: dt=31.104000, rms=0.504 (0.126%), neg=0, invalid=762
- 0404: dt=31.104000, rms=0.503 (0.108%), neg=0, invalid=762
- 0405: dt=31.104000, rms=0.503 (0.089%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0406: dt=497.664000, rms=0.502 (0.177%), neg=0, invalid=762
- 0407: dt=36.288000, rms=0.502 (0.078%), neg=0, invalid=762
- 0408: dt=36.288000, rms=0.501 (0.035%), neg=0, invalid=762
- 0409: dt=36.288000, rms=0.501 (0.030%), neg=0, invalid=762
- 0410: dt=36.288000, rms=0.501 (0.027%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.502, neg=0, invalid=762
- 0411: dt=11.200000, rms=0.501 (0.215%), neg=0, invalid=762
- 0412: dt=11.200000, rms=0.500 (0.095%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0413: dt=11.200000, rms=0.500 (0.073%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0414: dt=11.200000, rms=0.500 (0.042%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 2 iterations, nbhd size=0, neg = 0
- 0415: dt=11.200000, rms=0.500 (-0.037%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.500, neg=0, invalid=762
- 0416: dt=41.612403, rms=0.494 (1.279%), neg=0, invalid=762
- 0417: dt=25.181818, rms=0.492 (0.326%), neg=0, invalid=762
- 0418: dt=44.800000, rms=0.490 (0.321%), neg=0, invalid=762
- 0419: dt=24.205128, rms=0.489 (0.200%), neg=0, invalid=762
- 0420: dt=24.205128, rms=0.489 (0.158%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0421: dt=24.205128, rms=0.487 (0.243%), neg=0, invalid=762
- 0422: dt=24.205128, rms=0.486 (0.309%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0423: dt=24.205128, rms=0.485 (0.273%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 4 iterations, nbhd size=0, neg = 0
- 0424: dt=24.205128, rms=0.483 (0.327%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0425: dt=24.205128, rms=0.482 (0.313%), neg=0, invalid=762
- 0426: dt=24.205128, rms=0.480 (0.281%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0427: dt=24.205128, rms=0.479 (0.213%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 2 iterations, nbhd size=0, neg = 0
- 0428: dt=24.205128, rms=0.478 (0.190%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0429: dt=24.205128, rms=0.477 (0.195%), neg=0, invalid=762
- 0430: dt=24.205128, rms=0.477 (0.158%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 0 iterations, nbhd size=0, neg = 0
- 0431: dt=24.205128, rms=0.476 (0.111%), neg=0, invalid=762
- 0432: dt=24.205128, rms=0.476 (0.081%), neg=0, invalid=762
- 0433: dt=25.600000, rms=0.475 (0.036%), neg=0, invalid=762
- 0434: dt=25.600000, rms=0.475 (-0.006%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.482, neg=0, invalid=762
- 0435: dt=0.252000, rms=0.482 (0.041%), neg=0, invalid=762
- 0436: dt=0.108000, rms=0.482 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.482, neg=0, invalid=762
- 0437: dt=2.769231, rms=0.482 (0.070%), neg=0, invalid=762
- 0438: dt=1.500000, rms=0.482 (0.009%), neg=0, invalid=762
- 0439: dt=1.500000, rms=0.482 (0.001%), neg=0, invalid=762
- 0440: dt=1.500000, rms=0.482 (-0.017%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.493, neg=0, invalid=762
- 0441: dt=0.448000, rms=0.493 (0.087%), neg=0, invalid=762
- 0442: dt=0.256000, rms=0.493 (0.005%), neg=0, invalid=762
- 0443: dt=0.256000, rms=0.493 (-0.004%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.493, neg=0, invalid=762
- 0444: dt=1.280000, rms=0.492 (0.227%), neg=0, invalid=762
- 0445: dt=1.024000, rms=0.492 (0.044%), neg=0, invalid=762
- 0446: dt=1.024000, rms=0.492 (-0.001%), neg=0, invalid=762
- resetting metric properties...
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.480, neg=0, invalid=762
- iter 0, gcam->neg = 552
- after 12 iterations, nbhd size=1, neg = 0
- 0447: dt=1.934443, rms=0.456 (5.046%), neg=0, invalid=762
- 0448: dt=0.064000, rms=0.456 (0.039%), neg=0, invalid=762
- 0449: dt=0.064000, rms=0.456 (-0.033%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.456, neg=0, invalid=762
- 0450: dt=0.096000, rms=0.456 (0.124%), neg=0, invalid=762
- 0451: dt=0.007000, rms=0.456 (0.003%), neg=0, invalid=762
- 0452: dt=0.007000, rms=0.456 (-0.001%), 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=0.444, neg=0, invalid=762
- 0453: dt=0.000000, rms=0.444 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.444, neg=0, invalid=762
- 0454: dt=32.368000, rms=0.444 (0.007%), neg=0, invalid=762
- 0455: dt=27.744000, rms=0.444 (0.001%), neg=0, invalid=762
- 0456: dt=27.744000, rms=0.444 (-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=0.445, neg=0, invalid=762
- 0457: dt=0.000000, rms=0.445 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.445, neg=0, invalid=762
- 0458: dt=36.288000, rms=0.444 (0.039%), neg=0, invalid=762
- 0459: dt=103.680000, rms=0.444 (0.037%), neg=0, invalid=762
- 0460: dt=103.680000, rms=0.444 (0.065%), neg=0, invalid=762
- 0461: dt=103.680000, rms=0.444 (0.041%), neg=0, invalid=762
- 0462: dt=103.680000, rms=0.444 (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=0.444, neg=0, invalid=762
- 0463: dt=2.800000, rms=0.444 (0.017%), neg=0, invalid=762
- 0464: dt=2.000000, rms=0.444 (0.004%), neg=0, invalid=762
- 0465: dt=2.000000, rms=0.444 (-0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.444, neg=0, invalid=762
- 0466: dt=87.266451, rms=0.441 (0.806%), neg=0, invalid=762
- 0467: dt=11.200000, rms=0.440 (0.135%), neg=0, invalid=762
- 0468: dt=11.200000, rms=0.440 (0.048%), neg=0, invalid=762
- 0469: dt=11.200000, rms=0.440 (0.038%), neg=0, invalid=762
- 0470: dt=11.200000, rms=0.440 (0.027%), neg=0, invalid=762
- 0471: dt=44.800000, rms=0.439 (0.204%), neg=0, invalid=762
- 0472: dt=11.200000, rms=0.439 (0.024%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.441, neg=0, invalid=762
- 0473: dt=1.728000, rms=0.441 (0.024%), neg=0, invalid=762
- 0474: dt=0.576000, rms=0.441 (0.001%), neg=0, invalid=762
- 0475: dt=0.576000, rms=0.441 (-0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.441, neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 2 iterations, nbhd size=0, neg = 0
- 0476: dt=28.571429, rms=0.438 (0.737%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 7 iterations, nbhd size=1, neg = 0
- 0477: dt=11.520000, rms=0.436 (0.274%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 6 iterations, nbhd size=0, neg = 0
- 0478: dt=13.128205, rms=0.436 (0.082%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 4 iterations, nbhd size=0, neg = 0
- 0479: dt=13.128205, rms=0.436 (0.072%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 3 iterations, nbhd size=0, neg = 0
- 0480: dt=13.128205, rms=0.435 (0.140%), neg=0, invalid=762
- iter 0, gcam->neg = 11
- after 5 iterations, nbhd size=0, neg = 0
- 0481: dt=13.128205, rms=0.435 (0.116%), neg=0, invalid=762
- iter 0, gcam->neg = 14
- after 6 iterations, nbhd size=0, neg = 0
- 0482: dt=13.128205, rms=0.434 (0.133%), neg=0, invalid=762
- iter 0, gcam->neg = 16
- after 4 iterations, nbhd size=0, neg = 0
- 0483: dt=13.128205, rms=0.434 (0.096%), neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 3 iterations, nbhd size=0, neg = 0
- 0484: dt=13.128205, rms=0.433 (0.104%), neg=0, invalid=762
- iter 0, gcam->neg = 16
- after 7 iterations, nbhd size=0, neg = 0
- 0485: dt=13.128205, rms=0.433 (0.064%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 3 iterations, nbhd size=0, neg = 0
- 0486: dt=8.000000, rms=0.433 (0.021%), neg=0, invalid=762
- iter 0, gcam->neg = 8
- after 5 iterations, nbhd size=0, neg = 0
- 0487: dt=8.000000, rms=0.433 (-0.001%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.439, neg=0, invalid=762
- 0488: dt=0.000000, rms=0.439 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.439, neg=0, invalid=762
- 0489: dt=0.000050, rms=0.439 (0.000%), neg=0, invalid=762
- 0490: dt=0.000000, rms=0.439 (-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=0.429, neg=0, invalid=762
- iter 0, gcam->neg = 323
- after 13 iterations, nbhd size=1, neg = 0
- 0491: dt=1.169832, rms=0.423 (1.459%), neg=0, invalid=762
- 0492: dt=0.000023, rms=0.423 (0.000%), neg=0, invalid=762
- 0493: dt=0.000023, 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
- 0494: dt=0.192000, rms=0.422 (0.173%), neg=0, invalid=762
- 0495: dt=0.256000, rms=0.421 (0.128%), neg=0, invalid=762
- 0496: dt=0.256000, rms=0.421 (0.151%), neg=0, invalid=762
- 0497: dt=0.256000, rms=0.420 (0.152%), neg=0, invalid=762
- iter 0, gcam->neg = 40
- after 5 iterations, nbhd size=0, neg = 0
- 0498: dt=0.256000, rms=0.420 (-0.022%), neg=0, invalid=762
- 0499: dt=0.448000, rms=0.420 (0.111%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0500: dt=0.448000, rms=0.419 (0.133%), neg=0, invalid=762
- 0501: dt=0.112000, rms=0.419 (0.014%), neg=0, invalid=762
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- mri_ca_register took 2 hours, 38 minutes and 48 seconds.
- mri_ca_register utimesec 10452.348001
- mri_ca_register stimesec 10.840352
- mri_ca_register ru_maxrss 1341476
- mri_ca_register ru_ixrss 0
- mri_ca_register ru_idrss 0
- mri_ca_register ru_isrss 0
- mri_ca_register ru_minflt 5610217
- mri_ca_register ru_majflt 0
- mri_ca_register ru_nswap 0
- mri_ca_register ru_inblock 0
- mri_ca_register ru_oublock 64576
- mri_ca_register ru_msgsnd 0
- mri_ca_register ru_msgrcv 0
- mri_ca_register ru_nsignals 0
- mri_ca_register ru_nvcsw 7875
- mri_ca_register ru_nivcsw 43076
- FSRUNTIME@ mri_ca_register 2.6466 hours 2 threads
- #--------------------------------------
- #@# SubCort Seg Sat Oct 7 19:30:15 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-582
- 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-6.0.0/0051492/mri
- mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz
- == Number of threads available to mri_ca_label for OpenMP = 2 ==
- relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
- using Gibbs prior factor = 0.500
- renormalizing sequences with structure alignment, equivalent to:
- -renormalize
- -renormalize_mean 0.500
- -regularize 0.500
- reading 1 input volumes
- reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
- reading input volume from norm.mgz
- average std[0] = 7.3
- reading transform from transforms/talairach.m3z
- setting orig areas to linear transform determinant scaled 7.97
- 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 = 0.12322 (30)
- Left_Lateral_Ventricle (4): linear fit = 1.53 x + 0.0 (445 voxels, overlap=0.106)
- Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (445 voxels, peak = 31), gca=30.0
- gca peak = 0.17677 (13)
- mri peak = 0.11562 (32)
- Right_Lateral_Ventricle (43): linear fit = 2.15 x + 0.0 (421 voxels, overlap=0.108)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (421 voxels, peak = 28), gca=19.5
- gca peak = 0.28129 (95)
- mri peak = 0.10781 (94)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1010 voxels, overlap=1.013)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1010 voxels, peak = 95), gca=94.5
- gca peak = 0.16930 (96)
- mri peak = 0.10996 (98)
- Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1061 voxels, overlap=0.984)
- Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1061 voxels, peak = 98), gca=98.4
- gca peak = 0.24553 (55)
- mri peak = 0.09439 (72)
- Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1404 voxels, overlap=0.022)
- Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1404 voxels, peak = 70), gca=69.6
- gca peak = 0.30264 (59)
- mri peak = 0.09047 (72)
- Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (1221 voxels, overlap=0.021)
- Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (1221 voxels, peak = 73), gca=73.5
- gca peak = 0.07580 (103)
- mri peak = 0.11868 (103)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (66465 voxels, overlap=0.703)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (66465 voxels, peak = 102), gca=102.5
- gca peak = 0.07714 (104)
- mri peak = 0.10180 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (70066 voxels, overlap=0.735)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (70066 voxels, peak = 103), gca=103.5
- gca peak = 0.09712 (58)
- mri peak = 0.04582 (84)
- Left_Cerebral_Cortex (3): linear fit = 1.40 x + 0.0 (51106 voxels, overlap=0.000)
- Left_Cerebral_Cortex (3): linear fit = 1.40 x + 0.0 (51106 voxels, peak = 81), gca=81.5
- gca peak = 0.11620 (58)
- mri peak = 0.04152 (84)
- Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (53019 voxels, overlap=0.000)
- Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (53019 voxels, peak = 81), gca=81.5
- gca peak = 0.30970 (66)
- mri peak = 0.13087 (84)
- Right_Caudate (50): linear fit = 1.26 x + 0.0 (997 voxels, overlap=0.020)
- Right_Caudate (50): linear fit = 1.26 x + 0.0 (997 voxels, peak = 83), gca=83.5
- gca peak = 0.15280 (69)
- mri peak = 0.13548 (85)
- Left_Caudate (11): linear fit = 1.12 x + 0.0 (927 voxels, overlap=0.214)
- Left_Caudate (11): linear fit = 1.12 x + 0.0 (927 voxels, peak = 78), gca=77.6
- gca peak = 0.13902 (56)
- mri peak = 0.06630 (78)
- Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (28543 voxels, overlap=0.001)
- Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (28543 voxels, peak = 77), gca=77.0
- gca peak = 0.14777 (55)
- mri peak = 0.07011 (72)
- Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (30243 voxels, overlap=0.003)
- Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (30243 voxels, peak = 70), gca=69.6
- gca peak = 0.16765 (84)
- mri peak = 0.12230 (88)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (6655 voxels, overlap=0.729)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (6655 voxels, peak = 88), gca=87.8
- gca peak = 0.18739 (84)
- mri peak = 0.12525 (85)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6536 voxels, overlap=0.862)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6536 voxels, peak = 87), gca=86.9
- gca peak = 0.29869 (57)
- mri peak = 0.10677 (77)
- Left_Amygdala (18): linear fit = 1.32 x + 0.0 (768 voxels, overlap=0.061)
- Left_Amygdala (18): linear fit = 1.32 x + 0.0 (768 voxels, peak = 75), gca=75.0
- gca peak = 0.33601 (57)
- mri peak = 0.10219 (74)
- Right_Amygdala (54): linear fit = 1.28 x + 0.0 (821 voxels, overlap=0.049)
- Right_Amygdala (54): linear fit = 1.28 x + 0.0 (821 voxels, peak = 73), gca=73.2
- gca peak = 0.11131 (90)
- mri peak = 0.07429 (90)
- Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (5399 voxels, overlap=0.835)
- Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (5399 voxels, peak = 94), gca=94.0
- gca peak = 0.11793 (83)
- mri peak = 0.07746 (92)
- Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5716 voxels, overlap=0.607)
- Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5716 voxels, peak = 91), gca=90.9
- gca peak = 0.08324 (81)
- mri peak = 0.11389 (89)
- Left_Putamen (12): linear fit = 1.12 x + 0.0 (2933 voxels, overlap=0.154)
- Left_Putamen (12): linear fit = 1.12 x + 0.0 (2933 voxels, peak = 91), gca=91.1
- gca peak = 0.10360 (77)
- mri peak = 0.09672 (88)
- Right_Putamen (51): linear fit = 1.12 x + 0.0 (2737 voxels, overlap=0.321)
- Right_Putamen (51): linear fit = 1.12 x + 0.0 (2737 voxels, peak = 87), gca=86.6
- gca peak = 0.08424 (78)
- mri peak = 0.08873 (86)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (15349 voxels, overlap=0.476)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (15349 voxels, peak = 85), gca=85.4
- gca peak = 0.12631 (89)
- mri peak = 0.06541 (95)
- Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1891 voxels, overlap=0.563)
- Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1891 voxels, peak = 97), gca=97.5
- gca peak = 0.14500 (87)
- mri peak = 0.07900 (92)
- Left_VentralDC (28): linear fit = 1.08 x + 0.0 (2111 voxels, overlap=0.724)
- Left_VentralDC (28): linear fit = 1.08 x + 0.0 (2111 voxels, peak = 94), gca=93.5
- gca peak = 0.14975 (24)
- mri peak = 0.19055 (32)
- gca peak = 0.19357 (14)
- mri peak = 0.13752 (31)
- Fourth_Ventricle (15): linear fit = 1.90 x + 0.0 (252 voxels, overlap=0.147)
- Fourth_Ventricle (15): linear fit = 1.90 x + 0.0 (252 voxels, peak = 27), gca=26.7
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.16825 (27)
- gca peak Left_Thalamus = 1.00000 (94)
- gca peak Third_Ventricle = 0.14975 (24)
- gca peak Fourth_Ventricle = 0.19357 (14)
- gca peak CSF = 0.23379 (36)
- gca peak Left_Accumbens_area = 0.70037 (62)
- gca peak Left_undetermined = 1.00000 (26)
- gca peak Left_vessel = 0.75997 (52)
- gca peak Left_choroid_plexus = 0.12089 (35)
- gca peak Right_Inf_Lat_Vent = 0.24655 (23)
- gca peak Right_Accumbens_area = 0.45042 (65)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14516 (37)
- gca peak Fifth_Ventricle = 0.65475 (32)
- gca peak WM_hypointensities = 0.07854 (76)
- gca peak non_WM_hypointensities = 0.08491 (43)
- gca peak Optic_Chiasm = 0.71127 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.32 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 1.50 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.12544 (31)
- mri peak = 0.12322 (30)
- Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (445 voxels, overlap=0.711)
- Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (445 voxels, peak = 32), gca=32.4
- gca peak = 0.13981 (19)
- mri peak = 0.11562 (32)
- Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (421 voxels, overlap=0.313)
- Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (421 voxels, peak = 27), gca=26.7
- gca peak = 0.26724 (93)
- mri peak = 0.10781 (94)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1010 voxels, overlap=1.011)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1010 voxels, peak = 93), gca=92.5
- gca peak = 0.16267 (97)
- mri peak = 0.10996 (98)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (1061 voxels, overlap=1.004)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (1061 voxels, peak = 97), gca=97.5
- gca peak = 0.20044 (70)
- mri peak = 0.09439 (72)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1404 voxels, overlap=0.990)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1404 voxels, peak = 70), gca=70.0
- gca peak = 0.29103 (70)
- mri peak = 0.09047 (72)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1221 voxels, overlap=1.002)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1221 voxels, peak = 70), gca=70.0
- gca peak = 0.07829 (102)
- mri peak = 0.11868 (103)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (66465 voxels, overlap=0.698)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (66465 voxels, peak = 101), gca=101.5
- gca peak = 0.08042 (104)
- mri peak = 0.10180 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (70066 voxels, overlap=0.742)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (70066 voxels, peak = 103), gca=103.5
- gca peak = 0.06963 (81)
- mri peak = 0.04582 (84)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (51106 voxels, overlap=0.975)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (51106 voxels, peak = 81), gca=81.0
- gca peak = 0.08194 (81)
- mri peak = 0.04152 (84)
- Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (53019 voxels, overlap=0.971)
- Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (53019 voxels, peak = 79), gca=79.0
- gca peak = 0.21465 (83)
- mri peak = 0.13087 (84)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (997 voxels, overlap=0.999)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (997 voxels, peak = 82), gca=81.8
- gca peak = 0.16641 (87)
- mri peak = 0.13548 (85)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (927 voxels, overlap=0.977)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (927 voxels, peak = 87), gca=87.0
- gca peak = 0.10605 (76)
- mri peak = 0.06630 (78)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (28543 voxels, overlap=0.951)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (28543 voxels, peak = 75), gca=74.9
- gca peak = 0.12203 (69)
- mri peak = 0.07011 (72)
- Right_Cerebellum_Cortex (47): linear fit = 1.01 x + 0.0 (30243 voxels, overlap=0.969)
- Right_Cerebellum_Cortex (47): linear fit = 1.01 x + 0.0 (30243 voxels, peak = 70), gca=70.0
- gca peak = 0.15195 (88)
- mri peak = 0.12230 (88)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6655 voxels, overlap=0.927)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6655 voxels, peak = 88), gca=87.6
- gca peak = 0.18296 (87)
- mri peak = 0.12525 (85)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6536 voxels, overlap=0.963)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6536 voxels, peak = 87), gca=87.0
- gca peak = 0.29474 (75)
- mri peak = 0.10677 (77)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (768 voxels, overlap=1.004)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (768 voxels, peak = 75), gca=75.0
- gca peak = 0.34895 (73)
- mri peak = 0.10219 (74)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (821 voxels, overlap=0.997)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (821 voxels, peak = 73), gca=73.0
- gca peak = 0.11142 (94)
- mri peak = 0.07429 (90)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5399 voxels, overlap=0.957)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5399 voxels, peak = 94), gca=93.5
- gca peak = 0.09484 (88)
- mri peak = 0.07746 (92)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5716 voxels, overlap=0.967)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5716 voxels, peak = 88), gca=87.6
- gca peak = 0.09344 (91)
- mri peak = 0.11389 (89)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2933 voxels, overlap=0.700)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2933 voxels, peak = 91), gca=90.5
- gca peak = 0.08154 (84)
- mri peak = 0.09672 (88)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (2737 voxels, overlap=0.822)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (2737 voxels, peak = 84), gca=84.0
- gca peak = 0.07758 (86)
- mri peak = 0.08873 (86)
- Brain_Stem (16): linear fit = 0.99 x + 0.0 (15349 voxels, overlap=0.767)
- Brain_Stem (16): linear fit = 0.99 x + 0.0 (15349 voxels, peak = 85), gca=84.7
- gca peak = 0.11832 (92)
- mri peak = 0.06541 (95)
- Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1891 voxels, overlap=0.840)
- Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1891 voxels, peak = 90), gca=89.7
- gca peak = 0.16749 (92)
- mri peak = 0.07900 (92)
- Left_VentralDC (28): linear fit = 0.99 x + 0.0 (2111 voxels, overlap=0.915)
- Left_VentralDC (28): linear fit = 0.99 x + 0.0 (2111 voxels, peak = 91), gca=90.6
- gca peak = 0.12656 (38)
- mri peak = 0.19055 (32)
- gca peak = 0.16542 (24)
- mri peak = 0.13752 (31)
- Fourth_Ventricle (15): linear fit = 1.23 x + 0.0 (252 voxels, overlap=0.366)
- Fourth_Ventricle (15): linear fit = 1.23 x + 0.0 (252 voxels, peak = 29), gca=29.4
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.14119 (42)
- gca peak Left_Thalamus = 0.36646 (102)
- gca peak Third_Ventricle = 0.12656 (38)
- gca peak CSF = 0.15446 (55)
- gca peak Left_Accumbens_area = 0.41457 (70)
- gca peak Left_undetermined = 0.95280 (34)
- gca peak Left_vessel = 0.75997 (52)
- gca peak Left_choroid_plexus = 0.12303 (35)
- gca peak Right_Inf_Lat_Vent = 0.19572 (29)
- gca peak Right_Accumbens_area = 0.39758 (82)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14504 (37)
- gca peak Fifth_Ventricle = 0.51780 (46)
- gca peak WM_hypointensities = 0.07738 (75)
- gca peak non_WM_hypointensities = 0.11534 (54)
- gca peak Optic_Chiasm = 0.68905 (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 1.22 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
- 108327 voxels changed in iteration 0 of unlikely voxel relabeling
- 367 voxels changed in iteration 1 of unlikely voxel relabeling
- 0 voxels changed in iteration 2 of unlikely voxel relabeling
- 167252 gm and wm labels changed (%31 to gray, %69 to white out of all changed labels)
- 673 hippocampal voxels changed.
- 0 amygdala voxels changed.
- pass 1: 102754 changed. image ll: -2.154, PF=0.500
- pass 2: 29792 changed. image ll: -2.151, PF=0.500
- pass 3: 9747 changed.
- pass 4: 3610 changed.
- 136831 voxels changed in iteration 0 of unlikely voxel relabeling
- 1001 voxels changed in iteration 1 of unlikely voxel relabeling
- 16 voxels changed in iteration 2 of unlikely voxel relabeling
- 20 voxels changed in iteration 3 of unlikely voxel relabeling
- 4 voxels changed in iteration 4 of unlikely voxel relabeling
- 6816 voxels changed in iteration 0 of unlikely voxel relabeling
- 74 voxels changed in iteration 1 of unlikely voxel relabeling
- 10 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 6136 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
- 5345 voxels changed in iteration 0 of unlikely voxel relabeling
- 37 voxels changed in iteration 1 of unlikely voxel relabeling
- 0 voxels changed in iteration 2 of unlikely voxel relabeling
- MRItoUCHAR: min=0, max=85
- MRItoUCHAR: converting to UCHAR
- writing labeled volume to aseg.auto_noCCseg.mgz
- mri_ca_label utimesec 5397.181503
- mri_ca_label stimesec 1.681744
- mri_ca_label ru_maxrss 2115308
- mri_ca_label ru_ixrss 0
- mri_ca_label ru_idrss 0
- mri_ca_label ru_isrss 0
- mri_ca_label ru_minflt 688908
- mri_ca_label ru_majflt 0
- mri_ca_label ru_nswap 0
- mri_ca_label ru_inblock 64568
- mri_ca_label ru_oublock 504
- mri_ca_label ru_msgsnd 0
- mri_ca_label ru_msgrcv 0
- mri_ca_label ru_nsignals 0
- mri_ca_label ru_nvcsw 411
- mri_ca_label ru_nivcsw 14457
- auto-labeling took 89 minutes and 25 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/transforms/cc_up.lta 0051492
- 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-6.0.0/0051492/mri/transforms/cc_up.lta
- reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/aseg.auto_noCCseg.mgz
- reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/norm.mgz
- 93398 voxels in left wm, 69611 in right wm, xrange [121, 135]
- searching rotation angles z=[-8 6], y=[-4 10]
-
searching scale 1 Z rot -7.5
searching scale 1 Z rot -7.3
searching scale 1 Z rot -7.0
searching scale 1 Z rot -6.8
searching scale 1 Z rot -6.5
searching scale 1 Z rot -6.3
searching scale 1 Z rot -6.0
searching scale 1 Z rot -5.8
searching scale 1 Z rot -5.5
searching scale 1 Z rot -5.3
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.8
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.3
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.8
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.3
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.8
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.3
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.8
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.3
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.8
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.3
searching scale 1 Z rot -0.0
searching scale 1 Z rot 0.2
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.7
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.2
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.7
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.2
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.7
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.2
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.7
searching scale 1 Z rot 4.0
searching scale 1 Z rot 4.2
searching scale 1 Z rot 4.5
searching scale 1 Z rot 4.7
searching scale 1 Z rot 5.0
searching scale 1 Z rot 5.2
searching scale 1 Z rot 5.5
searching scale 1 Z rot 5.7
searching scale 1 Z rot 6.0
searching scale 1 Z rot 6.2 global minimum found at slice 126.7, rotations (2.66, -0.51)
- final transformation (x=126.7, yr=2.663, zr=-0.510):
- 0.99888 0.00891 0.04647 -4.32541;
- -0.00890 0.99996 -0.00041 56.17591;
- -0.04647 0.00000 0.99892 23.00558;
- 0.00000 0.00000 0.00000 1.00000;
- updating x range to be [126, 130] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 73 111
- eigenvectors:
- 0.00106 -0.00147 1.00000;
- -0.00338 -0.99999 -0.00147;
- 0.99999 -0.00338 -0.00107;
- writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/aseg.auto.mgz...
- corpus callosum segmentation took 1.7 minutes
- #--------------------------------------
- #@# Merge ASeg Sat Oct 7 21:01:23 CEST 2017
- cp aseg.auto.mgz aseg.presurf.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Sat Oct 7 21:01:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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...
- 1950 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 110
- gm peak at 88 (88), valley at 24 (24)
- csf peak at 44, setting threshold to 73
- 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 88 (88), valley at 24 (24)
- csf peak at 45, setting threshold to 73
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 3 minutes and 24 seconds.
- #--------------------------------------------
- #@# Mask BFS Sat Oct 7 21:04:49 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1829615 voxels in mask (pct= 10.91)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Sat Oct 7 21:04:50 CEST 2017
- mri_segment -mprage brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (104.0): 104.5 +- 5.4 [79.0 --> 125.0]
- GM (81.0) : 77.4 +- 13.2 [30.0 --> 95.0]
- setting bottom of white matter range to 90.6
- setting top of gray matter range to 103.8
- 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...
- 11791 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 3787 filled
- 2482 bright non-wm voxels segmented.
- 6765 diagonally connected voxels added...
- white matter segmentation took 2.2 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 0.48 minutes
- reading wm segmentation from wm.seg.mgz...
- 145 voxels added to wm to prevent paths from MTL structures to cortex
- 6197 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 42214 voxels turned on, 48476 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 0 new 0
- 115,126,128 old 0 new 0
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 24 found - 24 modified | TOTAL: 24
- pass 2 (xy+): 0 found - 24 modified | TOTAL: 24
- pass 1 (xy-): 37 found - 37 modified | TOTAL: 61
- pass 2 (xy-): 0 found - 37 modified | TOTAL: 61
- pass 1 (yz+): 39 found - 39 modified | TOTAL: 100
- pass 2 (yz+): 0 found - 39 modified | TOTAL: 100
- pass 1 (yz-): 46 found - 46 modified | TOTAL: 146
- pass 2 (yz-): 0 found - 46 modified | TOTAL: 146
- pass 1 (xz+): 50 found - 50 modified | TOTAL: 196
- pass 2 (xz+): 0 found - 50 modified | TOTAL: 196
- pass 1 (xz-): 54 found - 54 modified | TOTAL: 250
- pass 2 (xz-): 0 found - 54 modified | TOTAL: 250
- Iteration Number : 1
- pass 1 (+++): 30 found - 30 modified | TOTAL: 30
- pass 2 (+++): 0 found - 30 modified | TOTAL: 30
- pass 1 (+++): 27 found - 27 modified | TOTAL: 57
- pass 2 (+++): 0 found - 27 modified | TOTAL: 57
- pass 1 (+++): 18 found - 18 modified | TOTAL: 75
- pass 2 (+++): 0 found - 18 modified | TOTAL: 75
- pass 1 (+++): 39 found - 39 modified | TOTAL: 114
- pass 2 (+++): 0 found - 39 modified | TOTAL: 114
- Iteration Number : 1
- pass 1 (++): 178 found - 178 modified | TOTAL: 178
- pass 2 (++): 0 found - 178 modified | TOTAL: 178
- pass 1 (+-): 209 found - 209 modified | TOTAL: 387
- pass 2 (+-): 0 found - 209 modified | TOTAL: 387
- pass 1 (--): 187 found - 187 modified | TOTAL: 574
- pass 2 (--): 0 found - 187 modified | TOTAL: 574
- pass 1 (-+): 202 found - 202 modified | TOTAL: 776
- pass 2 (-+): 0 found - 202 modified | TOTAL: 776
- Iteration Number : 2
- pass 1 (xy+): 15 found - 15 modified | TOTAL: 15
- pass 2 (xy+): 0 found - 15 modified | TOTAL: 15
- pass 1 (xy-): 11 found - 11 modified | TOTAL: 26
- pass 2 (xy-): 0 found - 11 modified | TOTAL: 26
- pass 1 (yz+): 15 found - 15 modified | TOTAL: 41
- pass 2 (yz+): 0 found - 15 modified | TOTAL: 41
- pass 1 (yz-): 18 found - 18 modified | TOTAL: 59
- pass 2 (yz-): 0 found - 18 modified | TOTAL: 59
- pass 1 (xz+): 9 found - 9 modified | TOTAL: 68
- pass 2 (xz+): 0 found - 9 modified | TOTAL: 68
- pass 1 (xz-): 10 found - 10 modified | TOTAL: 78
- pass 2 (xz-): 0 found - 10 modified | TOTAL: 78
- Iteration Number : 2
- pass 1 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+++): 2 found - 2 modified | TOTAL: 4
- pass 2 (+++): 0 found - 2 modified | TOTAL: 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 4
- pass 1 (+++): 1 found - 1 modified | TOTAL: 5
- pass 2 (+++): 0 found - 1 modified | TOTAL: 5
- Iteration Number : 2
- pass 1 (++): 9 found - 9 modified | TOTAL: 9
- pass 2 (++): 0 found - 9 modified | TOTAL: 9
- pass 1 (+-): 7 found - 7 modified | TOTAL: 16
- pass 2 (+-): 0 found - 7 modified | TOTAL: 16
- pass 1 (--): 6 found - 6 modified | TOTAL: 22
- pass 2 (--): 0 found - 6 modified | TOTAL: 22
- pass 1 (-+): 3 found - 3 modified | TOTAL: 25
- pass 2 (-+): 0 found - 3 modified | TOTAL: 25
- Iteration Number : 3
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 3 found - 3 modified | TOTAL: 4
- pass 2 (xy-): 0 found - 3 modified | TOTAL: 4
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 5
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 5
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 5
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 5
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 5
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 1 found - 1 modified | TOTAL: 1
- pass 2 (+-): 0 found - 1 modified | TOTAL: 1
- pass 1 (--): 0 found - 0 modified | TOTAL: 1
- pass 1 (-+): 1 found - 1 modified | TOTAL: 2
- pass 2 (-+): 0 found - 1 modified | TOTAL: 2
- 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-): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz-): 0 found - 1 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 : 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
- Iteration Number : 5
- 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 : 5
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 5
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 1257 (out of 673233: 0.186711)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Sat Oct 7 21:07:37 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri
- mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
- logging cutting plane coordinates to ../scripts/ponscc.cut.log...
- INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
- using segmentation aseg.auto_noCCseg.mgz...
- reading input volume...done.
- searching for cutting planes...voxel to talairach voxel transform
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09242 1.06364 0.09253 21.59372;
- -0.05707 -0.11609 0.94472 16.61148;
- 0.00000 0.00000 0.00000 1.00000;
- voxel to talairach voxel transform
- 0.97679 0.09095 0.05660 -12.73767;
- -0.09242 1.06364 0.09253 21.59372;
- -0.05707 -0.11609 0.94472 16.61148;
- 0.00000 0.00000 0.00000 1.00000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 2666 (min = 350, max = 1400), aspect = 1.14 (min = 0.10, max = 0.75)
- need search nearby
- using seed (126, 123, 146), TAL = (2.0, 18.0, 5.0)
- talairach voxel to voxel transform
- 1.01203 -0.09217 -0.05161 15.73845;
- 0.08174 0.92278 -0.09528 -17.30231;
- 0.07118 0.10782 1.04369 -18.75876;
- 0.00000 0.00000 0.00000 1.00000;
- segmentation indicates cc at (126, 123, 146) --> (2.0, 18.0, 5.0)
- done.
- writing output to filled.mgz...
- filling took 0.8 minutes
- talairach cc position changed to (2.00, 18.00, 5.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, 18.00, 5.00) SRC: (106.17, 91.12, 154.57)
- search lh wm seed point around talairach space (-16.00, 18.00, 5.00), SRC: (142.60, 94.06, 157.13)
- 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 Sat Oct 7 21:08:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 2 found - 2 modified | TOTAL: 3
- pass 2 (xy-): 0 found - 2 modified | TOTAL: 3
- pass 1 (yz+): 4 found - 4 modified | TOTAL: 7
- pass 2 (yz+): 0 found - 4 modified | TOTAL: 7
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 8
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 8
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 9
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 9
- pass 1 (xz-): 4 found - 4 modified | TOTAL: 13
- pass 2 (xz-): 0 found - 4 modified | TOTAL: 13
- 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 (+-): 2 found - 2 modified | TOTAL: 3
- pass 2 (+-): 0 found - 2 modified | TOTAL: 3
- pass 1 (--): 1 found - 1 modified | TOTAL: 4
- pass 2 (--): 0 found - 1 modified | TOTAL: 4
- pass 1 (-+): 1 found - 1 modified | TOTAL: 5
- pass 2 (-+): 0 found - 1 modified | TOTAL: 5
- 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 = 18 (out of 326727: 0.005509)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- slice 30: 320 vertices, 366 faces
- slice 40: 4047 vertices, 4221 faces
- slice 50: 11043 vertices, 11330 faces
- slice 60: 21152 vertices, 21511 faces
- slice 70: 32258 vertices, 32685 faces
- slice 80: 44602 vertices, 45040 faces
- slice 90: 57135 vertices, 57565 faces
- slice 100: 69718 vertices, 70228 faces
- slice 110: 82603 vertices, 83049 faces
- slice 120: 95958 vertices, 96482 faces
- slice 130: 109386 vertices, 109919 faces
- slice 140: 123450 vertices, 123977 faces
- slice 150: 135439 vertices, 135936 faces
- slice 160: 144987 vertices, 145389 faces
- slice 170: 153346 vertices, 153708 faces
- slice 180: 161503 vertices, 161876 faces
- slice 190: 167785 vertices, 168105 faces
- slice 200: 173171 vertices, 173434 faces
- slice 210: 174336 vertices, 174458 faces
- slice 220: 174336 vertices, 174458 faces
- slice 230: 174336 vertices, 174458 faces
- slice 240: 174336 vertices, 174458 faces
- slice 250: 174336 vertices, 174458 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...
- 174336 voxel in cpt #1: X=-122 [v=174336,e=523374,f=348916] located at (-27.211189, -15.077953, 40.670544)
- For the whole surface: X=-122 [v=174336,e=523374,f=348916]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Tessellate rh Sat Oct 7 21:08:30 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 2
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 2
- pass 1 (yz+): 3 found - 3 modified | TOTAL: 5
- pass 2 (yz+): 0 found - 3 modified | TOTAL: 5
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 6
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 6
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 6
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 6
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 6 (out of 326308: 0.001839)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
- $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- slice 30: 1113 vertices, 1219 faces
- slice 40: 6164 vertices, 6373 faces
- slice 50: 13736 vertices, 14025 faces
- slice 60: 24186 vertices, 24588 faces
- slice 70: 36798 vertices, 37254 faces
- slice 80: 49243 vertices, 49697 faces
- slice 90: 61640 vertices, 62100 faces
- slice 100: 74717 vertices, 75196 faces
- slice 110: 87582 vertices, 88073 faces
- slice 120: 101234 vertices, 101727 faces
- slice 130: 114101 vertices, 114603 faces
- slice 140: 126999 vertices, 127479 faces
- slice 150: 137549 vertices, 137949 faces
- slice 160: 145898 vertices, 146273 faces
- slice 170: 154375 vertices, 154731 faces
- slice 180: 161588 vertices, 161953 faces
- slice 190: 168387 vertices, 168726 faces
- slice 200: 173274 vertices, 173491 faces
- slice 210: 174102 vertices, 174224 faces
- slice 220: 174102 vertices, 174224 faces
- slice 230: 174102 vertices, 174224 faces
- slice 240: 174102 vertices, 174224 faces
- slice 250: 174102 vertices, 174224 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...
- 174102 voxel in cpt #1: X=-122 [v=174102,e=522672,f=348448] located at (29.865562, -18.113951, 40.961079)
- For the whole surface: X=-122 [v=174102,e=522672,f=348448]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Sat Oct 7 21:08:37 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- #--------------------------------------------
- #@# Smooth1 rh Sat Oct 7 21:08:37 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- Waiting for PID 13040 of (13040 13043) to complete...
- Waiting for PID 13043 of (13040 13043) 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 (13040 13043) completed and logs appended.
- #--------------------------------------------
- #@# Inflation1 lh Sat Oct 7 21:08:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- #--------------------------------------------
- #@# Inflation1 rh Sat Oct 7 21:08:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Waiting for PID 13107 of (13107 13110) to complete...
- Waiting for PID 13110 of (13107 13110) 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 = 50.4 mm, total surface area = 90694 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 1.5 minutes
-
step 000: RMS=0.159 (target=0.015)
step 005: RMS=0.122 (target=0.015)
step 010: RMS=0.094 (target=0.015)
step 015: RMS=0.080 (target=0.015)
step 020: RMS=0.070 (target=0.015)
step 025: RMS=0.062 (target=0.015)
step 030: RMS=0.057 (target=0.015)
step 035: RMS=0.052 (target=0.015)
step 040: RMS=0.048 (target=0.015)
step 045: RMS=0.046 (target=0.015)
step 050: RMS=0.045 (target=0.015)
step 055: RMS=0.044 (target=0.015)
step 060: RMS=0.044 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 89.884335
- mris_inflate stimesec 0.141978
- mris_inflate ru_maxrss 254480
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 36474
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 12288
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2168
- mris_inflate ru_nivcsw 9929
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Not saving sulc
- Reading ../surf/rh.smoothwm.nofix
- avg radius = 50.7 mm, total surface area = 90965 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 1.8 minutes
-
step 000: RMS=0.158 (target=0.015)
step 005: RMS=0.121 (target=0.015)
step 010: RMS=0.092 (target=0.015)
step 015: RMS=0.078 (target=0.015)
step 020: RMS=0.066 (target=0.015)
step 025: RMS=0.058 (target=0.015)
step 030: RMS=0.052 (target=0.015)
step 035: RMS=0.048 (target=0.015)
step 040: RMS=0.044 (target=0.015)
step 045: RMS=0.043 (target=0.015)
step 050: RMS=0.041 (target=0.015)
step 055: RMS=0.040 (target=0.015)
step 060: RMS=0.040 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 113.245784
- mris_inflate stimesec 0.194970
- mris_inflate ru_maxrss 254164
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 36905
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 12272
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 7592
- mris_inflate ru_nivcsw 7208
- PIDs (13107 13110) completed and logs appended.
- #--------------------------------------------
- #@# QSphere lh Sat Oct 7 21:10:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- #--------------------------------------------
- #@# QSphere rh Sat Oct 7 21:10:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- Waiting for PID 13210 of (13210 13214) to complete...
- Waiting for PID 13214 of (13210 13214) 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 0.88 +- 0.54 (0.00-->7.69) (max @ vno 116002 --> 116003)
- face area 0.02 +- 0.03 (-0.22-->0.48)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.274...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=177.205, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.945, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.386, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.652, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.819, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.928, avgs=0
- 030/300: dt: 0.9000, rms radial error=173.006, avgs=0
- 035/300: dt: 0.9000, rms radial error=172.066, avgs=0
- 040/300: dt: 0.9000, rms radial error=171.119, avgs=0
- 045/300: dt: 0.9000, rms radial error=170.170, avgs=0
- 050/300: dt: 0.9000, rms radial error=169.222, avgs=0
- 055/300: dt: 0.9000, rms radial error=168.277, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.336, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.399, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.466, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.537, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.613, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.696, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.782, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.873, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.969, avgs=0
- 105/300: dt: 0.9000, rms radial error=159.071, avgs=0
- 110/300: dt: 0.9000, rms radial error=158.174, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.288, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.402, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.522, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.646, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.775, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.913, avgs=0
- 145/300: dt: 0.9000, rms radial error=152.050, avgs=0
- 150/300: dt: 0.9000, rms radial error=151.195, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.344, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.497, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.657, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.821, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.990, avgs=0
- 180/300: dt: 0.9000, rms radial error=146.163, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.340, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.521, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.707, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.898, avgs=0
- 205/300: dt: 0.9000, rms radial error=142.093, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.292, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.496, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.704, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.917, avgs=0
- 230/300: dt: 0.9000, rms radial error=138.133, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.355, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.580, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.810, avgs=0
- 250/300: dt: 0.9000, rms radial error=135.045, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.283, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.526, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.773, avgs=0
- 270/300: dt: 0.9000, rms radial error=132.024, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.279, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.539, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.803, avgs=0
- 290/300: dt: 0.9000, rms radial error=129.071, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.342, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.618, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 21216.61
- 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 = 3867.50
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
- epoch 3 (K=160.0), pass 1, starting sse = 454.67
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.03/10 = 0.00270
- epoch 4 (K=640.0), pass 1, starting sse = 34.55
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.04/10 = 0.00435
- final distance error %29.37
- writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.14 hours
- mris_sphere utimesec 509.380562
- mris_sphere stimesec 0.335948
- mris_sphere ru_maxrss 254684
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 36530
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 12312
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 13121
- mris_sphere ru_nivcsw 33058
- FSRUNTIME@ mris_sphere 0.1368 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 0.88 +- 0.53 (0.00-->5.78) (max @ vno 124323 --> 124324)
- face area 0.02 +- 0.02 (-0.12-->0.52)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.271...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=177.340, avgs=0
- 005/300: dt: 0.9000, rms radial error=177.078, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.515, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.776, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.934, avgs=0
- 025/300: dt: 0.9000, rms radial error=174.037, avgs=0
- 030/300: dt: 0.9000, rms radial error=173.107, avgs=0
- 035/300: dt: 0.9000, rms radial error=172.162, avgs=0
- 040/300: dt: 0.9000, rms radial error=171.209, avgs=0
- 045/300: dt: 0.9000, rms radial error=170.254, avgs=0
- 050/300: dt: 0.9000, rms radial error=169.300, avgs=0
- 055/300: dt: 0.9000, rms radial error=168.349, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.401, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.459, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.521, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.589, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.662, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.741, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.825, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.914, avgs=0
- 100/300: dt: 0.9000, rms radial error=160.008, avgs=0
- 105/300: dt: 0.9000, rms radial error=159.107, avgs=0
- 110/300: dt: 0.9000, rms radial error=158.211, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.320, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.434, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.553, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.677, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.806, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.939, avgs=0
- 145/300: dt: 0.9000, rms radial error=152.078, avgs=0
- 150/300: dt: 0.9000, rms radial error=151.221, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.368, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.520, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.677, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.839, avgs=0
- 175/300: dt: 0.9000, rms radial error=147.006, avgs=0
- 180/300: dt: 0.9000, rms radial error=146.177, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.352, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.532, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.717, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.906, avgs=0
- 205/300: dt: 0.9000, rms radial error=142.100, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.299, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.502, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.709, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.921, avgs=0
- 230/300: dt: 0.9000, rms radial error=138.137, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.358, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.583, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.812, avgs=0
- 250/300: dt: 0.9000, rms radial error=135.046, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.284, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.527, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.773, avgs=0
- 270/300: dt: 0.9000, rms radial error=132.024, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.279, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.538, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.801, avgs=0
- 290/300: dt: 0.9000, rms radial error=129.068, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.340, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.616, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 21223.90
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
- epoch 2 (K=40.0), pass 1, starting sse = 3855.86
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00002
- epoch 3 (K=160.0), pass 1, starting sse = 462.08
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.06/11 = 0.00545
- epoch 4 (K=640.0), pass 1, starting sse = 34.63
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.13/13 = 0.00963
- final distance error %28.95
- writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.13 hours
- mris_sphere utimesec 457.417461
- mris_sphere stimesec 0.204968
- mris_sphere ru_maxrss 254364
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 36443
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 12296
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 13259
- mris_sphere ru_nivcsw 33244
- FSRUNTIME@ mris_sphere 0.1272 hours 1 threads
- PIDs (13210 13214) completed and logs appended.
- #--------------------------------------------
- #@# Fix Topology Copy lh Sat Oct 7 21:18:46 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- #--------------------------------------------
- #@# Fix Topology Copy rh Sat Oct 7 21:18:46 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- #@# Fix Topology lh Sat Oct 7 21:18:46 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051492 lh
- #@# Fix Topology rh Sat Oct 7 21:18:46 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051492 rh
- Waiting for PID 13604 of (13604 13607) to complete...
- Waiting for PID 13607 of (13604 13607) to complete...
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051492 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=-122 (nv=174336, nf=348916, ne=523374, g=62)
- 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 12 iterations
- marking ambiguous vertices...
- 7761 ambiguous faces found in tessellation
- segmenting defects...
- 73 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 36 into 35
- -merging segment 60 into 50
- 71 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.0978 (-4.5489)
- -vertex loglikelihood: -5.5885 (-2.7942)
- -normal dot loglikelihood: -3.6544 (-3.6544)
- -quad curv loglikelihood: -5.9334 (-2.9667)
- Total Loglikelihood : -24.2741
- CORRECTING DEFECT 0 (vertices=258, convex hull=181, v0=590)
- After retessellation of defect 0 (v0=590), euler #=-70 (169547,506547,336930) : difference with theory (-68) = 2
- CORRECTING DEFECT 1 (vertices=77, convex hull=114, v0=658)
- After retessellation of defect 1 (v0=658), euler #=-69 (169558,506630,337003) : difference with theory (-67) = 2
- CORRECTING DEFECT 2 (vertices=19, convex hull=19, v0=10132)
- After retessellation of defect 2 (v0=10132), euler #=-68 (169559,506639,337012) : difference with theory (-66) = 2
- CORRECTING DEFECT 3 (vertices=23, convex hull=52, v0=11660)
- After retessellation of defect 3 (v0=11660), euler #=-67 (169570,506694,337057) : difference with theory (-65) = 2
- CORRECTING DEFECT 4 (vertices=17, convex hull=21, v0=13329)
- After retessellation of defect 4 (v0=13329), euler #=-66 (169572,506706,337068) : difference with theory (-64) = 2
- CORRECTING DEFECT 5 (vertices=47, convex hull=98, v0=13336)
- After retessellation of defect 5 (v0=13336), euler #=-65 (169581,506777,337131) : difference with theory (-63) = 2
- CORRECTING DEFECT 6 (vertices=35, convex hull=65, v0=18871)
- After retessellation of defect 6 (v0=18871), euler #=-64 (169593,506840,337183) : difference with theory (-62) = 2
- CORRECTING DEFECT 7 (vertices=30, convex hull=44, v0=19627)
- After retessellation of defect 7 (v0=19627), euler #=-63 (169600,506881,337218) : difference with theory (-61) = 2
- CORRECTING DEFECT 8 (vertices=28, convex hull=26, v0=21015)
- After retessellation of defect 8 (v0=21015), euler #=-62 (169601,506895,337232) : difference with theory (-60) = 2
- CORRECTING DEFECT 9 (vertices=32, convex hull=77, v0=24216)
- After retessellation of defect 9 (v0=24216), euler #=-61 (169616,506969,337292) : difference with theory (-59) = 2
- CORRECTING DEFECT 10 (vertices=25, convex hull=63, v0=24597)
- After retessellation of defect 10 (v0=24597), euler #=-60 (169625,507019,337334) : difference with theory (-58) = 2
- CORRECTING DEFECT 11 (vertices=24, convex hull=58, v0=30111)
- After retessellation of defect 11 (v0=30111), euler #=-59 (169635,507074,337380) : difference with theory (-57) = 2
- CORRECTING DEFECT 12 (vertices=63, convex hull=75, v0=31873)
- After retessellation of defect 12 (v0=31873), euler #=-58 (169644,507137,337435) : difference with theory (-56) = 2
- CORRECTING DEFECT 13 (vertices=73, convex hull=72, v0=40693)
- After retessellation of defect 13 (v0=40693), euler #=-57 (169661,507219,337501) : difference with theory (-55) = 2
- CORRECTING DEFECT 14 (vertices=38, convex hull=67, v0=45082)
- After retessellation of defect 14 (v0=45082), euler #=-56 (169679,507299,337564) : difference with theory (-54) = 2
- CORRECTING DEFECT 15 (vertices=27, convex hull=55, v0=48325)
- After retessellation of defect 15 (v0=48325), euler #=-55 (169688,507347,337604) : difference with theory (-53) = 2
- CORRECTING DEFECT 16 (vertices=70, convex hull=87, v0=49616)
- After retessellation of defect 16 (v0=49616), euler #=-54 (169706,507440,337680) : difference with theory (-52) = 2
- CORRECTING DEFECT 17 (vertices=18, convex hull=24, v0=51825)
- After retessellation of defect 17 (v0=51825), euler #=-53 (169709,507455,337693) : difference with theory (-51) = 2
- CORRECTING DEFECT 18 (vertices=262, convex hull=226, v0=61673)
- After retessellation of defect 18 (v0=61673), euler #=-52 (169718,507596,337826) : difference with theory (-50) = 2
- CORRECTING DEFECT 19 (vertices=15, convex hull=26, v0=66504)
- After retessellation of defect 19 (v0=66504), euler #=-51 (169719,507608,337838) : difference with theory (-49) = 2
- CORRECTING DEFECT 20 (vertices=179, convex hull=120, v0=66647)
- After retessellation of defect 20 (v0=66647), euler #=-50 (169767,507807,337990) : difference with theory (-48) = 2
- CORRECTING DEFECT 21 (vertices=35, convex hull=58, v0=68123)
- After retessellation of defect 21 (v0=68123), euler #=-49 (169790,507898,338059) : difference with theory (-47) = 2
- CORRECTING DEFECT 22 (vertices=46, convex hull=71, v0=73518)
- After retessellation of defect 22 (v0=73518), euler #=-48 (169806,507973,338119) : difference with theory (-46) = 2
- CORRECTING DEFECT 23 (vertices=35, convex hull=69, v0=80405)
- After retessellation of defect 23 (v0=80405), euler #=-47 (169826,508063,338190) : difference with theory (-45) = 2
- CORRECTING DEFECT 24 (vertices=47, convex hull=35, v0=87731)
- After retessellation of defect 24 (v0=87731), euler #=-46 (169833,508097,338218) : difference with theory (-44) = 2
- CORRECTING DEFECT 25 (vertices=14, convex hull=32, v0=96923)
- After retessellation of defect 25 (v0=96923), euler #=-45 (169838,508123,338240) : difference with theory (-43) = 2
- CORRECTING DEFECT 26 (vertices=25, convex hull=28, v0=97083)
- After retessellation of defect 26 (v0=97083), euler #=-44 (169844,508152,338264) : difference with theory (-42) = 2
- CORRECTING DEFECT 27 (vertices=28, convex hull=65, v0=97443)
- After retessellation of defect 27 (v0=97443), euler #=-43 (169859,508221,338319) : difference with theory (-41) = 2
- CORRECTING DEFECT 28 (vertices=38, convex hull=76, v0=102378)
- After retessellation of defect 28 (v0=102378), euler #=-42 (169868,508279,338369) : difference with theory (-40) = 2
- CORRECTING DEFECT 29 (vertices=26, convex hull=48, v0=103035)
- After retessellation of defect 29 (v0=103035), euler #=-41 (169877,508325,338407) : difference with theory (-39) = 2
- CORRECTING DEFECT 30 (vertices=50, convex hull=53, v0=105265)
- After retessellation of defect 30 (v0=105265), euler #=-40 (169886,508372,338446) : difference with theory (-38) = 2
- CORRECTING DEFECT 31 (vertices=10, convex hull=20, v0=108766)
- After retessellation of defect 31 (v0=108766), euler #=-39 (169887,508381,338455) : difference with theory (-37) = 2
- CORRECTING DEFECT 32 (vertices=94, convex hull=40, v0=109213)
- After retessellation of defect 32 (v0=109213), euler #=-38 (169897,508424,338489) : difference with theory (-36) = 2
- CORRECTING DEFECT 33 (vertices=41, convex hull=87, v0=109321)
- After retessellation of defect 33 (v0=109321), euler #=-37 (169919,508524,338568) : difference with theory (-35) = 2
- CORRECTING DEFECT 34 (vertices=6, convex hull=24, v0=110382)
- After retessellation of defect 34 (v0=110382), euler #=-36 (169921,508536,338579) : difference with theory (-34) = 2
- CORRECTING DEFECT 35 (vertices=251, convex hull=262, v0=110392)
- After retessellation of defect 35 (v0=110392), euler #=-34 (170042,509031,338955) : difference with theory (-33) = 1
- CORRECTING DEFECT 36 (vertices=97, convex hull=76, v0=113627)
- After retessellation of defect 36 (v0=113627), euler #=-33 (170059,509119,339027) : difference with theory (-32) = 1
- CORRECTING DEFECT 37 (vertices=7, convex hull=21, v0=114622)
- After retessellation of defect 37 (v0=114622), euler #=-32 (170061,509130,339037) : difference with theory (-31) = 1
- CORRECTING DEFECT 38 (vertices=72, convex hull=57, v0=115056)
- After retessellation of defect 38 (v0=115056), euler #=-31 (170079,509208,339098) : difference with theory (-30) = 1
- CORRECTING DEFECT 39 (vertices=46, convex hull=34, v0=115823)
- After retessellation of defect 39 (v0=115823), euler #=-30 (170086,509242,339126) : difference with theory (-29) = 1
- CORRECTING DEFECT 40 (vertices=170, convex hull=100, v0=117188)
- After retessellation of defect 40 (v0=117188), euler #=-29 (170141,509452,339282) : difference with theory (-28) = 1
- CORRECTING DEFECT 41 (vertices=41, convex hull=78, v0=117382)
- After retessellation of defect 41 (v0=117382), euler #=-28 (170151,509517,339338) : difference with theory (-27) = 1
- CORRECTING DEFECT 42 (vertices=47, convex hull=45, v0=117521)
- After retessellation of defect 42 (v0=117521), euler #=-27 (170167,509581,339387) : difference with theory (-26) = 1
- CORRECTING DEFECT 43 (vertices=165, convex hull=141, v0=117712)
- After retessellation of defect 43 (v0=117712), euler #=-26 (170216,509791,339549) : difference with theory (-25) = 1
- CORRECTING DEFECT 44 (vertices=20, convex hull=27, v0=117917)
- After retessellation of defect 44 (v0=117917), euler #=-25 (170218,509810,339567) : difference with theory (-24) = 1
- CORRECTING DEFECT 45 (vertices=39, convex hull=66, v0=118529)
- After retessellation of defect 45 (v0=118529), euler #=-24 (170239,509899,339636) : difference with theory (-23) = 1
- CORRECTING DEFECT 46 (vertices=34, convex hull=85, v0=119206)
- After retessellation of defect 46 (v0=119206), euler #=-23 (170257,509982,339702) : difference with theory (-22) = 1
- CORRECTING DEFECT 47 (vertices=174, convex hull=67, v0=120264)
- After retessellation of defect 47 (v0=120264), euler #=-22 (170270,510048,339756) : difference with theory (-21) = 1
- CORRECTING DEFECT 48 (vertices=107, convex hull=109, v0=124195)
- After retessellation of defect 48 (v0=124195), euler #=-21 (170304,510200,339875) : difference with theory (-20) = 1
- CORRECTING DEFECT 49 (vertices=462, convex hull=335, v0=125772)
- After retessellation of defect 49 (v0=125772), euler #=-19 (170452,510806,340335) : difference with theory (-19) = 0
- CORRECTING DEFECT 50 (vertices=286, convex hull=168, v0=125960)
- After retessellation of defect 50 (v0=125960), euler #=-18 (170511,511058,340529) : difference with theory (-18) = 0
- CORRECTING DEFECT 51 (vertices=54, convex hull=58, v0=131181)
- After retessellation of defect 51 (v0=131181), euler #=-17 (170528,511130,340585) : difference with theory (-17) = 0
- CORRECTING DEFECT 52 (vertices=76, convex hull=99, v0=131460)
- After retessellation of defect 52 (v0=131460), euler #=-16 (170568,511290,340706) : difference with theory (-16) = 0
- CORRECTING DEFECT 53 (vertices=38, convex hull=34, v0=131481)
- After retessellation of defect 53 (v0=131481), euler #=-15 (170576,511327,340736) : difference with theory (-15) = 0
- CORRECTING DEFECT 54 (vertices=28, convex hull=34, v0=133732)
- After retessellation of defect 54 (v0=133732), euler #=-14 (170581,511354,340759) : difference with theory (-14) = 0
- CORRECTING DEFECT 55 (vertices=12, convex hull=25, v0=133776)
- After retessellation of defect 55 (v0=133776), euler #=-13 (170583,511365,340769) : difference with theory (-13) = 0
- CORRECTING DEFECT 56 (vertices=35, convex hull=41, v0=137346)
- After retessellation of defect 56 (v0=137346), euler #=-12 (170585,511389,340792) : difference with theory (-12) = 0
- CORRECTING DEFECT 57 (vertices=171, convex hull=64, v0=138265)
- After retessellation of defect 57 (v0=138265), euler #=-11 (170600,511463,340852) : difference with theory (-11) = 0
- CORRECTING DEFECT 58 (vertices=36, convex hull=29, v0=139168)
- After retessellation of defect 58 (v0=139168), euler #=-10 (170605,511489,340874) : difference with theory (-10) = 0
- CORRECTING DEFECT 59 (vertices=30, convex hull=65, v0=150046)
- After retessellation of defect 59 (v0=150046), euler #=-9 (170615,511543,340919) : difference with theory (-9) = 0
- CORRECTING DEFECT 60 (vertices=30, convex hull=60, v0=151267)
- After retessellation of defect 60 (v0=151267), euler #=-8 (170627,511602,340967) : difference with theory (-8) = 0
- CORRECTING DEFECT 61 (vertices=74, convex hull=37, v0=154805)
- After retessellation of defect 61 (v0=154805), euler #=-7 (170635,511640,340998) : difference with theory (-7) = 0
- CORRECTING DEFECT 62 (vertices=26, convex hull=49, v0=159716)
- After retessellation of defect 62 (v0=159716), euler #=-6 (170643,511686,341037) : difference with theory (-6) = 0
- CORRECTING DEFECT 63 (vertices=93, convex hull=97, v0=161439)
- After retessellation of defect 63 (v0=161439), euler #=-5 (170661,511779,341113) : difference with theory (-5) = 0
- CORRECTING DEFECT 64 (vertices=19, convex hull=58, v0=165620)
- After retessellation of defect 64 (v0=165620), euler #=-4 (170673,511838,341161) : difference with theory (-4) = 0
- CORRECTING DEFECT 65 (vertices=32, convex hull=69, v0=168379)
- After retessellation of defect 65 (v0=168379), euler #=-3 (170684,511898,341211) : difference with theory (-3) = 0
- CORRECTING DEFECT 66 (vertices=48, convex hull=77, v0=169310)
- After retessellation of defect 66 (v0=169310), euler #=-2 (170708,511998,341288) : difference with theory (-2) = 0
- CORRECTING DEFECT 67 (vertices=39, convex hull=68, v0=171254)
- After retessellation of defect 67 (v0=171254), euler #=-1 (170717,512057,341339) : difference with theory (-1) = 0
- CORRECTING DEFECT 68 (vertices=38, convex hull=76, v0=171408)
- After retessellation of defect 68 (v0=171408), euler #=0 (170729,512122,341393) : difference with theory (0) = 0
- CORRECTING DEFECT 69 (vertices=54, convex hull=81, v0=171748)
- After retessellation of defect 69 (v0=171748), euler #=1 (170746,512208,341463) : difference with theory (1) = 0
- CORRECTING DEFECT 70 (vertices=24, convex hull=61, v0=172523)
- After retessellation of defect 70 (v0=172523), euler #=2 (170760,512274,341516) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.25 (0.05-->17.66) (max @ vno 124159 --> 133822)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.25 (0.05-->17.66) (max @ vno 124159 --> 133822)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 276 mutations (34.2%), 530 crossovers (65.8%), 303 vertices were eliminated
- building final representation...
- 3576 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=170760, nf=341516, ne=512274, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 57.3 minutes
- 0 defective edges
- removing intersecting faces
- 000: 501 intersecting
- 001: 4 intersecting
- mris_fix_topology utimesec 3437.800374
- mris_fix_topology stimesec 0.224965
- mris_fix_topology ru_maxrss 536108
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 57688
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 12272
- mris_fix_topology ru_oublock 16536
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 720
- mris_fix_topology ru_nivcsw 7707
- FSRUNTIME@ mris_fix_topology lh 0.9546 hours 1 threads
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051492 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=-122 (nv=174102, nf=348448, ne=522672, g=62)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 10 iterations
- marking ambiguous vertices...
- 6704 ambiguous faces found in tessellation
- segmenting defects...
- 78 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 78 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.0026 (-4.5013)
- -vertex loglikelihood: -5.6097 (-2.8048)
- -normal dot loglikelihood: -3.5757 (-3.5757)
- -quad curv loglikelihood: -6.3193 (-3.1597)
- Total Loglikelihood : -24.5072
- CORRECTING DEFECT 0 (vertices=203, convex hull=114, v0=206)
- After retessellation of defect 0 (v0=206), euler #=-73 (169926,507798,337799) : difference with theory (-75) = -2
- CORRECTING DEFECT 1 (vertices=97, convex hull=95, v0=1362)
- After retessellation of defect 1 (v0=1362), euler #=-72 (169947,507904,337885) : difference with theory (-74) = -2
- CORRECTING DEFECT 2 (vertices=577, convex hull=322, v0=7838)
- After retessellation of defect 2 (v0=7838), euler #=-71 (170051,508376,338254) : difference with theory (-73) = -2
- CORRECTING DEFECT 3 (vertices=63, convex hull=67, v0=12516)
- After retessellation of defect 3 (v0=12516), euler #=-70 (170060,508428,338298) : difference with theory (-72) = -2
- CORRECTING DEFECT 4 (vertices=26, convex hull=70, v0=15808)
- After retessellation of defect 4 (v0=15808), euler #=-69 (170070,508486,338347) : difference with theory (-71) = -2
- CORRECTING DEFECT 5 (vertices=78, convex hull=93, v0=22936)
- After retessellation of defect 5 (v0=22936), euler #=-68 (170088,508579,338423) : difference with theory (-70) = -2
- CORRECTING DEFECT 6 (vertices=27, convex hull=58, v0=24122)
- After retessellation of defect 6 (v0=24122), euler #=-67 (170100,508637,338470) : difference with theory (-69) = -2
- CORRECTING DEFECT 7 (vertices=7, convex hull=25, v0=27176)
- After retessellation of defect 7 (v0=27176), euler #=-66 (170102,508649,338481) : difference with theory (-68) = -2
- CORRECTING DEFECT 8 (vertices=21, convex hull=26, v0=27366)
- After retessellation of defect 8 (v0=27366), euler #=-65 (170103,508661,338493) : difference with theory (-67) = -2
- CORRECTING DEFECT 9 (vertices=15, convex hull=61, v0=27536)
- After retessellation of defect 9 (v0=27536), euler #=-64 (170114,508719,338541) : difference with theory (-66) = -2
- CORRECTING DEFECT 10 (vertices=24, convex hull=51, v0=27597)
- After retessellation of defect 10 (v0=27597), euler #=-63 (170124,508769,338582) : difference with theory (-65) = -2
- CORRECTING DEFECT 11 (vertices=32, convex hull=63, v0=36376)
- After retessellation of defect 11 (v0=36376), euler #=-62 (170137,508833,338634) : difference with theory (-64) = -2
- CORRECTING DEFECT 12 (vertices=33, convex hull=67, v0=39478)
- After retessellation of defect 12 (v0=39478), euler #=-61 (170151,508902,338690) : difference with theory (-63) = -2
- CORRECTING DEFECT 13 (vertices=24, convex hull=61, v0=41820)
- After retessellation of defect 13 (v0=41820), euler #=-60 (170160,508962,338742) : difference with theory (-62) = -2
- CORRECTING DEFECT 14 (vertices=45, convex hull=89, v0=42252)
- After retessellation of defect 14 (v0=42252), euler #=-59 (170176,509045,338810) : difference with theory (-61) = -2
- CORRECTING DEFECT 15 (vertices=79, convex hull=54, v0=45499)
- After retessellation of defect 15 (v0=45499), euler #=-58 (170184,509091,338849) : difference with theory (-60) = -2
- CORRECTING DEFECT 16 (vertices=55, convex hull=92, v0=45755)
- After retessellation of defect 16 (v0=45755), euler #=-57 (170214,509220,338949) : difference with theory (-59) = -2
- CORRECTING DEFECT 17 (vertices=30, convex hull=77, v0=46479)
- After retessellation of defect 17 (v0=46479), euler #=-56 (170223,509278,338999) : difference with theory (-58) = -2
- CORRECTING DEFECT 18 (vertices=34, convex hull=54, v0=60312)
- After retessellation of defect 18 (v0=60312), euler #=-55 (170241,509351,339055) : difference with theory (-57) = -2
- CORRECTING DEFECT 19 (vertices=20, convex hull=55, v0=63221)
- After retessellation of defect 19 (v0=63221), euler #=-54 (170251,509400,339095) : difference with theory (-56) = -2
- CORRECTING DEFECT 20 (vertices=27, convex hull=28, v0=64273)
- After retessellation of defect 20 (v0=64273), euler #=-53 (170259,509433,339121) : difference with theory (-55) = -2
- CORRECTING DEFECT 21 (vertices=29, convex hull=57, v0=73713)
- After retessellation of defect 21 (v0=73713), euler #=-52 (170271,509491,339168) : difference with theory (-54) = -2
- CORRECTING DEFECT 22 (vertices=56, convex hull=57, v0=76708)
- After retessellation of defect 22 (v0=76708), euler #=-51 (170290,509567,339226) : difference with theory (-53) = -2
- CORRECTING DEFECT 23 (vertices=47, convex hull=56, v0=76874)
- After retessellation of defect 23 (v0=76874), euler #=-50 (170303,509632,339279) : difference with theory (-52) = -2
- CORRECTING DEFECT 24 (vertices=47, convex hull=62, v0=79781)
- After retessellation of defect 24 (v0=79781), euler #=-49 (170314,509689,339326) : difference with theory (-51) = -2
- CORRECTING DEFECT 25 (vertices=6, convex hull=29, v0=81962)
- After retessellation of defect 25 (v0=81962), euler #=-48 (170315,509700,339337) : difference with theory (-50) = -2
- CORRECTING DEFECT 26 (vertices=44, convex hull=51, v0=86286)
- After retessellation of defect 26 (v0=86286), euler #=-47 (170331,509764,339386) : difference with theory (-49) = -2
- CORRECTING DEFECT 27 (vertices=45, convex hull=84, v0=88879)
- After retessellation of defect 27 (v0=88879), euler #=-46 (170351,509858,339461) : difference with theory (-48) = -2
- CORRECTING DEFECT 28 (vertices=30, convex hull=69, v0=90422)
- After retessellation of defect 28 (v0=90422), euler #=-45 (170360,509910,339505) : difference with theory (-47) = -2
- CORRECTING DEFECT 29 (vertices=5, convex hull=26, v0=90994)
- After retessellation of defect 29 (v0=90994), euler #=-44 (170361,509918,339513) : difference with theory (-46) = -2
- CORRECTING DEFECT 30 (vertices=26, convex hull=49, v0=98850)
- After retessellation of defect 30 (v0=98850), euler #=-43 (170373,509973,339557) : difference with theory (-45) = -2
- CORRECTING DEFECT 31 (vertices=32, convex hull=40, v0=100379)
- After retessellation of defect 31 (v0=100379), euler #=-42 (170386,510028,339600) : difference with theory (-44) = -2
- CORRECTING DEFECT 32 (vertices=45, convex hull=34, v0=104781)
- After retessellation of defect 32 (v0=104781), euler #=-41 (170390,510056,339625) : difference with theory (-43) = -2
- CORRECTING DEFECT 33 (vertices=10, convex hull=26, v0=105925)
- After retessellation of defect 33 (v0=105925), euler #=-40 (170393,510073,339640) : difference with theory (-42) = -2
- CORRECTING DEFECT 34 (vertices=25, convex hull=69, v0=106334)
- After retessellation of defect 34 (v0=106334), euler #=-39 (170406,510142,339697) : difference with theory (-41) = -2
- CORRECTING DEFECT 35 (vertices=25, convex hull=47, v0=107725)
- After retessellation of defect 35 (v0=107725), euler #=-38 (170415,510186,339733) : difference with theory (-40) = -2
- CORRECTING DEFECT 36 (vertices=6, convex hull=16, v0=110630)
- After retessellation of defect 36 (v0=110630), euler #=-37 (170415,510191,339739) : difference with theory (-39) = -2
- CORRECTING DEFECT 37 (vertices=23, convex hull=46, v0=113749)
- After retessellation of defect 37 (v0=113749), euler #=-36 (170424,510238,339778) : difference with theory (-38) = -2
- CORRECTING DEFECT 38 (vertices=67, convex hull=80, v0=114903)
- After retessellation of defect 38 (v0=114903), euler #=-35 (170439,510312,339838) : difference with theory (-37) = -2
- CORRECTING DEFECT 39 (vertices=90, convex hull=77, v0=114946)
- After retessellation of defect 39 (v0=114946), euler #=-35 (170484,510487,339968) : difference with theory (-36) = -1
- CORRECTING DEFECT 40 (vertices=10, convex hull=24, v0=118328)
- After retessellation of defect 40 (v0=118328), euler #=-34 (170484,510494,339976) : difference with theory (-35) = -1
- CORRECTING DEFECT 41 (vertices=118, convex hull=126, v0=119388)
- After retessellation of defect 41 (v0=119388), euler #=-33 (170515,510650,340102) : difference with theory (-34) = -1
- CORRECTING DEFECT 42 (vertices=9, convex hull=20, v0=121699)
- After retessellation of defect 42 (v0=121699), euler #=-32 (170519,510665,340114) : difference with theory (-33) = -1
- CORRECTING DEFECT 43 (vertices=94, convex hull=85, v0=122764)
- After retessellation of defect 43 (v0=122764), euler #=-31 (170533,510749,340185) : difference with theory (-32) = -1
- CORRECTING DEFECT 44 (vertices=22, convex hull=22, v0=122897)
- After retessellation of defect 44 (v0=122897), euler #=-30 (170538,510770,340202) : difference with theory (-31) = -1
- CORRECTING DEFECT 45 (vertices=65, convex hull=89, v0=123066)
- After retessellation of defect 45 (v0=123066), euler #=-29 (170566,510888,340293) : difference with theory (-30) = -1
- CORRECTING DEFECT 46 (vertices=17, convex hull=33, v0=123649)
- After retessellation of defect 46 (v0=123649), euler #=-28 (170567,510904,340309) : difference with theory (-29) = -1
- CORRECTING DEFECT 47 (vertices=52, convex hull=50, v0=125501)
- After retessellation of defect 47 (v0=125501), euler #=-28 (170574,510949,340347) : difference with theory (-28) = 0
- CORRECTING DEFECT 48 (vertices=6, convex hull=26, v0=125569)
- After retessellation of defect 48 (v0=125569), euler #=-27 (170577,510965,340361) : difference with theory (-27) = 0
- CORRECTING DEFECT 49 (vertices=29, convex hull=41, v0=126782)
- After retessellation of defect 49 (v0=126782), euler #=-26 (170583,510997,340388) : difference with theory (-26) = 0
- CORRECTING DEFECT 50 (vertices=26, convex hull=62, v0=127693)
- After retessellation of defect 50 (v0=127693), euler #=-25 (170593,511049,340431) : difference with theory (-25) = 0
- CORRECTING DEFECT 51 (vertices=28, convex hull=51, v0=127751)
- After retessellation of defect 51 (v0=127751), euler #=-24 (170605,511102,340473) : difference with theory (-24) = 0
- CORRECTING DEFECT 52 (vertices=6, convex hull=13, v0=127834)
- After retessellation of defect 52 (v0=127834), euler #=-23 (170606,511107,340478) : difference with theory (-23) = 0
- CORRECTING DEFECT 53 (vertices=22, convex hull=41, v0=127988)
- After retessellation of defect 53 (v0=127988), euler #=-22 (170613,511145,340510) : difference with theory (-22) = 0
- CORRECTING DEFECT 54 (vertices=28, convex hull=63, v0=130287)
- After retessellation of defect 54 (v0=130287), euler #=-21 (170627,511215,340567) : difference with theory (-21) = 0
- CORRECTING DEFECT 55 (vertices=12, convex hull=26, v0=131436)
- After retessellation of defect 55 (v0=131436), euler #=-20 (170630,511233,340583) : difference with theory (-20) = 0
- CORRECTING DEFECT 56 (vertices=17, convex hull=15, v0=132200)
- After retessellation of defect 56 (v0=132200), euler #=-19 (170634,511247,340594) : difference with theory (-19) = 0
- CORRECTING DEFECT 57 (vertices=33, convex hull=73, v0=132546)
- After retessellation of defect 57 (v0=132546), euler #=-18 (170649,511318,340651) : difference with theory (-18) = 0
- CORRECTING DEFECT 58 (vertices=38, convex hull=36, v0=133254)
- After retessellation of defect 58 (v0=133254), euler #=-17 (170656,511352,340679) : difference with theory (-17) = 0
- CORRECTING DEFECT 59 (vertices=32, convex hull=61, v0=135405)
- After retessellation of defect 59 (v0=135405), euler #=-16 (170674,511430,340740) : difference with theory (-16) = 0
- CORRECTING DEFECT 60 (vertices=38, convex hull=81, v0=136675)
- After retessellation of defect 60 (v0=136675), euler #=-15 (170690,511513,340808) : difference with theory (-15) = 0
- CORRECTING DEFECT 61 (vertices=41, convex hull=32, v0=139444)
- After retessellation of defect 61 (v0=139444), euler #=-14 (170693,511534,340827) : difference with theory (-14) = 0
- CORRECTING DEFECT 62 (vertices=83, convex hull=78, v0=140145)
- After retessellation of defect 62 (v0=140145), euler #=-13 (170713,511625,340899) : difference with theory (-13) = 0
- CORRECTING DEFECT 63 (vertices=421, convex hull=204, v0=149275)
- After retessellation of defect 63 (v0=149275), euler #=-12 (170802,512014,341200) : difference with theory (-12) = 0
- CORRECTING DEFECT 64 (vertices=42, convex hull=30, v0=152045)
- After retessellation of defect 64 (v0=152045), euler #=-11 (170807,512042,341224) : difference with theory (-11) = 0
- CORRECTING DEFECT 65 (vertices=14, convex hull=16, v0=154008)
- After retessellation of defect 65 (v0=154008), euler #=-10 (170808,512050,341232) : difference with theory (-10) = 0
- CORRECTING DEFECT 66 (vertices=30, convex hull=47, v0=154964)
- After retessellation of defect 66 (v0=154964), euler #=-9 (170815,512089,341265) : difference with theory (-9) = 0
- CORRECTING DEFECT 67 (vertices=37, convex hull=70, v0=155047)
- After retessellation of defect 67 (v0=155047), euler #=-8 (170833,512171,341330) : difference with theory (-8) = 0
- CORRECTING DEFECT 68 (vertices=45, convex hull=41, v0=158598)
- After retessellation of defect 68 (v0=158598), euler #=-7 (170838,512199,341354) : difference with theory (-7) = 0
- CORRECTING DEFECT 69 (vertices=56, convex hull=38, v0=164693)
- After retessellation of defect 69 (v0=164693), euler #=-6 (170847,512244,341391) : difference with theory (-6) = 0
- CORRECTING DEFECT 70 (vertices=22, convex hull=57, v0=165805)
- After retessellation of defect 70 (v0=165805), euler #=-5 (170854,512286,341427) : difference with theory (-5) = 0
- CORRECTING DEFECT 71 (vertices=92, convex hull=87, v0=166268)
- After retessellation of defect 71 (v0=166268), euler #=-4 (170876,512393,341513) : difference with theory (-4) = 0
- CORRECTING DEFECT 72 (vertices=38, convex hull=90, v0=169236)
- After retessellation of defect 72 (v0=169236), euler #=-3 (170886,512459,341570) : difference with theory (-3) = 0
- CORRECTING DEFECT 73 (vertices=141, convex hull=77, v0=170170)
- After retessellation of defect 73 (v0=170170), euler #=-2 (170910,512567,341655) : difference with theory (-2) = 0
- CORRECTING DEFECT 74 (vertices=20, convex hull=58, v0=170400)
- After retessellation of defect 74 (v0=170400), euler #=-1 (170918,512615,341696) : difference with theory (-1) = 0
- CORRECTING DEFECT 75 (vertices=51, convex hull=85, v0=170908)
- After retessellation of defect 75 (v0=170908), euler #=0 (170932,512699,341767) : difference with theory (0) = 0
- CORRECTING DEFECT 76 (vertices=151, convex hull=133, v0=171643)
- After retessellation of defect 76 (v0=171643), euler #=1 (170959,512838,341880) : difference with theory (1) = 0
- CORRECTING DEFECT 77 (vertices=30, convex hull=78, v0=172128)
- After retessellation of defect 77 (v0=172128), euler #=2 (170973,512913,341942) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.24 (0.06-->11.57) (max @ vno 879 --> 1199)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.24 (0.06-->11.57) (max @ vno 879 --> 1199)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 296 mutations (34.2%), 569 crossovers (65.8%), 300 vertices were eliminated
- building final representation...
- 3129 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=170973, nf=341942, ne=512913, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 44.9 minutes
- 0 defective edges
- removing intersecting faces
- 000: 514 intersecting
- 001: 5 intersecting
- mris_fix_topology utimesec 2694.451381
- mris_fix_topology stimesec 0.377942
- mris_fix_topology ru_maxrss 536768
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 57518
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 11520
- mris_fix_topology ru_oublock 16552
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 741
- mris_fix_topology ru_nivcsw 5466
- FSRUNTIME@ mris_fix_topology rh 0.7482 hours 1 threads
- PIDs (13604 13607) completed and logs appended.
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 170760 - 512274 + 341516 = 2 --> 0 holes
- F =2V-4: 341516 = 341520-4 (0)
- 2E=3F: 1024548 = 1024548 (0)
- total defect index = 0
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 170973 - 512913 + 341942 = 2 --> 0 holes
- F =2V-4: 341942 = 341946-4 (0)
- 2E=3F: 1025826 = 1025826 (0)
- total defect index = 0
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 110 intersecting
- 001: 4 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 45 intersecting
- 001: 3 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Sat Oct 7 22:16:18 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051492 lh
- #--------------------------------------------
- #@# Make White Surf rh Sat Oct 7 22:16:18 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051492 rh
- Waiting for PID 16015 of (16015 16018) to complete...
- Waiting for PID 16018 of (16015 16018) to complete...
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051492 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-6.0.0/0051492/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- 41718 bright wm thresholded.
- 2651 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.orig...
- computing class statistics...
- border white: 358475 voxels (2.14%)
- border gray 362870 voxels (2.16%)
- WM (105.0): 104.5 +- 5.4 [70.0 --> 110.0]
- GM (87.0) : 86.1 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 74.8 (was 70)
- setting MAX_BORDER_WHITE to 112.4 (was 105)
- setting MIN_BORDER_WHITE to 85.0 (was 85)
- setting MAX_CSF to 64.6 (was 40)
- setting MAX_GRAY to 101.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 74.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 54.4 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.03-->4.85) (max @ vno 63290 --> 69592)
- face area 0.28 +- 0.13 (0.00-->4.77)
- mean absolute distance = 0.81 +- 0.97
- 4951 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=107+-3.5, GM=85+-7.0
- mean inside = 101.6, mean outside = 89.3
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=91.9, 90 (90) missing vertices, mean dist 0.4 [0.7 (%30.4)->0.9 (%69.6))]
- %66 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.26 (0.05-->5.82) (max @ vno 63290 --> 69592)
- face area 0.28 +- 0.13 (0.00-->4.17)
- mean absolute distance = 0.43 +- 0.64
- 6167 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2363402.5, rms=7.071
- 001: dt: 0.5000, sse=1531875.6, rms=5.096 (27.926%)
- 002: dt: 0.5000, sse=1143679.9, rms=3.789 (25.663%)
- 003: dt: 0.5000, sse=954915.0, rms=2.939 (22.411%)
- 004: dt: 0.5000, sse=868865.2, rms=2.435 (17.174%)
- 005: dt: 0.5000, sse=828204.9, rms=2.172 (10.789%)
- 006: dt: 0.5000, sse=811209.2, rms=2.037 (6.231%)
- 007: dt: 0.5000, sse=804437.3, rms=1.967 (3.418%)
- rms = 1.92, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=798272.6, rms=1.924 (2.164%)
- 009: dt: 0.2500, sse=752100.9, rms=1.401 (27.195%)
- 010: dt: 0.2500, sse=745837.0, rms=1.323 (5.587%)
- rms = 1.31, time step reduction 2 of 3 to 0.125...
- 011: dt: 0.2500, sse=744395.2, rms=1.308 (1.095%)
- rms = 1.29, time step reduction 3 of 3 to 0.062...
- 012: dt: 0.1250, sse=743737.4, rms=1.295 (1.026%)
- positioning took 1.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- mean border=94.0, 51 (10) missing vertices, mean dist -0.3 [0.5 (%70.0)->0.3 (%30.0))]
- %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.06-->5.94) (max @ vno 63290 --> 69592)
- face area 0.35 +- 0.17 (0.00-->5.30)
- mean absolute distance = 0.31 +- 0.42
- 6692 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1228879.1, rms=3.366
- 013: dt: 0.5000, sse=1004129.8, rms=2.144 (36.314%)
- 014: dt: 0.5000, sse=943748.2, rms=1.696 (20.899%)
- 015: dt: 0.5000, sse=928066.2, rms=1.559 (8.063%)
- rms = 1.52, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.5000, sse=920324.6, rms=1.523 (2.325%)
- 017: dt: 0.2500, sse=900603.9, rms=1.188 (21.966%)
- 018: dt: 0.2500, sse=895252.6, rms=1.136 (4.388%)
- rms = 1.13, time step reduction 2 of 3 to 0.125...
- 019: dt: 0.2500, sse=895514.3, rms=1.130 (0.588%)
- rms = 1.12, time step reduction 3 of 3 to 0.062...
- 020: dt: 0.1250, sse=894358.2, rms=1.119 (0.962%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=95.8, 59 (5) missing vertices, mean dist -0.2 [0.3 (%72.2)->0.2 (%27.8))]
- %89 local maxima, % 7 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 0.88 +- 0.25 (0.08-->5.97) (max @ vno 63290 --> 69592)
- face area 0.33 +- 0.16 (0.00-->5.05)
- mean absolute distance = 0.24 +- 0.33
- 4983 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1016797.7, rms=2.473
- 021: dt: 0.5000, sse=893656.8, rms=1.470 (40.558%)
- 022: dt: 0.5000, sse=878125.2, rms=1.294 (11.948%)
- rms = 1.35, time step reduction 1 of 3 to 0.250...
- 023: dt: 0.2500, sse=861915.8, rms=1.118 (13.616%)
- 024: dt: 0.2500, sse=861739.7, rms=1.037 (7.247%)
- rms = 1.03, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.2500, sse=855576.6, rms=1.032 (0.520%)
- rms = 1.02, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=855755.2, rms=1.024 (0.751%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=96.3, 78 (3) missing vertices, mean dist -0.1 [0.3 (%57.7)->0.2 (%42.3))]
- %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white.preaparc...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=858501.9, rms=1.289
- 027: dt: 0.5000, sse=843050.1, rms=0.868 (32.602%)
- rms = 1.16, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=823042.8, rms=0.802 (7.651%)
- rms = 0.84, time step reduction 2 of 3 to 0.125...
- rms = 0.80, time step reduction 3 of 3 to 0.062...
- 029: dt: 0.1250, sse=821269.6, rms=0.798 (0.548%)
- positioning took 0.6 minutes
- generating cortex label...
- 19 non-cortical segments detected
- only using segment with 8035 vertices
- erasing segment 1 (vno[0] = 59129)
- erasing segment 2 (vno[0] = 76749)
- erasing segment 3 (vno[0] = 99012)
- erasing segment 4 (vno[0] = 99020)
- erasing segment 5 (vno[0] = 102822)
- erasing segment 6 (vno[0] = 112230)
- erasing segment 7 (vno[0] = 113872)
- erasing segment 8 (vno[0] = 114802)
- erasing segment 9 (vno[0] = 116473)
- erasing segment 10 (vno[0] = 118661)
- erasing segment 11 (vno[0] = 119040)
- erasing segment 12 (vno[0] = 120313)
- erasing segment 13 (vno[0] = 120321)
- erasing segment 14 (vno[0] = 121457)
- erasing segment 15 (vno[0] = 122669)
- erasing segment 16 (vno[0] = 122693)
- erasing segment 17 (vno[0] = 123923)
- erasing segment 18 (vno[0] = 126117)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.area
- vertex spacing 0.88 +- 0.25 (0.05-->5.97) (max @ vno 63290 --> 69592)
- face area 0.32 +- 0.16 (0.00-->4.98)
- refinement took 6.2 minutes
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051492 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-6.0.0/0051492/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- 41718 bright wm thresholded.
- 2651 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.orig...
- computing class statistics...
- border white: 358475 voxels (2.14%)
- border gray 362870 voxels (2.16%)
- WM (105.0): 104.5 +- 5.4 [70.0 --> 110.0]
- GM (87.0) : 86.1 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 73.8 (was 70)
- setting MAX_BORDER_WHITE to 112.4 (was 105)
- setting MIN_BORDER_WHITE to 84.0 (was 85)
- setting MAX_CSF to 63.6 (was 40)
- setting MAX_GRAY to 101.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 73.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 53.4 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.03-->4.67) (max @ vno 170790 --> 170793)
- face area 0.28 +- 0.12 (0.00-->2.64)
- mean absolute distance = 0.82 +- 0.96
- 5769 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=107+-3.5, GM=84+-7.0
- mean inside = 101.6, mean outside = 89.1
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=91.5, 74 (74) missing vertices, mean dist 0.4 [0.6 (%29.2)->0.9 (%70.8))]
- %67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.26 (0.11-->4.60) (max @ vno 170790 --> 170793)
- face area 0.28 +- 0.13 (0.00-->2.27)
- mean absolute distance = 0.44 +- 0.65
- 6790 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2496965.2, rms=7.323
- 001: dt: 0.5000, sse=1610151.1, rms=5.312 (27.461%)
- 002: dt: 0.5000, sse=1191631.6, rms=3.959 (25.472%)
- 003: dt: 0.5000, sse=981213.0, rms=3.050 (22.956%)
- 004: dt: 0.5000, sse=880023.6, rms=2.496 (18.182%)
- 005: dt: 0.5000, sse=838417.8, rms=2.206 (11.619%)
- 006: dt: 0.5000, sse=819281.2, rms=2.074 (5.967%)
- 007: dt: 0.5000, sse=812105.6, rms=2.010 (3.084%)
- rms = 1.98, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=808772.8, rms=1.979 (1.533%)
- 009: dt: 0.2500, sse=759492.4, rms=1.428 (27.836%)
- 010: dt: 0.2500, sse=753083.6, rms=1.347 (5.684%)
- rms = 1.33, time step reduction 2 of 3 to 0.125...
- 011: dt: 0.2500, sse=750738.4, rms=1.332 (1.123%)
- rms = 1.32, time step reduction 3 of 3 to 0.062...
- 012: dt: 0.1250, sse=749366.1, rms=1.318 (1.032%)
- positioning took 1.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- mean border=93.7, 63 (19) missing vertices, mean dist -0.3 [0.5 (%71.2)->0.3 (%28.8))]
- %79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.04-->4.53) (max @ vno 170790 --> 170793)
- face area 0.35 +- 0.16 (0.00-->2.86)
- mean absolute distance = 0.31 +- 0.41
- 6946 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1248712.5, rms=3.408
- 013: dt: 0.5000, sse=1017960.8, rms=2.171 (36.309%)
- 014: dt: 0.5000, sse=960446.1, rms=1.744 (19.648%)
- 015: dt: 0.5000, sse=941507.8, rms=1.611 (7.661%)
- rms = 1.58, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.5000, sse=935838.2, rms=1.576 (2.163%)
- 017: dt: 0.2500, sse=910177.2, rms=1.224 (22.308%)
- 018: dt: 0.2500, sse=906165.8, rms=1.164 (4.886%)
- rms = 1.15, time step reduction 2 of 3 to 0.125...
- 019: dt: 0.2500, sse=905446.3, rms=1.152 (1.050%)
- rms = 1.14, time step reduction 3 of 3 to 0.062...
- 020: dt: 0.1250, sse=903687.4, rms=1.138 (1.216%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=95.5, 59 (8) missing vertices, mean dist -0.2 [0.3 (%72.7)->0.2 (%27.3))]
- %89 local maxima, % 7 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 0.88 +- 0.25 (0.04-->4.54) (max @ vno 170790 --> 170793)
- face area 0.33 +- 0.16 (0.00-->2.96)
- mean absolute distance = 0.23 +- 0.33
- 4759 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1041709.7, rms=2.578
- 021: dt: 0.5000, sse=904870.3, rms=1.540 (40.280%)
- 022: dt: 0.5000, sse=890973.9, rms=1.345 (12.641%)
- rms = 1.38, time step reduction 1 of 3 to 0.250...
- 023: dt: 0.2500, sse=869228.0, rms=1.154 (14.213%)
- 024: dt: 0.2500, sse=862688.4, rms=1.058 (8.329%)
- rms = 1.05, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.2500, sse=862401.2, rms=1.049 (0.847%)
- rms = 1.04, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=861998.5, rms=1.038 (1.047%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- mean border=96.1, 77 (3) missing vertices, mean dist -0.1 [0.2 (%58.3)->0.2 (%41.7))]
- %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.white.preaparc...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=867152.4, rms=1.323
- 027: dt: 0.5000, sse=837409.9, rms=0.896 (32.299%)
- rms = 1.18, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=828858.4, rms=0.813 (9.231%)
- rms = 0.85, time step reduction 2 of 3 to 0.125...
- rms = 0.81, time step reduction 3 of 3 to 0.062...
- 029: dt: 0.1250, sse=826868.3, rms=0.806 (0.892%)
- positioning took 0.6 minutes
- generating cortex label...
- 7 non-cortical segments detected
- only using segment with 8211 vertices
- erasing segment 1 (vno[0] = 83179)
- erasing segment 2 (vno[0] = 120658)
- erasing segment 3 (vno[0] = 121875)
- erasing segment 4 (vno[0] = 123014)
- erasing segment 5 (vno[0] = 124133)
- erasing segment 6 (vno[0] = 129413)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.area
- vertex spacing 0.88 +- 0.25 (0.04-->4.52) (max @ vno 170790 --> 170793)
- face area 0.33 +- 0.16 (0.00-->2.92)
- refinement took 6.4 minutes
- PIDs (16015 16018) completed and logs appended.
- #--------------------------------------------
- #@# Smooth2 lh Sat Oct 7 22:22:41 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
- #--------------------------------------------
- #@# Smooth2 rh Sat Oct 7 22:22:41 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
- Waiting for PID 16252 of (16252 16255) to complete...
- Waiting for PID 16255 of (16252 16255) 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 (16252 16255) completed and logs appended.
- #--------------------------------------------
- #@# Inflation2 lh Sat Oct 7 22:22:49 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- #--------------------------------------------
- #@# Inflation2 rh Sat Oct 7 22:22:49 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Waiting for PID 16305 of (16305 16308) to complete...
- Waiting for PID 16308 of (16305 16308) to complete...
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- Reading ../surf/lh.smoothwm
- avg radius = 50.4 mm, total surface area = 100824 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.176 (target=0.015)
step 005: RMS=0.125 (target=0.015)
step 010: RMS=0.094 (target=0.015)
step 015: RMS=0.077 (target=0.015)
step 020: RMS=0.064 (target=0.015)
step 025: RMS=0.053 (target=0.015)
step 030: RMS=0.045 (target=0.015)
step 035: RMS=0.038 (target=0.015)
step 040: RMS=0.033 (target=0.015)
step 045: RMS=0.029 (target=0.015)
step 050: RMS=0.026 (target=0.015)
step 055: RMS=0.024 (target=0.015)
step 060: RMS=0.022 (target=0.015)
- inflation complete.
- inflation took 0.9 minutes
- mris_inflate utimesec 52.077083
- mris_inflate stimesec 0.120981
- mris_inflate ru_maxrss 249492
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 35866
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 13368
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2405
- mris_inflate ru_nivcsw 3659
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Reading ../surf/rh.smoothwm
- avg radius = 50.7 mm, total surface area = 101197 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.176 (target=0.015)
step 005: RMS=0.124 (target=0.015)
step 010: RMS=0.093 (target=0.015)
step 015: RMS=0.076 (target=0.015)
step 020: RMS=0.062 (target=0.015)
step 025: RMS=0.052 (target=0.015)
step 030: RMS=0.044 (target=0.015)
step 035: RMS=0.037 (target=0.015)
step 040: RMS=0.032 (target=0.015)
step 045: RMS=0.029 (target=0.015)
step 050: RMS=0.026 (target=0.015)
step 055: RMS=0.024 (target=0.015)
step 060: RMS=0.022 (target=0.015)
- inflation complete.
- inflation took 0.9 minutes
- mris_inflate utimesec 53.609850
- mris_inflate stimesec 0.110983
- mris_inflate ru_maxrss 249752
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 35930
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 13384
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2304
- mris_inflate ru_nivcsw 3869
- PIDs (16305 16308) completed and logs appended.
- #--------------------------------------------
- #@# Curv .H and .K lh Sat Oct 7 22:23:43 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 Sat Oct 7 22:23:43 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/surf
- reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 16401 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- Waiting for PID 16404 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- Waiting for PID 16407 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- Waiting for PID 16410 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- Waiting for PID 16413 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- Waiting for PID 16416 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- Waiting for PID 16419 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- Waiting for PID 16422 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- Waiting for PID 16425 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- Waiting for PID 16428 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- Waiting for PID 16431 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- Waiting for PID 16434 of (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) to complete...
- mris_curvature -w lh.white.preaparc
- total integrated curvature = 9.465*4pi (118.939) --> -8 handles
- ICI = 215.9, FI = 2093.5, variation=33443.211
- 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
- 255 vertices thresholded to be in k1 ~ [-0.20 0.93], k2 ~ [-0.11 0.09]
- total integrated curvature = 0.507*4pi (6.370) --> 0 handles
- ICI = 1.6, FI = 10.6, variation=179.021
- 150 vertices thresholded to be in [-0.02 0.01]
- writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 157 vertices thresholded to be in [-0.12 0.16]
- done.
- writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.021
- done.
- mris_curvature -w rh.white.preaparc
- total integrated curvature = 2.931*4pi (36.830) --> -2 handles
- ICI = 215.5, FI = 2105.2, variation=33673.399
- 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
- 225 vertices thresholded to be in k1 ~ [-0.20 0.46], k2 ~ [-0.10 0.05]
- total integrated curvature = 0.471*4pi (5.916) --> 1 handles
- ICI = 1.7, FI = 11.6, variation=195.286
- 162 vertices thresholded to be in [-0.01 0.01]
- writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 179 vertices thresholded to be in [-0.13 0.20]
- done.
- writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.023
- done.
- PIDs (16401 16404 16407 16410 16413 16416 16419 16422 16425 16428 16431 16434) completed and logs appended.
- #-----------------------------------------
- #@# Curvature Stats lh Sat Oct 7 22:25:29 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051492 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 [ 0051492/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 [ 285 ]
- Gb_filter = 0
- WARN: S lookup min: -0.350887
- WARN: S explicit min: 0.000000 vertex = 709
- #-----------------------------------------
- #@# Curvature Stats rh Sat Oct 7 22:25:35 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051492 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 [ 0051492/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 [ 300 ]
- Gb_filter = 0
- WARN: S lookup min: -0.229070
- WARN: S explicit min: 0.000000 vertex = 484
- #--------------------------------------------
- #@# Sphere lh Sat Oct 7 22:25:41 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- #--------------------------------------------
- #@# Sphere rh Sat Oct 7 22:25:41 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- Waiting for PID 16594 of (16594 16597) to complete...
- Waiting for PID 16597 of (16594 16597) to complete...
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0.258...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.68
- pass 1: epoch 2 of 3 starting distance error %20.67
- unfolding complete - removing small folds...
- starting distance error %20.59
- removing remaining folds...
- final distance error %20.61
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 267 negative triangles
- 181: dt=0.9900, 267 negative triangles
- 182: dt=0.9900, 140 negative triangles
- 183: dt=0.9900, 96 negative triangles
- 184: dt=0.9900, 82 negative triangles
- 185: dt=0.9900, 78 negative triangles
- 186: dt=0.9900, 54 negative triangles
- 187: dt=0.9900, 49 negative triangles
- 188: dt=0.9900, 42 negative triangles
- 189: dt=0.9900, 23 negative triangles
- 190: dt=0.9900, 25 negative triangles
- 191: dt=0.9900, 20 negative triangles
- 192: dt=0.9900, 26 negative triangles
- 193: dt=0.9900, 15 negative triangles
- 194: dt=0.9900, 15 negative triangles
- 195: dt=0.9900, 9 negative triangles
- 196: dt=0.9900, 13 negative triangles
- 197: dt=0.9900, 7 negative triangles
- 198: dt=0.9900, 6 negative triangles
- 199: dt=0.9900, 7 negative triangles
- 200: dt=0.9900, 2 negative triangles
- 201: dt=0.9900, 1 negative triangles
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 1.51 hours
- mris_sphere utimesec 5457.094395
- mris_sphere stimesec 3.795423
- mris_sphere ru_maxrss 350588
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 61272
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 12048
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 126780
- mris_sphere ru_nivcsw 452817
- FSRUNTIME@ mris_sphere 1.5128 hours 1 threads
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0.258...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %21.00
- pass 1: epoch 2 of 3 starting distance error %21.00
- unfolding complete - removing small folds...
- starting distance error %20.95
- removing remaining folds...
- final distance error %20.96
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 353 negative triangles
- 153: dt=0.9900, 353 negative triangles
- 154: dt=0.9900, 158 negative triangles
- 155: dt=0.9900, 116 negative triangles
- 156: dt=0.9900, 109 negative triangles
- 157: dt=0.9900, 93 negative triangles
- 158: dt=0.9900, 82 negative triangles
- 159: dt=0.9900, 84 negative triangles
- 160: dt=0.9900, 82 negative triangles
- 161: dt=0.9900, 72 negative triangles
- 162: dt=0.9900, 72 negative triangles
- 163: dt=0.9900, 66 negative triangles
- 164: dt=0.9900, 73 negative triangles
- 165: dt=0.9900, 61 negative triangles
- 166: dt=0.9900, 55 negative triangles
- 167: dt=0.9900, 60 negative triangles
- 168: dt=0.9900, 63 negative triangles
- 169: dt=0.9900, 59 negative triangles
- 170: dt=0.9900, 56 negative triangles
- 171: dt=0.9900, 55 negative triangles
- 172: dt=0.9900, 49 negative triangles
- 173: dt=0.9900, 55 negative triangles
- 174: dt=0.9900, 49 negative triangles
- 175: dt=0.9900, 47 negative triangles
- 176: dt=0.9900, 45 negative triangles
- 177: dt=0.9900, 37 negative triangles
- 178: dt=0.9900, 44 negative triangles
- 179: dt=0.9900, 35 negative triangles
- 180: dt=0.9900, 38 negative triangles
- 181: dt=0.9900, 35 negative triangles
- 182: dt=0.9900, 33 negative triangles
- 183: dt=0.9900, 30 negative triangles
- 184: dt=0.9900, 29 negative triangles
- 185: dt=0.9900, 26 negative triangles
- 186: dt=0.9900, 26 negative triangles
- 187: dt=0.9900, 23 negative triangles
- 188: dt=0.9900, 22 negative triangles
- 189: dt=0.9900, 21 negative triangles
- 190: dt=0.9900, 19 negative triangles
- 191: dt=0.9900, 26 negative triangles
- 192: dt=0.9900, 22 negative triangles
- 193: dt=0.9900, 19 negative triangles
- 194: dt=0.9900, 17 negative triangles
- 195: dt=0.9900, 18 negative triangles
- 196: dt=0.9900, 15 negative triangles
- 197: dt=0.9900, 11 negative triangles
- 198: dt=0.9900, 8 negative triangles
- 199: dt=0.9900, 11 negative triangles
- 200: dt=0.9900, 9 negative triangles
- 201: dt=0.9900, 8 negative triangles
- 202: dt=0.9900, 5 negative triangles
- 203: dt=0.9900, 2 negative triangles
- 204: dt=0.9900, 4 negative triangles
- 205: dt=0.9900, 2 negative triangles
- 206: dt=0.9900, 3 negative triangles
- 207: dt=0.9900, 2 negative triangles
- 208: dt=0.9900, 1 negative triangles
- 209: dt=0.9900, 1 negative triangles
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.51 hours
- mris_sphere utimesec 5430.954369
- mris_sphere stimesec 1.170822
- mris_sphere ru_maxrss 351348
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 61971
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 12104
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 130721
- mris_sphere ru_nivcsw 445678
- FSRUNTIME@ mris_sphere 1.5084 hours 1 threads
- PIDs (16594 16597) completed and logs appended.
- #--------------------------------------------
- #@# Surf Reg lh Sat Oct 7 23:56:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 Sat Oct 7 23:56:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 22465 of (22465 22468) to complete...
- Waiting for PID 22468 of (22465 22468) to complete...
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 = 5.582
- curvature mean = 0.003, std = 0.815
- curvature mean = 0.022, std = 0.840
- Starting MRISrigidBodyAlignGlobal()
- d=32.00 min @ (0.00, -8.00, 8.00) sse = 298537.8, tmin=3.3273
- d=16.00 min @ (0.00, 0.00, -4.00) sse = 273796.4, tmin=4.9984
- d=4.00 min @ (0.00, 1.00, 1.00) sse = 271728.1, tmin=8.3877
- d=2.00 min @ (0.00, -0.50, -0.50) sse = 270795.2, tmin=10.1015
- d=1.00 min @ (0.25, 0.25, 0.00) sse = 270653.9, tmin=11.8161
- d=0.50 min @ (-0.12, -0.12, 0.12) sse = 270610.2, tmin=13.5403
- 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 13.54 min
- curvature mean = -0.042, std = 0.817
- curvature mean = 0.009, std = 0.939
- curvature mean = -0.053, std = 0.822
- curvature mean = 0.003, std = 0.974
- curvature mean = -0.058, std = 0.821
- curvature mean = 0.001, std = 0.989
- 2 Reading smoothwm
- curvature mean = -0.026, std = 0.315
- curvature mean = 0.029, std = 0.244
- curvature mean = 0.062, std = 0.298
- curvature mean = 0.027, std = 0.302
- curvature mean = 0.035, std = 0.471
- curvature mean = 0.026, std = 0.330
- curvature mean = 0.021, std = 0.607
- curvature mean = 0.025, std = 0.342
- curvature mean = 0.008, std = 0.719
- MRISregister() return, current seed 0
- -01: dt=0.0000, 45 negative triangles
- 128: dt=0.9900, 45 negative triangles
- expanding nbhd size to 1
- 129: dt=0.9900, 66 negative triangles
- 130: dt=0.9900, 43 negative triangles
- 131: dt=0.9900, 37 negative triangles
- 132: dt=0.9900, 37 negative triangles
- 133: dt=0.9900, 34 negative triangles
- 134: dt=0.9900, 35 negative triangles
- 135: dt=0.9900, 28 negative triangles
- 136: dt=0.9900, 28 negative triangles
- 137: dt=0.9900, 21 negative triangles
- 138: dt=0.9900, 21 negative triangles
- 139: dt=0.9900, 24 negative triangles
- 140: dt=0.9900, 22 negative triangles
- 141: dt=0.9900, 15 negative triangles
- 142: dt=0.9900, 14 negative triangles
- 143: dt=0.9900, 10 negative triangles
- 144: dt=0.9900, 10 negative triangles
- 145: dt=0.9900, 6 negative triangles
- 146: dt=0.9900, 6 negative triangles
- 147: dt=0.9900, 4 negative triangles
- 148: dt=0.9900, 1 negative triangles
- 149: dt=0.9900, 1 negative triangles
- 150: dt=0.9900, 2 negative triangles
- writing registered surface to ../surf/lh.sphere.reg...
- registration took 2.71 hours
- mris_register utimesec 9946.216945
- mris_register stimesec 3.454474
- mris_register ru_maxrss 306592
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 42544
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 12096
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 419958
- mris_register ru_nivcsw 558355
- FSRUNTIME@ mris_register 2.7102 hours 1 threads
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 = 5.566
- curvature mean = 0.019, std = 0.808
- curvature mean = 0.020, std = 0.840
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 476508.6, tmin=1.6442
- d=32.00 min @ (8.00, 8.00, 8.00) sse = 284152.9, tmin=3.3059
- d=4.00 min @ (1.00, 1.00, 0.00) sse = 280840.6, tmin=8.3312
- d=2.00 min @ (-0.50, 0.00, 0.50) sse = 280467.1, tmin=10.0285
- d=1.00 min @ (0.25, 0.25, -0.25) sse = 280230.8, tmin=11.7360
- d=0.50 min @ (0.00, -0.12, 0.12) sse = 280196.0, tmin=13.4651
- 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 13.47 min
- curvature mean = -0.015, std = 0.809
- curvature mean = 0.008, std = 0.938
- curvature mean = -0.023, std = 0.812
- curvature mean = 0.003, std = 0.975
- curvature mean = -0.026, std = 0.812
- curvature mean = 0.001, std = 0.990
- 2 Reading smoothwm
- curvature mean = -0.026, std = 0.288
- curvature mean = 0.032, std = 0.240
- curvature mean = 0.066, std = 0.329
- curvature mean = 0.028, std = 0.297
- curvature mean = 0.039, std = 0.512
- curvature mean = 0.028, std = 0.323
- curvature mean = 0.023, std = 0.654
- curvature mean = 0.028, std = 0.334
- curvature mean = 0.009, std = 0.764
- MRISregister() return, current seed 0
- -01: dt=0.0000, 56 negative triangles
- 123: dt=0.9900, 56 negative triangles
- expanding nbhd size to 1
- 124: dt=0.9900, 79 negative triangles
- 125: dt=0.9900, 46 negative triangles
- 126: dt=0.9900, 50 negative triangles
- 127: dt=0.9900, 48 negative triangles
- 128: dt=0.9900, 46 negative triangles
- 129: dt=0.9900, 45 negative triangles
- 130: dt=0.9900, 51 negative triangles
- 131: dt=0.9900, 36 negative triangles
- 132: dt=0.9900, 35 negative triangles
- 133: dt=0.9900, 36 negative triangles
- 134: dt=0.9900, 26 negative triangles
- 135: dt=0.9900, 30 negative triangles
- 136: dt=0.9900, 19 negative triangles
- 137: dt=0.9900, 21 negative triangles
- 138: dt=0.9900, 17 negative triangles
- 139: dt=0.9900, 15 negative triangles
- 140: dt=0.9900, 9 negative triangles
- 141: dt=0.9900, 6 negative triangles
- 142: dt=0.9900, 5 negative triangles
- 143: dt=0.9900, 5 negative triangles
- 144: dt=0.9900, 6 negative triangles
- 145: dt=0.9900, 4 negative triangles
- 146: dt=0.9900, 3 negative triangles
- 147: dt=0.9900, 1 negative triangles
- writing registered surface to ../surf/rh.sphere.reg...
- registration took 2.52 hours
- mris_register utimesec 9085.761754
- mris_register stimesec 3.983394
- mris_register ru_maxrss 304364
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 42474
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 12120
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 414029
- mris_register ru_nivcsw 524818
- FSRUNTIME@ mris_register 2.5219 hours 1 threads
- PIDs (22465 22468) completed and logs appended.
- #--------------------------------------------
- #@# Jacobian white lh Sun Oct 8 02:39:04 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# Jacobian white rh Sun Oct 8 02:39:04 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- Waiting for PID 31788 of (31788 31791) to complete...
- Waiting for PID 31791 of (31788 31791) 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 (31788 31791) completed and logs appended.
- #--------------------------------------------
- #@# AvgCurv lh Sun Oct 8 02:39:07 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 02:39:07 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 31832 of (31832 31835) to complete...
- Waiting for PID 31835 of (31832 31835) 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 (31832 31835) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc lh Sun Oct 8 02:39:09 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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 02:39:09 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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 31876 of (31876 31879) to complete...
- Waiting for PID 31879 of (31876 31879) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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...
- 1802 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3702 changed, 170760 examined...
- 001: 938 changed, 15402 examined...
- 002: 245 changed, 4994 examined...
- 003: 99 changed, 1458 examined...
- 004: 33 changed, 621 examined...
- 005: 11 changed, 198 examined...
- 006: 8 changed, 59 examined...
- 007: 5 changed, 41 examined...
- 008: 3 changed, 26 examined...
- 009: 0 changed, 14 examined...
- 305 labels changed using aseg
- 000: 132 total segments, 87 labels (443 vertices) changed
- 001: 46 total segments, 2 labels (3 vertices) changed
- 002: 44 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 3 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 2288 vertices marked for relabeling...
- 2288 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 19 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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...
- 1553 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3258 changed, 170973 examined...
- 001: 799 changed, 13937 examined...
- 002: 171 changed, 4423 examined...
- 003: 71 changed, 1073 examined...
- 004: 24 changed, 436 examined...
- 005: 13 changed, 152 examined...
- 006: 6 changed, 76 examined...
- 007: 2 changed, 39 examined...
- 008: 0 changed, 15 examined...
- 192 labels changed using aseg
- 000: 104 total segments, 67 labels (286 vertices) changed
- 001: 44 total segments, 7 labels (16 vertices) changed
- 002: 38 total segments, 1 labels (1 vertices) changed
- 003: 37 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 4 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1868 vertices marked for relabeling...
- 1868 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 18 seconds.
- PIDs (31876 31879) completed and logs appended.
- #--------------------------------------------
- #@# Make Pial Surf lh Sun Oct 8 02:39:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051492 lh
- #--------------------------------------------
- #@# Make Pial Surf rh Sun Oct 8 02:39:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051492 rh
- Waiting for PID 31923 of (31923 31926) to complete...
- Waiting for PID 31926 of (31923 31926) to complete...
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051492 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-6.0.0/0051492/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- 41718 bright wm thresholded.
- 2651 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.orig...
- computing class statistics...
- border white: 358475 voxels (2.14%)
- border gray 362870 voxels (2.16%)
- WM (105.0): 104.5 +- 5.4 [70.0 --> 110.0]
- GM (87.0) : 86.1 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 74.8 (was 70)
- setting MAX_BORDER_WHITE to 112.4 (was 105)
- setting MIN_BORDER_WHITE to 85.0 (was 85)
- setting MAX_CSF to 64.6 (was 40)
- setting MAX_GRAY to 101.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 74.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 54.4 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=107+-3.5, GM=85+-7.0
- mean inside = 101.6, mean outside = 89.3
- 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 0.88 +- 0.25 (0.05-->5.97) (max @ vno 63290 --> 69592)
- face area 0.32 +- 0.16 (0.00-->4.97)
- mean absolute distance = 0.74 +- 0.91
- 3318 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 52 points - only 0.00% unknown
- deleting segment 2 with 153 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 7 with 43 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- deleting segment 10 with 150 points - only 0.00% unknown
- deleting segment 12 with 68 points - only 0.00% unknown
- deleting segment 13 with 20 points - only 0.00% unknown
- deleting segment 14 with 38 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 15 with 4 points - only 0.00% unknown
- mean border=91.9, 97 (97) missing vertices, mean dist 0.5 [1.1 (%13.2)->0.7 (%86.8))]
- %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.26 (0.08-->5.96) (max @ vno 63290 --> 69592)
- face area 0.32 +- 0.16 (0.00-->5.04)
- mean absolute distance = 0.42 +- 0.62
- 4539 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1835085.1, rms=5.608
- 001: dt: 0.5000, sse=1174207.2, rms=3.371 (39.894%)
- 002: dt: 0.5000, sse=967112.2, rms=2.274 (32.531%)
- 003: dt: 0.5000, sse=914898.3, rms=1.897 (16.579%)
- 004: dt: 0.5000, sse=893859.4, rms=1.736 (8.506%)
- rms = 1.70, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.5000, sse=891495.7, rms=1.700 (2.062%)
- 006: dt: 0.2500, sse=863920.8, rms=1.370 (19.440%)
- 007: dt: 0.2500, sse=862323.6, rms=1.313 (4.126%)
- rms = 1.30, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=861126.3, rms=1.296 (1.290%)
- rms = 1.28, time step reduction 3 of 3 to 0.062...
- 009: dt: 0.1250, sse=858473.4, rms=1.282 (1.096%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 41 points - only 0.00% unknown
- deleting segment 1 with 145 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 29 points - only 0.00% unknown
- deleting segment 5 with 11 points - only 0.00% unknown
- deleting segment 6 with 74 points - only 0.00% unknown
- deleting segment 8 with 50 points - only 0.00% unknown
- deleting segment 9 with 8 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 10 with 4 points - only 0.00% unknown
- deleting segment 11 with 54 points - only 0.00% unknown
- mean border=94.0, 54 (22) missing vertices, mean dist -0.3 [0.5 (%68.8)->0.3 (%31.2))]
- %79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.08-->5.94) (max @ vno 63290 --> 69592)
- face area 0.35 +- 0.17 (0.00-->5.56)
- mean absolute distance = 0.31 +- 0.41
- 6541 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1195345.0, rms=3.192
- 010: dt: 0.5000, sse=992719.7, rms=2.000 (37.341%)
- 011: dt: 0.5000, sse=944513.7, rms=1.553 (22.339%)
- 012: dt: 0.5000, sse=924982.0, rms=1.451 (6.555%)
- rms = 1.44, time step reduction 1 of 3 to 0.250...
- 013: dt: 0.5000, sse=919569.0, rms=1.439 (0.846%)
- 014: dt: 0.2500, sse=900499.2, rms=1.118 (22.312%)
- rms = 1.08, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=899383.9, rms=1.083 (3.144%)
- rms = 1.07, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=897591.1, rms=1.075 (0.764%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 44 points - only 0.00% unknown
- deleting segment 1 with 143 points - only 0.00% unknown
- deleting segment 2 with 27 points - only 0.00% unknown
- deleting segment 3 with 14 points - only 0.00% unknown
- deleting segment 4 with 85 points - only 0.00% unknown
- deleting segment 6 with 47 points - only 0.00% unknown
- deleting segment 7 with 16 points - only 0.00% unknown
- deleting segment 8 with 38 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- mean border=95.7, 54 (11) missing vertices, mean dist -0.2 [0.3 (%72.3)->0.2 (%27.7))]
- %89 local maxima, % 7 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 0.88 +- 0.25 (0.04-->5.91) (max @ vno 63290 --> 69592)
- face area 0.33 +- 0.17 (0.00-->5.31)
- mean absolute distance = 0.23 +- 0.33
- 4772 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1023151.0, rms=2.464
- 017: dt: 0.5000, sse=901146.9, rms=1.459 (40.776%)
- 018: dt: 0.5000, sse=877906.9, rms=1.276 (12.556%)
- rms = 1.33, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=865936.6, rms=1.098 (13.939%)
- 020: dt: 0.2500, sse=863609.2, rms=1.018 (7.285%)
- rms = 1.01, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=861590.4, rms=1.013 (0.512%)
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=860708.0, rms=1.006 (0.637%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 44 points - only 0.00% unknown
- deleting segment 1 with 143 points - only 0.00% unknown
- deleting segment 2 with 26 points - only 0.00% unknown
- deleting segment 3 with 18 points - only 0.00% unknown
- deleting segment 4 with 13 points - only 0.00% unknown
- deleting segment 5 with 83 points - only 0.00% unknown
- deleting segment 6 with 46 points - only 0.00% unknown
- deleting segment 7 with 17 points - only 0.00% unknown
- deleting segment 8 with 35 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- mean border=96.3, 71 (7) missing vertices, mean dist -0.1 [0.3 (%57.6)->0.2 (%42.4))]
- %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=864082.9, rms=1.283
- 023: dt: 0.5000, sse=855140.8, rms=0.865 (32.581%)
- rms = 1.14, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=831221.8, rms=0.794 (8.194%)
- rms = 0.83, time step reduction 2 of 3 to 0.125...
- rms = 0.79, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=829608.3, rms=0.789 (0.723%)
- positioning took 0.6 minutes
- generating cortex label...
- 17 non-cortical segments detected
- only using segment with 8047 vertices
- erasing segment 1 (vno[0] = 57893)
- erasing segment 2 (vno[0] = 76761)
- erasing segment 3 (vno[0] = 90487)
- erasing segment 4 (vno[0] = 99012)
- erasing segment 5 (vno[0] = 99020)
- erasing segment 6 (vno[0] = 102822)
- erasing segment 7 (vno[0] = 116473)
- erasing segment 8 (vno[0] = 118661)
- erasing segment 9 (vno[0] = 119040)
- erasing segment 10 (vno[0] = 120306)
- erasing segment 11 (vno[0] = 120321)
- erasing segment 12 (vno[0] = 121457)
- erasing segment 13 (vno[0] = 122669)
- erasing segment 14 (vno[0] = 122693)
- erasing segment 15 (vno[0] = 123923)
- erasing segment 16 (vno[0] = 126117)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.area
- vertex spacing 0.88 +- 0.26 (0.05-->5.90) (max @ vno 63290 --> 69592)
- face area 0.33 +- 0.16 (0.00-->5.42)
- 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 69 points - only 0.00% unknown
- deleting segment 1 with 16 points - only 0.00% unknown
- deleting segment 2 with 18 points - only 0.00% unknown
- deleting segment 3 with 29 points - only 0.00% unknown
- deleting segment 4 with 43 points - only 0.00% unknown
- deleting segment 5 with 263 points - only 0.00% unknown
- deleting segment 7 with 106 points - only 0.00% unknown
- deleting segment 8 with 182 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- deleting segment 13 with 124 points - only 0.00% unknown
- deleting segment 14 with 112 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 15 with 4 points - only 0.00% unknown
- deleting segment 16 with 5 points - only 0.00% unknown
- deleting segment 17 with 45 points - only 0.00% unknown
- deleting segment 18 with 103 points - only 0.00% unknown
- deleting segment 19 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 20 with 4 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=72.5, 119 (119) missing vertices, mean dist 1.6 [0.5 (%0.0)->3.1 (%100.0))]
- %14 local maxima, %35 large gradients and %47 min vals, 415 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=20820754.0, rms=24.723
- 001: dt: 0.0500, sse=18946628.0, rms=23.537 (4.796%)
- 002: dt: 0.0500, sse=17598468.0, rms=22.646 (3.787%)
- 003: dt: 0.0500, sse=16565929.0, rms=21.939 (3.124%)
- 004: dt: 0.0500, sse=15731298.0, rms=21.350 (2.685%)
- 005: dt: 0.0500, sse=15030129.0, rms=20.842 (2.379%)
- 006: dt: 0.0500, sse=14423257.0, rms=20.392 (2.158%)
- 007: dt: 0.0500, sse=13887125.0, rms=19.986 (1.990%)
- 008: dt: 0.0500, sse=13405444.0, rms=19.614 (1.861%)
- 009: dt: 0.0500, sse=12967481.0, rms=19.270 (1.756%)
- 010: dt: 0.0500, sse=12565037.0, rms=18.948 (1.671%)
- positioning took 1.3 minutes
- mean border=72.4, 101 (65) missing vertices, mean dist 1.3 [0.2 (%0.1)->2.5 (%99.9))]
- %15 local maxima, %35 large gradients and %46 min vals, 401 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=13493323.0, rms=19.684
- 011: dt: 0.0500, sse=13118228.0, rms=19.390 (1.491%)
- 012: dt: 0.0500, sse=12769069.0, rms=19.113 (1.431%)
- 013: dt: 0.0500, sse=12442737.0, rms=18.850 (1.376%)
- 014: dt: 0.0500, sse=12136736.0, rms=18.599 (1.327%)
- 015: dt: 0.0500, sse=11848755.0, rms=18.361 (1.282%)
- 016: dt: 0.0500, sse=11577161.0, rms=18.133 (1.241%)
- 017: dt: 0.0500, sse=11319737.0, rms=17.914 (1.206%)
- 018: dt: 0.0500, sse=11075391.0, rms=17.704 (1.174%)
- 019: dt: 0.0500, sse=10842828.0, rms=17.502 (1.144%)
- 020: dt: 0.0500, sse=10620605.0, rms=17.306 (1.119%)
- positioning took 1.3 minutes
- mean border=72.3, 102 (48) missing vertices, mean dist 1.1 [0.1 (%0.3)->2.2 (%99.7))]
- %15 local maxima, %35 large gradients and %46 min vals, 380 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=10730645.0, rms=17.408
- 021: dt: 0.0500, sse=10514116.0, rms=17.216 (1.102%)
- 022: dt: 0.0500, sse=10306355.0, rms=17.030 (1.081%)
- 023: dt: 0.0500, sse=10105674.0, rms=16.848 (1.068%)
- 024: dt: 0.0500, sse=9911325.0, rms=16.670 (1.057%)
- 025: dt: 0.0500, sse=9722553.0, rms=16.495 (1.049%)
- 026: dt: 0.0500, sse=9538536.0, rms=16.323 (1.045%)
- 027: dt: 0.0500, sse=9358777.0, rms=16.152 (1.043%)
- 028: dt: 0.0500, sse=9182244.0, rms=15.984 (1.046%)
- 029: dt: 0.0500, sse=9008478.0, rms=15.815 (1.052%)
- 030: dt: 0.0500, sse=8837322.0, rms=15.648 (1.059%)
- positioning took 1.3 minutes
- mean border=72.2, 124 (40) missing vertices, mean dist 1.0 [0.1 (%2.0)->1.9 (%98.0))]
- %15 local maxima, %35 large gradients and %45 min vals, 345 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=8896341.0, rms=15.706
- 031: dt: 0.5000, sse=7576545.5, rms=14.355 (8.604%)
- 032: dt: 0.5000, sse=6449793.0, rms=13.087 (8.830%)
- 033: dt: 0.5000, sse=5485988.0, rms=11.898 (9.090%)
- 034: dt: 0.5000, sse=4588319.0, rms=10.669 (10.325%)
- 035: dt: 0.5000, sse=3822529.0, rms=9.499 (10.970%)
- 036: dt: 0.5000, sse=3118038.8, rms=8.276 (12.873%)
- 037: dt: 0.5000, sse=2565275.8, rms=7.176 (13.292%)
- 038: dt: 0.5000, sse=2137081.2, rms=6.188 (13.773%)
- 039: dt: 0.5000, sse=1887004.4, rms=5.534 (10.573%)
- 040: dt: 0.5000, sse=1726939.2, rms=5.064 (8.476%)
- 041: dt: 0.5000, sse=1652538.0, rms=4.835 (4.525%)
- 042: dt: 0.5000, sse=1595035.1, rms=4.643 (3.976%)
- rms = 4.60, time step reduction 1 of 3 to 0.250...
- 043: dt: 0.5000, sse=1581532.4, rms=4.600 (0.936%)
- 044: dt: 0.2500, sse=1399395.0, rms=3.884 (15.551%)
- 045: dt: 0.2500, sse=1353467.5, rms=3.699 (4.773%)
- rms = 3.73, time step reduction 2 of 3 to 0.125...
- 046: dt: 0.1250, sse=1329286.2, rms=3.593 (2.876%)
- 047: dt: 0.1250, sse=1297986.0, rms=3.448 (4.018%)
- rms = 3.41, time step reduction 3 of 3 to 0.062...
- 048: dt: 0.1250, sse=1290511.4, rms=3.413 (1.023%)
- positioning took 3.2 minutes
- mean border=71.5, 3254 (15) missing vertices, mean dist 0.1 [0.2 (%47.6)->0.5 (%52.4))]
- %27 local maxima, %26 large gradients and %41 min vals, 203 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=1590053.8, rms=3.898
- rms = 4.35, time step reduction 1 of 3 to 0.250...
- 049: dt: 0.2500, sse=1473088.5, rms=3.386 (13.139%)
- 050: dt: 0.2500, sse=1421504.8, rms=3.132 (7.492%)
- rms = 3.20, time step reduction 2 of 3 to 0.125...
- 051: dt: 0.1250, sse=1397217.9, rms=3.005 (4.069%)
- 052: dt: 0.1250, sse=1364359.9, rms=2.825 (5.978%)
- 053: dt: 0.1250, sse=1351003.5, rms=2.752 (2.589%)
- rms = 2.71, time step reduction 3 of 3 to 0.062...
- 054: dt: 0.1250, sse=1343575.5, rms=2.713 (1.424%)
- positioning took 1.5 minutes
- mean border=71.1, 3699 (12) missing vertices, mean dist 0.1 [0.1 (%46.8)->0.3 (%53.2))]
- %38 local maxima, %16 large gradients and %40 min vals, 258 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=1362932.0, rms=2.870
- rms = 3.33, time step reduction 1 of 3 to 0.250...
- 055: dt: 0.2500, sse=1337596.1, rms=2.728 (4.955%)
- rms = 2.69, time step reduction 2 of 3 to 0.125...
- 056: dt: 0.2500, sse=1328968.8, rms=2.692 (1.332%)
- 057: dt: 0.1250, sse=1316428.9, rms=2.614 (2.887%)
- rms = 2.58, time step reduction 3 of 3 to 0.062...
- 058: dt: 0.1250, sse=1310093.5, rms=2.580 (1.308%)
- positioning took 1.0 minutes
- mean border=70.7, 7382 (11) missing vertices, mean dist 0.0 [0.1 (%48.2)->0.2 (%51.8))]
- %40 local maxima, %14 large gradients and %39 min vals, 213 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-6.0.0/0051492/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1323954.8, rms=2.638
- rms = 3.07, time step reduction 1 of 3 to 0.250...
- 059: dt: 0.2500, sse=1307836.9, rms=2.542 (3.649%)
- rms = 2.51, time step reduction 2 of 3 to 0.125...
- 060: dt: 0.2500, sse=1299322.8, rms=2.510 (1.250%)
- 061: dt: 0.1250, sse=1288258.0, rms=2.435 (2.977%)
- rms = 2.40, time step reduction 3 of 3 to 0.062...
- 062: dt: 0.1250, sse=1281805.9, rms=2.400 (1.476%)
- positioning took 1.0 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.area.pial
- vertex spacing 0.98 +- 0.43 (0.06-->6.97) (max @ vno 69591 --> 69592)
- face area 0.38 +- 0.30 (0.00-->10.05)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 170760 vertices processed
- 25000 of 170760 vertices processed
- 50000 of 170760 vertices processed
- 75000 of 170760 vertices processed
- 100000 of 170760 vertices processed
- 125000 of 170760 vertices processed
- 150000 of 170760 vertices processed
- 0 of 170760 vertices processed
- 25000 of 170760 vertices processed
- 50000 of 170760 vertices processed
- 75000 of 170760 vertices processed
- 100000 of 170760 vertices processed
- 125000 of 170760 vertices processed
- 150000 of 170760 vertices processed
- thickness calculation complete, 260:662 truncations.
- 42457 vertices at 0 distance
- 124517 vertices at 1 distance
- 100991 vertices at 2 distance
- 40955 vertices at 3 distance
- 12964 vertices at 4 distance
- 4023 vertices at 5 distance
- 1161 vertices at 6 distance
- 348 vertices at 7 distance
- 111 vertices at 8 distance
- 44 vertices at 9 distance
- 38 vertices at 10 distance
- 21 vertices at 11 distance
- 16 vertices at 12 distance
- 18 vertices at 13 distance
- 11 vertices at 14 distance
- 11 vertices at 15 distance
- 9 vertices at 16 distance
- 12 vertices at 17 distance
- 15 vertices at 18 distance
- 13 vertices at 19 distance
- 7 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.thickness
- positioning took 19.4 minutes
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051492 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-6.0.0/0051492/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- 41718 bright wm thresholded.
- 2651 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.orig...
- computing class statistics...
- border white: 358475 voxels (2.14%)
- border gray 362870 voxels (2.16%)
- WM (105.0): 104.5 +- 5.4 [70.0 --> 110.0]
- GM (87.0) : 86.1 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 73.8 (was 70)
- setting MAX_BORDER_WHITE to 112.4 (was 105)
- setting MIN_BORDER_WHITE to 84.0 (was 85)
- setting MAX_CSF to 63.6 (was 40)
- setting MAX_GRAY to 101.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 73.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 53.4 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=107+-3.5, GM=84+-7.0
- mean inside = 101.6, mean outside = 89.1
- 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 0.88 +- 0.25 (0.04-->4.52) (max @ vno 170790 --> 170793)
- face area 0.33 +- 0.16 (0.00-->2.92)
- mean absolute distance = 0.74 +- 0.91
- 3002 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 46 points - only 0.00% unknown
- deleting segment 3 with 152 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 61 points - only 0.00% unknown
- deleting segment 6 with 99 points - only 0.00% unknown
- mean border=91.5, 113 (113) missing vertices, mean dist 0.5 [1.1 (%12.0)->0.7 (%88.0))]
- %65 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.26 (0.11-->4.42) (max @ vno 170790 --> 170793)
- face area 0.33 +- 0.16 (0.00-->2.46)
- mean absolute distance = 0.42 +- 0.62
- 4929 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1893678.0, rms=5.746
- 001: dt: 0.5000, sse=1200143.5, rms=3.457 (39.835%)
- 002: dt: 0.5000, sse=985775.8, rms=2.343 (32.240%)
- 003: dt: 0.5000, sse=927797.5, rms=1.957 (16.473%)
- 004: dt: 0.5000, sse=906739.2, rms=1.799 (8.075%)
- rms = 1.76, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.5000, sse=902186.8, rms=1.763 (1.967%)
- 006: dt: 0.2500, sse=876775.1, rms=1.415 (19.765%)
- 007: dt: 0.2500, sse=870079.8, rms=1.352 (4.412%)
- rms = 1.33, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=868545.0, rms=1.331 (1.545%)
- rms = 1.32, time step reduction 3 of 3 to 0.062...
- 009: dt: 0.1250, sse=866850.8, rms=1.315 (1.199%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 1 with 39 points - only 0.00% unknown
- deleting segment 2 with 8 points - only 0.00% unknown
- deleting segment 4 with 82 points - only 0.00% unknown
- deleting segment 5 with 48 points - only 0.00% unknown
- deleting segment 6 with 88 points - only 0.00% unknown
- mean border=93.7, 52 (20) missing vertices, mean dist -0.3 [0.5 (%70.1)->0.3 (%29.9))]
- %79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.07-->4.44) (max @ vno 170790 --> 170793)
- face area 0.35 +- 0.17 (0.00-->2.76)
- mean absolute distance = 0.31 +- 0.41
- 6719 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1211533.4, rms=3.231
- 010: dt: 0.5000, sse=1008421.2, rms=2.036 (36.979%)
- 011: dt: 0.5000, sse=954891.3, rms=1.606 (21.132%)
- 012: dt: 0.5000, sse=935963.8, rms=1.496 (6.843%)
- rms = 1.48, time step reduction 1 of 3 to 0.250...
- 013: dt: 0.5000, sse=930446.1, rms=1.479 (1.141%)
- 014: dt: 0.2500, sse=910477.9, rms=1.141 (22.887%)
- rms = 1.10, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=906916.7, rms=1.101 (3.461%)
- rms = 1.09, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=905491.6, rms=1.092 (0.782%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 1 with 37 points - only 0.00% unknown
- deleting segment 2 with 13 points - only 0.00% unknown
- deleting segment 3 with 93 points - only 0.00% unknown
- deleting segment 4 with 47 points - only 0.00% unknown
- deleting segment 5 with 94 points - only 0.00% unknown
- mean border=95.5, 59 (12) missing vertices, mean dist -0.2 [0.3 (%72.9)->0.2 (%27.1))]
- %89 local maxima, % 7 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 0.88 +- 0.25 (0.04-->4.41) (max @ vno 170790 --> 170793)
- face area 0.33 +- 0.16 (0.00-->2.63)
- mean absolute distance = 0.23 +- 0.32
- 4775 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1044041.1, rms=2.559
- 017: dt: 0.5000, sse=909533.2, rms=1.522 (40.530%)
- 018: dt: 0.5000, sse=889020.9, rms=1.330 (12.649%)
- rms = 1.37, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=872656.7, rms=1.135 (14.651%)
- 020: dt: 0.2500, sse=869239.4, rms=1.042 (8.172%)
- rms = 1.03, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=866931.6, rms=1.033 (0.883%)
- rms = 1.02, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=866071.0, rms=1.023 (0.991%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 36 points - only 0.00% unknown
- deleting segment 1 with 124 points - only 0.00% unknown
- deleting segment 2 with 53 points - only 0.00% unknown
- deleting segment 3 with 94 points - only 0.00% unknown
- mean border=96.0, 80 (10) missing vertices, mean dist -0.1 [0.2 (%58.2)->0.2 (%41.8))]
- %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=872023.9, rms=1.315
- 023: dt: 0.5000, sse=842856.8, rms=0.884 (32.755%)
- rms = 1.17, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=834824.3, rms=0.804 (9.058%)
- rms = 0.84, time step reduction 2 of 3 to 0.125...
- rms = 0.80, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=833294.9, rms=0.798 (0.834%)
- positioning took 0.6 minutes
- generating cortex label...
- 8 non-cortical segments detected
- only using segment with 8223 vertices
- erasing segment 1 (vno[0] = 83198)
- erasing segment 2 (vno[0] = 104015)
- erasing segment 3 (vno[0] = 120658)
- erasing segment 4 (vno[0] = 121875)
- erasing segment 5 (vno[0] = 123014)
- erasing segment 6 (vno[0] = 124133)
- erasing segment 7 (vno[0] = 129413)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.area
- vertex spacing 0.88 +- 0.26 (0.04-->4.40) (max @ vno 170790 --> 170793)
- face area 0.33 +- 0.16 (0.00-->2.59)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 22 points - only 0.00% unknown
- deleting segment 1 with 71 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 4 with 4 points - only 0.00% unknown
- deleting segment 5 with 9 points - only 0.00% unknown
- deleting segment 6 with 99 points - only 0.00% unknown
- deleting segment 7 with 71 points - only 0.00% unknown
- deleting segment 8 with 16 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 points - only 0.00% unknown
- deleting segment 10 with 10 points - only 0.00% unknown
- deleting segment 11 with 8 points - only 0.00% unknown
- deleting segment 12 with 99 points - only 0.00% unknown
- deleting segment 13 with 17 points - only 0.00% unknown
- deleting segment 14 with 16 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=71.6, 116 (116) missing vertices, mean dist 1.6 [0.4 (%0.0)->3.1 (%100.0))]
- %13 local maxima, %35 large gradients and %48 min vals, 284 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=22113792.0, rms=25.460
- 001: dt: 0.0500, sse=20125278.0, rms=24.243 (4.781%)
- 002: dt: 0.0500, sse=18693698.0, rms=23.327 (3.778%)
- 003: dt: 0.0500, sse=17596524.0, rms=22.600 (3.117%)
- 004: dt: 0.0500, sse=16710513.0, rms=21.995 (2.677%)
- 005: dt: 0.0500, sse=15965756.0, rms=21.473 (2.372%)
- 006: dt: 0.0500, sse=15321063.0, rms=21.011 (2.152%)
- 007: dt: 0.0500, sse=14750621.0, rms=20.593 (1.988%)
- 008: dt: 0.0500, sse=14237369.0, rms=20.210 (1.861%)
- 009: dt: 0.0500, sse=13770568.0, rms=19.855 (1.757%)
- 010: dt: 0.0500, sse=13341931.0, rms=19.523 (1.671%)
- positioning took 1.3 minutes
- mean border=71.4, 102 (53) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.6 (%100.0))]
- %14 local maxima, %35 large gradients and %47 min vals, 269 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=14242280.0, rms=20.214
- 011: dt: 0.0500, sse=13841822.0, rms=19.910 (1.505%)
- 012: dt: 0.0500, sse=13468560.0, rms=19.622 (1.445%)
- 013: dt: 0.0500, sse=13118958.0, rms=19.349 (1.394%)
- 014: dt: 0.0500, sse=12790700.0, rms=19.089 (1.346%)
- 015: dt: 0.0500, sse=12481580.0, rms=18.840 (1.302%)
- 016: dt: 0.0500, sse=12189746.0, rms=18.602 (1.262%)
- 017: dt: 0.0500, sse=11913914.0, rms=18.374 (1.224%)
- 018: dt: 0.0500, sse=11652060.0, rms=18.156 (1.191%)
- 019: dt: 0.0500, sse=11402729.0, rms=17.945 (1.162%)
- 020: dt: 0.0500, sse=11164995.0, rms=17.741 (1.134%)
- positioning took 1.3 minutes
- mean border=71.3, 125 (46) missing vertices, mean dist 1.1 [0.1 (%0.4)->2.2 (%99.6))]
- %14 local maxima, %36 large gradients and %46 min vals, 253 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=11277973.0, rms=17.844
- 021: dt: 0.0500, sse=11046729.0, rms=17.644 (1.116%)
- 022: dt: 0.0500, sse=10825536.0, rms=17.452 (1.092%)
- 023: dt: 0.0500, sse=10612392.0, rms=17.264 (1.076%)
- 024: dt: 0.0500, sse=10406946.0, rms=17.081 (1.060%)
- 025: dt: 0.0500, sse=10208071.0, rms=16.902 (1.049%)
- 026: dt: 0.0500, sse=10015009.0, rms=16.726 (1.040%)
- 027: dt: 0.0500, sse=9826764.0, rms=16.553 (1.036%)
- 028: dt: 0.0500, sse=9641655.0, rms=16.380 (1.041%)
- 029: dt: 0.0500, sse=9459790.0, rms=16.209 (1.044%)
- 030: dt: 0.0500, sse=9280427.0, rms=16.039 (1.052%)
- positioning took 1.3 minutes
- mean border=71.2, 158 (42) missing vertices, mean dist 1.0 [0.1 (%2.1)->1.9 (%97.9))]
- %15 local maxima, %36 large gradients and %46 min vals, 262 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=9355574.0, rms=16.111
- 031: dt: 0.5000, sse=8013130.5, rms=14.778 (8.273%)
- 032: dt: 0.5000, sse=6819374.5, rms=13.479 (8.792%)
- 033: dt: 0.5000, sse=5741810.0, rms=12.190 (9.564%)
- 034: dt: 0.5000, sse=4743734.5, rms=10.858 (10.927%)
- 035: dt: 0.5000, sse=3898551.5, rms=9.589 (11.688%)
- 036: dt: 0.5000, sse=3148101.2, rms=8.299 (13.452%)
- 037: dt: 0.5000, sse=2583975.2, rms=7.183 (13.441%)
- 038: dt: 0.5000, sse=2181278.8, rms=6.261 (12.848%)
- 039: dt: 0.5000, sse=1946346.4, rms=5.659 (9.615%)
- 040: dt: 0.5000, sse=1793421.6, rms=5.222 (7.707%)
- 041: dt: 0.5000, sse=1714427.4, rms=4.986 (4.528%)
- 042: dt: 0.5000, sse=1656691.2, rms=4.800 (3.734%)
- 043: dt: 0.5000, sse=1633808.2, rms=4.728 (1.489%)
- 044: dt: 0.5000, sse=1605903.4, rms=4.632 (2.041%)
- rms = 4.63, time step reduction 1 of 3 to 0.250...
- 045: dt: 0.5000, sse=1603548.1, rms=4.627 (0.111%)
- 046: dt: 0.2500, sse=1424000.1, rms=3.927 (15.114%)
- 047: dt: 0.2500, sse=1377336.1, rms=3.742 (4.721%)
- rms = 3.79, time step reduction 2 of 3 to 0.125...
- 048: dt: 0.1250, sse=1352766.4, rms=3.636 (2.845%)
- 049: dt: 0.1250, sse=1322071.1, rms=3.496 (3.829%)
- rms = 3.47, time step reduction 3 of 3 to 0.062...
- 050: dt: 0.1250, sse=1315838.0, rms=3.467 (0.830%)
- positioning took 3.7 minutes
- mean border=70.5, 3475 (10) missing vertices, mean dist 0.1 [0.2 (%48.4)->0.5 (%51.6))]
- %26 local maxima, %27 large gradients and %41 min vals, 151 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=1618682.2, rms=3.896
- rms = 4.39, time step reduction 1 of 3 to 0.250...
- 051: dt: 0.2500, sse=1503200.1, rms=3.391 (12.971%)
- 052: dt: 0.2500, sse=1456494.8, rms=3.162 (6.752%)
- rms = 3.23, time step reduction 2 of 3 to 0.125...
- 053: dt: 0.1250, sse=1432378.6, rms=3.037 (3.950%)
- 054: dt: 0.1250, sse=1400704.8, rms=2.867 (5.590%)
- 055: dt: 0.1250, sse=1386963.4, rms=2.794 (2.541%)
- rms = 2.76, time step reduction 3 of 3 to 0.062...
- 056: dt: 0.1250, sse=1380025.8, rms=2.758 (1.295%)
- positioning took 1.5 minutes
- mean border=70.2, 3750 (9) missing vertices, mean dist 0.1 [0.1 (%48.7)->0.4 (%51.3))]
- %36 local maxima, %17 large gradients and %41 min vals, 160 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=1391254.1, rms=2.878
- rms = 3.40, time step reduction 1 of 3 to 0.250...
- 057: dt: 0.2500, sse=1367275.2, rms=2.746 (4.600%)
- rms = 2.73, time step reduction 2 of 3 to 0.125...
- 058: dt: 0.2500, sse=1362390.6, rms=2.732 (0.516%)
- 059: dt: 0.1250, sse=1350183.8, rms=2.658 (2.716%)
- rms = 2.63, time step reduction 3 of 3 to 0.062...
- 060: dt: 0.1250, sse=1344589.4, rms=2.629 (1.077%)
- positioning took 1.0 minutes
- mean border=69.8, 7399 (9) missing vertices, mean dist 0.0 [0.1 (%49.0)->0.3 (%51.0))]
- %38 local maxima, %14 large gradients and %39 min vals, 137 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-6.0.0/0051492/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=1355881.8, rms=2.675
- rms = 3.19, time step reduction 1 of 3 to 0.250...
- 061: dt: 0.2500, sse=1340403.4, rms=2.585 (3.370%)
- rms = 2.58, time step reduction 2 of 3 to 0.125...
- 062: dt: 0.2500, sse=1335736.4, rms=2.579 (0.252%)
- 063: dt: 0.1250, sse=1324446.6, rms=2.505 (2.844%)
- rms = 2.47, time step reduction 3 of 3 to 0.062...
- 064: dt: 0.1250, sse=1318359.4, rms=2.474 (1.259%)
- positioning took 1.1 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.area.pial
- vertex spacing 0.99 +- 0.44 (0.09-->8.08) (max @ vno 110425 --> 110426)
- face area 0.38 +- 0.31 (0.00-->8.65)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 170973 vertices processed
- 25000 of 170973 vertices processed
- 50000 of 170973 vertices processed
- 75000 of 170973 vertices processed
- 100000 of 170973 vertices processed
- 125000 of 170973 vertices processed
- 150000 of 170973 vertices processed
- 0 of 170973 vertices processed
- 25000 of 170973 vertices processed
- 50000 of 170973 vertices processed
- 75000 of 170973 vertices processed
- 100000 of 170973 vertices processed
- 125000 of 170973 vertices processed
- 150000 of 170973 vertices processed
- thickness calculation complete, 382:1020 truncations.
- 40373 vertices at 0 distance
- 122172 vertices at 1 distance
- 102669 vertices at 2 distance
- 42979 vertices at 3 distance
- 14182 vertices at 4 distance
- 4363 vertices at 5 distance
- 1294 vertices at 6 distance
- 421 vertices at 7 distance
- 171 vertices at 8 distance
- 79 vertices at 9 distance
- 30 vertices at 10 distance
- 32 vertices at 11 distance
- 34 vertices at 12 distance
- 24 vertices at 13 distance
- 20 vertices at 14 distance
- 11 vertices at 15 distance
- 8 vertices at 16 distance
- 11 vertices at 17 distance
- 12 vertices at 18 distance
- 11 vertices at 19 distance
- 32 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.thickness
- positioning took 19.9 minutes
- PIDs (31923 31926) completed and logs appended.
- #--------------------------------------------
- #@# Surf Volume lh Sun Oct 8 02:59:22 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0051492 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/lh.cortex.label
- Total face volume 305147
- Total vertex volume 301436 (mask=0)
- #@# 0051492 lh 301436
-
- vertexvol Done
- #--------------------------------------------
- #@# Surf Volume rh Sun Oct 8 02:59:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0051492 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/rh.cortex.label
- Total face volume 313446
- Total vertex volume 309132 (mask=0)
- #@# 0051492 rh 309132
-
- vertexvol Done
- #--------------------------------------------
- #@# Cortical ribbon mask Sun Oct 8 02:59:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0051492
- 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 = 24
- writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/ribbon.mgz
- mris_volmask took 23.36 minutes
- writing ribbon files
- #-----------------------------------------
- #@# Parcellation Stats lh Sun Oct 8 03:22:54 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0051492 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 0051492 lh pial
- #-----------------------------------------
- #@# Parcellation Stats rh Sun Oct 8 03:22:54 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0051492 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 0051492 rh pial
- Waiting for PID 2009 of (2009 2012 2015 2018) to complete...
- Waiting for PID 2012 of (2009 2012 2015 2018) to complete...
- Waiting for PID 2015 of (2009 2012 2015 2018) to complete...
- Waiting for PID 2018 of (2009 2012 2015 2018) 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 0051492 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 305147
- Total vertex volume 301436 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 1876 1290 3094 2.459 0.426 0.107 0.020 14 1.7 bankssts
- 1194 778 2497 2.888 0.841 0.144 0.032 21 1.4 caudalanteriorcingulate
- 4720 3096 9292 2.757 0.482 0.120 0.027 51 4.9 caudalmiddlefrontal
- 2955 1925 4029 1.945 0.483 0.145 0.039 42 4.7 cuneus
- 970 684 2942 3.204 0.925 0.126 0.032 9 1.2 entorhinal
- 5968 4127 13358 2.734 0.612 0.130 0.034 77 8.1 fusiform
- 7539 4891 13705 2.605 0.381 0.121 0.026 89 7.6 inferiorparietal
- 6168 4030 13814 2.881 0.659 0.123 0.035 88 8.6 inferiortemporal
- 1687 1115 2675 2.188 0.779 0.138 0.032 24 2.2 isthmuscingulate
- 10153 6259 13592 2.072 0.598 0.138 0.038 141 15.9 lateraloccipital
- 4851 3196 9394 2.810 0.700 0.127 0.033 65 6.5 lateralorbitofrontal
- 6059 3884 9326 2.163 0.560 0.143 0.043 91 10.6 lingual
- 3634 2499 7040 2.495 0.687 0.124 0.036 54 5.6 medialorbitofrontal
- 5971 4042 14356 2.879 0.615 0.117 0.024 67 6.1 middletemporal
- 1285 847 2719 2.915 0.757 0.122 0.033 18 1.6 parahippocampal
- 2506 1520 3870 2.418 0.465 0.109 0.027 22 2.6 paracentral
- 2576 1715 5084 2.743 0.398 0.110 0.022 25 2.2 parsopercularis
- 1307 761 2670 2.729 0.598 0.115 0.037 20 1.8 parsorbitalis
- 2422 1565 4184 2.500 0.609 0.118 0.033 35 3.2 parstriangularis
- 2612 1744 2806 1.796 0.516 0.140 0.039 34 4.3 pericalcarine
- 8125 4903 11772 2.200 0.622 0.108 0.026 78 8.8 postcentral
- 1936 1306 3270 2.340 0.705 0.139 0.033 32 2.6 posteriorcingulate
- 10008 6190 15653 2.420 0.614 0.115 0.032 131 13.5 precentral
- 6191 4119 10898 2.474 0.447 0.127 0.029 71 7.3 precuneus
- 1580 1034 3963 3.306 0.545 0.135 0.029 25 2.0 rostralanteriorcingulate
- 11374 7575 22707 2.650 0.517 0.130 0.029 148 13.8 rostralmiddlefrontal
- 14036 9176 30107 2.915 0.504 0.127 0.034 180 20.1 superiorfrontal
- 9364 5854 14435 2.310 0.460 0.122 0.027 106 10.3 superiorparietal
- 7397 4989 16319 2.862 0.690 0.109 0.022 68 6.6 superiortemporal
- 9056 6017 17215 2.671 0.458 0.128 0.029 114 11.1 supramarginal
- 649 395 1407 2.440 0.731 0.180 0.081 20 2.3 frontalpole
- 849 616 3093 3.365 0.850 0.140 0.036 11 1.4 temporalpole
- 864 518 1475 2.519 0.339 0.109 0.029 10 0.8 transversetemporal
- 4202 2728 8614 3.077 0.679 0.124 0.040 64 6.3 insula
- mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0051492 lh pial
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 305147
- Total vertex volume 301436 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 1876 1185 3094 2.459 0.426 0.114 0.030 24 2.4 bankssts
- 1194 903 2497 2.888 0.841 0.151 0.035 39 2.0 caudalanteriorcingulate
- 4720 3541 9292 2.757 0.482 0.116 0.024 44 5.0 caudalmiddlefrontal
- 2955 2227 4029 1.945 0.483 0.136 0.033 47 4.6 cuneus
- 970 1049 2942 3.204 0.925 0.177 0.037 18 1.8 entorhinal
- 5968 5394 13358 2.734 0.612 0.153 0.036 102 9.9 fusiform
- 7539 5651 13705 2.605 0.381 0.123 0.027 105 9.1 inferiorparietal
- 6168 5274 13814 2.881 0.659 0.140 0.035 115 10.3 inferiortemporal
- 1687 1297 2675 2.188 0.779 0.134 0.035 31 2.3 isthmuscingulate
- 10153 7021 13592 2.072 0.598 0.115 0.028 156 12.6 lateraloccipital
- 4851 3407 9394 2.810 0.700 0.131 0.103 1086 35.2 lateralorbitofrontal
- 6059 4741 9326 2.163 0.560 0.140 0.036 91 9.7 lingual
- 3634 3072 7040 2.495 0.687 0.154 0.062 145 13.0 medialorbitofrontal
- 5971 5579 14356 2.879 0.615 0.134 0.025 64 6.9 middletemporal
- 1285 1074 2719 2.915 0.757 0.132 0.033 13 1.8 parahippocampal
- 2506 1668 3870 2.418 0.465 0.108 0.021 26 2.3 paracentral
- 2576 1979 5084 2.743 0.398 0.127 0.025 29 3.0 parsopercularis
- 1307 1087 2670 2.729 0.598 0.124 0.021 10 1.3 parsorbitalis
- 2422 1736 4184 2.500 0.609 0.122 0.024 42 2.7 parstriangularis
- 2612 1477 2806 1.796 0.516 0.111 0.028 39 2.9 pericalcarine
- 8125 5800 11772 2.200 0.622 0.106 0.021 76 7.3 postcentral
- 1936 1493 3270 2.340 0.705 0.150 0.038 32 3.6 posteriorcingulate
- 10008 6593 15653 2.420 0.614 0.100 0.027 158 13.2 precentral
- 6191 4585 10898 2.474 0.447 0.129 0.028 84 8.1 precuneus
- 1580 1443 3963 3.306 0.545 0.180 0.051 254 4.2 rostralanteriorcingulate
- 11374 9158 22707 2.650 0.517 0.136 0.029 148 14.8 rostralmiddlefrontal
- 14036 11005 30107 2.915 0.504 0.130 0.030 188 18.1 superiorfrontal
- 9364 6453 14435 2.310 0.460 0.115 0.026 111 9.6 superiorparietal
- 7397 6132 16319 2.862 0.690 0.123 0.025 78 8.3 superiortemporal
- 9056 6775 17215 2.671 0.458 0.127 0.031 120 12.7 supramarginal
- 649 674 1407 2.440 0.731 0.179 0.049 9 1.5 frontalpole
- 849 1110 3093 3.365 0.850 0.182 0.035 10 1.4 temporalpole
- 864 680 1475 2.519 0.339 0.116 0.030 5 1.0 transversetemporal
- 4202 2671 8614 3.077 0.679 0.132 0.040 81 7.0 insula
- mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051492 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 313446
- Total vertex volume 309132 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 1434 1020 2555 2.641 0.362 0.104 0.018 9 1.1 bankssts
- 1376 919 2762 2.575 0.709 0.123 0.021 20 1.1 caudalanteriorcingulate
- 4019 2502 7483 2.721 0.490 0.114 0.035 45 5.9 caudalmiddlefrontal
- 2868 1818 3673 1.934 0.458 0.148 0.042 43 5.0 cuneus
- 723 500 2388 3.384 0.781 0.133 0.044 9 1.2 entorhinal
- 5693 3948 13107 2.808 0.575 0.133 0.032 77 7.3 fusiform
- 8953 5781 16484 2.630 0.419 0.121 0.026 107 9.2 inferiorparietal
- 6891 4647 15651 2.821 0.706 0.124 0.032 98 8.4 inferiortemporal
- 1624 1038 2839 2.343 0.833 0.140 0.045 27 2.9 isthmuscingulate
- 10566 6825 15640 2.162 0.590 0.138 0.034 140 15.0 lateraloccipital
- 4781 3168 9700 2.844 0.713 0.126 0.034 64 6.7 lateralorbitofrontal
- 5199 3410 8271 2.163 0.626 0.142 0.038 80 8.2 lingual
- 3233 2244 7020 2.801 0.588 0.126 0.027 52 3.6 medialorbitofrontal
- 7033 4887 16896 2.873 0.669 0.129 0.030 92 8.6 middletemporal
- 1157 747 2159 2.517 0.711 0.101 0.026 9 1.3 parahippocampal
- 2788 1727 4659 2.515 0.487 0.107 0.027 25 2.9 paracentral
- 2154 1451 4497 2.804 0.365 0.120 0.025 26 2.0 parsopercularis
- 2026 1280 4209 2.742 0.635 0.141 0.042 34 3.9 parsorbitalis
- 2799 1847 5892 2.757 0.446 0.119 0.026 29 2.9 parstriangularis
- 2697 1718 3201 1.934 0.518 0.122 0.035 31 3.6 pericalcarine
- 8008 4818 11714 2.233 0.601 0.109 0.027 79 8.6 postcentral
- 2338 1578 4034 2.387 0.745 0.143 0.037 37 3.7 posteriorcingulate
- 9741 5828 14628 2.443 0.593 0.107 0.027 79 10.9 precentral
- 7178 4813 12478 2.467 0.435 0.134 0.032 102 9.9 precuneus
- 907 608 2139 3.113 0.560 0.136 0.033 13 1.2 rostralanteriorcingulate
- 14367 9463 28057 2.636 0.519 0.129 0.031 196 18.6 rostralmiddlefrontal
- 12964 8305 27502 2.965 0.524 0.115 0.029 156 14.9 superiorfrontal
- 9492 6021 16276 2.425 0.463 0.122 0.025 107 9.6 superiorparietal
- 7012 4814 16588 2.994 0.630 0.115 0.025 69 7.6 superiortemporal
- 6571 4355 12851 2.734 0.472 0.133 0.033 89 8.4 supramarginal
- 461 342 1342 2.897 0.473 0.193 0.052 14 0.9 frontalpole
- 740 503 2783 3.875 0.753 0.129 0.034 8 1.2 temporalpole
- 593 366 1035 2.714 0.374 0.132 0.030 7 0.7 transversetemporal
- 3944 2581 8550 3.181 0.799 0.120 0.035 43 5.4 insula
- mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051492 rh pial
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 313446
- Total vertex volume 309132 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 1434 912 2555 2.641 0.362 0.114 0.026 16 1.7 bankssts
- 1376 1159 2762 2.575 0.709 0.136 0.030 23 1.6 caudalanteriorcingulate
- 4019 2848 7483 2.721 0.490 0.110 0.026 83 4.3 caudalmiddlefrontal
- 2868 2086 3673 1.934 0.458 0.135 0.035 48 4.7 cuneus
- 723 848 2388 3.384 0.781 0.193 0.040 13 1.4 entorhinal
- 5693 5155 13107 2.808 0.575 0.150 0.032 87 8.7 fusiform
- 8953 6618 16484 2.630 0.419 0.120 0.026 99 10.2 inferiorparietal
- 6891 6151 15651 2.821 0.706 0.143 0.040 165 14.0 inferiortemporal
- 1624 1254 2839 2.343 0.833 0.132 0.036 32 2.4 isthmuscingulate
- 10566 7726 15640 2.162 0.590 0.118 0.026 138 11.8 lateraloccipital
- 4781 3525 9700 2.844 0.713 0.129 0.031 69 6.2 lateralorbitofrontal
- 5199 4180 8271 2.163 0.626 0.137 0.034 74 7.8 lingual
- 3233 2806 7020 2.801 0.588 0.135 0.028 38 3.8 medialorbitofrontal
- 7033 6659 16896 2.873 0.669 0.144 0.029 94 9.4 middletemporal
- 1157 945 2159 2.517 0.711 0.123 0.029 11 1.7 parahippocampal
- 2788 1916 4659 2.515 0.487 0.105 0.025 28 3.0 paracentral
- 2154 1712 4497 2.804 0.365 0.130 0.028 33 2.7 parsopercularis
- 2026 1688 4209 2.742 0.635 0.132 0.025 23 2.4 parsorbitalis
- 2799 2306 5892 2.757 0.446 0.131 0.024 33 3.1 parstriangularis
- 2697 1595 3201 1.934 0.518 0.105 0.032 64 3.4 pericalcarine
- 8008 5605 11714 2.233 0.601 0.111 0.023 83 7.7 postcentral
- 2338 1763 4034 2.387 0.745 0.142 0.035 38 3.7 posteriorcingulate
- 9741 6051 14628 2.443 0.593 0.090 0.018 97 7.7 precentral
- 7178 5279 12478 2.467 0.435 0.137 0.035 115 10.7 precuneus
- 907 782 2139 3.113 0.560 0.143 0.033 19 1.1 rostralanteriorcingulate
- 14367 11390 28057 2.636 0.519 0.133 0.027 190 17.8 rostralmiddlefrontal
- 12964 9905 27502 2.965 0.524 0.122 0.027 183 15.9 superiorfrontal
- 9492 7209 16276 2.425 0.463 0.124 0.029 111 12.2 superiorparietal
- 7012 6077 16588 2.994 0.630 0.134 0.028 75 8.9 superiortemporal
- 6571 4894 12851 2.734 0.472 0.123 0.030 81 8.4 supramarginal
- 461 549 1342 2.897 0.473 0.211 0.043 9 1.0 frontalpole
- 740 899 2783 3.875 0.753 0.175 0.034 11 1.2 temporalpole
- 593 401 1035 2.714 0.374 0.111 0.025 4 0.7 transversetemporal
- 3944 2557 8550 3.181 0.799 0.133 0.036 70 6.1 insula
- PIDs (2009 2012 2015 2018) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 2 lh Sun Oct 8 03:24:39 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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 03:24:39 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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 2111 of (2111 2114) to complete...
- Waiting for PID 2114 of (2111 2114) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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...
- 28 labels changed using aseg
- relabeling using gibbs priors...
- 000: 10692 changed, 170760 examined...
- 001: 2527 changed, 41706 examined...
- 002: 763 changed, 13107 examined...
- 003: 323 changed, 4303 examined...
- 004: 177 changed, 1868 examined...
- 005: 88 changed, 973 examined...
- 006: 58 changed, 479 examined...
- 007: 35 changed, 298 examined...
- 008: 12 changed, 189 examined...
- 009: 7 changed, 75 examined...
- 010: 3 changed, 42 examined...
- 011: 2 changed, 21 examined...
- 012: 1 changed, 13 examined...
- 013: 1 changed, 6 examined...
- 014: 0 changed, 5 examined...
- 9 labels changed using aseg
- 000: 297 total segments, 212 labels (2848 vertices) changed
- 001: 98 total segments, 14 labels (52 vertices) changed
- 002: 84 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 49 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1459 vertices marked for relabeling...
- 1459 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 0 minutes and 23 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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...
- 9 labels changed using aseg
- relabeling using gibbs priors...
- 000: 10705 changed, 170973 examined...
- 001: 2558 changed, 42354 examined...
- 002: 781 changed, 13326 examined...
- 003: 308 changed, 4420 examined...
- 004: 181 changed, 1822 examined...
- 005: 83 changed, 992 examined...
- 006: 42 changed, 476 examined...
- 007: 21 changed, 242 examined...
- 008: 12 changed, 126 examined...
- 009: 8 changed, 57 examined...
- 010: 1 changed, 39 examined...
- 011: 2 changed, 7 examined...
- 012: 1 changed, 10 examined...
- 013: 0 changed, 5 examined...
- 1 labels changed using aseg
- 000: 301 total segments, 216 labels (2870 vertices) changed
- 001: 97 total segments, 12 labels (38 vertices) changed
- 002: 85 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 43 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1489 vertices marked for relabeling...
- 1489 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 0 minutes and 23 seconds.
- PIDs (2111 2114) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Sun Oct 8 03:25:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0051492 lh white
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Sun Oct 8 03:25:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0051492 rh white
- Waiting for PID 2179 of (2179 2182) to complete...
- Waiting for PID 2182 of (2179 2182) 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 0051492 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 305147
- Total vertex volume 301436 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 1665 1135 3332 2.561 0.601 0.151 0.041 29 2.8 G&S_frontomargin
- 2329 1395 3777 2.460 0.558 0.128 0.040 30 3.8 G&S_occipital_inf
- 1830 1048 2413 2.095 0.505 0.115 0.031 20 2.4 G&S_paracentral
- 2465 1649 5317 2.815 0.412 0.129 0.027 30 2.8 G&S_subcentral
- 1234 789 2439 2.514 0.603 0.159 0.053 27 2.9 G&S_transv_frontopol
- 2685 1828 5947 3.056 0.586 0.125 0.026 31 2.8 G&S_cingul-Ant
- 1624 1112 3194 2.801 0.530 0.125 0.027 19 1.8 G&S_cingul-Mid-Ant
- 1561 1076 2797 2.539 0.441 0.123 0.029 18 1.9 G&S_cingul-Mid-Post
- 682 466 1578 2.685 0.487 0.161 0.042 13 1.1 G_cingul-Post-dorsal
- 409 264 786 2.575 0.657 0.149 0.039 7 0.5 G_cingul-Post-ventral
- 2917 1862 3978 1.893 0.495 0.151 0.047 49 5.5 G_cuneus
- 1419 918 3470 2.821 0.362 0.129 0.039 24 2.2 G_front_inf-Opercular
- 486 282 1260 3.137 0.482 0.144 0.044 8 0.7 G_front_inf-Orbital
- 1492 919 3058 2.579 0.717 0.128 0.041 31 2.5 G_front_inf-Triangul
- 6752 4275 16254 2.912 0.497 0.136 0.033 110 8.6 G_front_middle
- 9908 6270 23072 2.983 0.533 0.133 0.040 151 17.0 G_front_sup
- 836 532 1963 3.242 0.726 0.119 0.040 14 1.3 G_Ins_lg&S_cent_ins
- 1041 682 3091 3.460 0.711 0.151 0.058 32 2.2 G_insular_short
- 2969 1756 5279 2.413 0.431 0.139 0.036 51 4.2 G_occipital_middle
- 1954 1227 2923 2.067 0.620 0.145 0.038 31 2.9 G_occipital_sup
- 2587 1755 6571 2.897 0.598 0.143 0.041 46 4.2 G_oc-temp_lat-fusifor
- 4682 2861 7278 2.126 0.576 0.148 0.049 79 9.4 G_oc-temp_med-Lingual
- 2028 1343 5698 3.170 0.800 0.130 0.037 28 2.9 G_oc-temp_med-Parahip
- 3101 1918 6905 2.768 0.744 0.132 0.043 58 5.6 G_orbital
- 3479 2157 7395 2.729 0.427 0.130 0.032 55 4.2 G_pariet_inf-Angular
- 4643 3011 10217 2.790 0.477 0.134 0.033 70 6.3 G_pariet_inf-Supramar
- 3520 2145 6257 2.417 0.467 0.124 0.030 46 4.2 G_parietal_sup
- 3147 1627 4389 2.215 0.551 0.102 0.031 35 3.8 G_postcentral
- 4115 2313 6952 2.471 0.760 0.116 0.038 47 6.4 G_precentral
- 3554 2239 7301 2.580 0.444 0.139 0.034 56 4.7 G_precuneus
- 1053 712 2942 2.828 0.633 0.140 0.046 25 2.1 G_rectus
- 947 636 1296 2.250 0.978 0.103 0.053 10 2.2 G_subcallosal
- 758 459 1425 2.565 0.351 0.110 0.029 9 0.8 G_temp_sup-G_T_transv
- 2648 1794 8100 3.229 0.715 0.139 0.033 43 3.3 G_temp_sup-Lateral
- 886 642 2545 3.350 0.619 0.099 0.019 4 0.8 G_temp_sup-Plan_polar
- 1318 915 2687 2.623 0.485 0.092 0.018 8 1.0 G_temp_sup-Plan_tempo
- 3147 1969 8345 3.052 0.686 0.140 0.051 65 6.4 G_temporal_inf
- 3442 2285 10139 3.117 0.578 0.133 0.031 52 4.5 G_temporal_middle
- 421 279 583 2.367 0.489 0.088 0.017 2 0.2 Lat_Fis-ant-Horizont
- 433 319 663 2.694 0.333 0.098 0.014 2 0.2 Lat_Fis-ant-Vertical
- 1281 855 1664 2.395 0.347 0.112 0.022 10 1.2 Lat_Fis-post
- 2918 1831 3050 1.615 0.510 0.147 0.043 45 5.6 Pole_occipital
- 2061 1481 6917 3.270 0.739 0.144 0.038 33 3.4 Pole_temporal
- 2882 1999 3440 2.009 0.662 0.133 0.032 29 4.1 S_calcarine
- 3773 2495 4101 1.899 0.537 0.107 0.025 53 4.5 S_central
- 1164 806 1620 2.320 0.291 0.099 0.016 6 0.8 S_cingul-Marginalis
- 675 465 1139 2.927 0.408 0.101 0.019 3 0.6 S_circular_insula_ant
- 1769 1151 2751 2.943 0.498 0.093 0.023 9 1.8 S_circular_insula_inf
- 1932 1294 2766 2.675 0.378 0.115 0.023 15 1.9 S_circular_insula_sup
- 1350 932 2003 2.427 0.391 0.089 0.013 5 0.8 S_collat_transv_ant
- 788 521 887 2.069 0.358 0.122 0.025 6 0.9 S_collat_transv_post
- 2680 1863 4372 2.511 0.382 0.114 0.021 18 2.4 S_front_inf
- 2065 1419 2925 2.317 0.343 0.123 0.027 20 2.5 S_front_middle
- 3623 2459 6160 2.672 0.383 0.105 0.020 26 2.7 S_front_sup
- 622 417 853 2.662 0.372 0.121 0.024 5 0.7 S_interm_prim-Jensen
- 3464 2258 4590 2.296 0.350 0.116 0.021 30 3.0 S_intrapariet&P_trans
- 1114 761 1322 2.118 0.334 0.125 0.024 9 1.1 S_oc_middle&Lunatus
- 1639 1083 2069 2.103 0.439 0.120 0.024 15 1.5 S_oc_sup&transversal
- 680 465 832 2.312 0.314 0.113 0.021 4 0.6 S_occipital_ant
- 1034 712 1649 2.574 0.426 0.106 0.022 7 0.8 S_oc-temp_lat
- 2251 1587 3541 2.438 0.535 0.120 0.025 20 2.1 S_oc-temp_med&Lingual
- 412 289 642 2.555 0.487 0.123 0.023 3 0.5 S_orbital_lateral
- 774 533 1073 2.440 0.565 0.118 0.022 7 0.6 S_orbital_med-olfact
- 1848 1238 3334 2.857 0.638 0.118 0.025 18 1.7 S_orbital-H_Shaped
- 2038 1395 2943 2.330 0.388 0.111 0.022 14 1.9 S_parieto_occipital
- 1616 970 1674 1.985 0.992 0.131 0.026 26 1.5 S_pericallosal
- 3425 2333 4949 2.369 0.418 0.119 0.024 29 3.5 S_postcentral
- 2239 1472 3372 2.534 0.360 0.099 0.017 15 1.5 S_precentral-inf-part
- 1872 1272 2845 2.560 0.396 0.108 0.021 14 1.5 S_precentral-sup-part
- 1207 834 2067 2.468 0.473 0.132 0.021 15 1.0 S_suborbital
- 1139 795 1660 2.321 0.343 0.117 0.023 9 1.1 S_subparietal
- 2032 1410 3041 2.547 0.465 0.104 0.016 12 1.4 S_temporal_inf
- 7098 4820 11012 2.494 0.413 0.104 0.019 51 5.6 S_temporal_sup
- 463 308 557 2.096 0.352 0.111 0.016 4 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 0051492 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 313446
- Total vertex volume 309132 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 1458 1059 3421 2.844 0.522 0.168 0.040 27 2.5 G&S_frontomargin
- 1641 1043 3115 2.579 0.503 0.128 0.040 24 2.5 G&S_occipital_inf
- 1760 975 2630 2.331 0.524 0.108 0.033 17 2.1 G&S_paracentral
- 1574 1089 3509 2.833 0.462 0.129 0.032 20 2.0 G&S_subcentral
- 1699 1170 4116 2.855 0.548 0.140 0.029 25 2.1 G&S_transv_frontopol
- 3970 2752 8874 3.003 0.500 0.126 0.027 44 4.6 G&S_cingul-Ant
- 1735 1184 3467 2.851 0.449 0.115 0.020 18 1.5 G&S_cingul-Mid-Ant
- 2006 1359 3784 2.613 0.542 0.132 0.036 25 3.2 G&S_cingul-Mid-Post
- 661 451 1666 2.767 0.461 0.157 0.039 12 1.1 G_cingul-Post-dorsal
- 335 225 897 2.977 0.601 0.152 0.057 8 0.6 G_cingul-Post-ventral
- 2651 1642 3673 1.982 0.473 0.150 0.048 45 5.0 G_cuneus
- 1345 873 3417 2.991 0.347 0.127 0.030 23 1.6 G_front_inf-Opercular
- 678 413 1974 3.144 0.475 0.141 0.034 11 0.9 G_front_inf-Orbital
- 1100 714 2681 2.841 0.413 0.126 0.030 13 1.3 G_front_inf-Triangul
- 6780 4067 15488 2.800 0.557 0.135 0.041 125 11.9 G_front_middle
- 8329 5017 18743 3.029 0.565 0.120 0.037 135 11.4 G_front_sup
- 628 432 1700 3.497 0.746 0.123 0.036 9 0.7 G_Ins_lg&S_cent_ins
- 1309 816 3470 3.234 0.970 0.138 0.051 23 2.7 G_insular_short
- 3212 2036 6352 2.527 0.472 0.149 0.037 61 4.8 G_occipital_middle
- 1832 1191 3443 2.324 0.638 0.135 0.031 24 2.2 G_occipital_sup
- 2587 1769 6500 2.877 0.491 0.141 0.038 42 3.9 G_oc-temp_lat-fusifor
- 3518 2242 6095 2.235 0.597 0.148 0.041 62 6.0 G_oc-temp_med-Lingual
- 1584 1040 4738 3.217 0.823 0.125 0.037 18 2.2 G_oc-temp_med-Parahip
- 3470 2287 8823 2.997 0.715 0.150 0.051 75 7.7 G_orbital
- 3017 1922 7205 2.803 0.449 0.131 0.030 46 3.4 G_pariet_inf-Angular
- 3785 2488 8708 2.866 0.494 0.142 0.037 65 5.6 G_pariet_inf-Supramar
- 3550 2148 6614 2.492 0.459 0.126 0.028 50 3.8 G_parietal_sup
- 3117 1668 4774 2.262 0.610 0.111 0.031 38 3.8 G_postcentral
- 3913 2091 6455 2.474 0.689 0.109 0.034 38 5.5 G_precentral
- 3356 2199 7336 2.601 0.482 0.150 0.040 70 5.6 G_precuneus
- 929 650 2537 2.728 0.539 0.146 0.036 25 1.5 G_rectus
- 660 419 1020 2.453 0.929 0.082 0.032 5 0.5 G_subcallosal
- 482 282 987 2.856 0.428 0.118 0.029 6 0.6 G_temp_sup-G_T_transv
- 2518 1736 7614 3.236 0.647 0.142 0.036 37 3.8 G_temp_sup-Lateral
- 817 557 2358 3.677 0.664 0.102 0.026 6 0.8 G_temp_sup-Plan_polar
- 1206 819 2397 2.687 0.492 0.113 0.025 12 1.1 G_temp_sup-Plan_tempo
- 4095 2690 10801 2.910 0.782 0.139 0.040 78 6.3 G_temporal_inf
- 4071 2822 11591 3.014 0.657 0.138 0.037 67 5.9 G_temporal_middle
- 378 264 563 2.689 0.308 0.101 0.014 2 0.3 Lat_Fis-ant-Horizont
- 145 112 302 2.911 0.403 0.109 0.016 1 0.1 Lat_Fis-ant-Vertical
- 1373 909 1957 2.657 0.386 0.124 0.030 12 1.6 Lat_Fis-post
- 5061 3147 5548 1.708 0.577 0.142 0.038 70 8.5 Pole_occipital
- 2136 1485 7656 3.489 0.717 0.145 0.041 38 3.8 Pole_temporal
- 2416 1664 3407 2.298 0.580 0.122 0.030 21 3.2 S_calcarine
- 3674 2326 4085 2.056 0.530 0.096 0.020 19 3.1 S_central
- 1450 1016 2143 2.326 0.337 0.102 0.016 8 1.0 S_cingul-Marginalis
- 859 568 1257 2.797 0.441 0.105 0.020 4 0.7 S_circular_insula_ant
- 1453 943 2337 3.063 0.584 0.083 0.016 5 1.0 S_circular_insula_inf
- 1463 996 2184 2.622 0.390 0.106 0.019 7 1.3 S_circular_insula_sup
- 1415 981 2494 2.741 0.527 0.091 0.014 6 0.9 S_collat_transv_ant
- 578 400 807 2.275 0.335 0.133 0.028 4 0.7 S_collat_transv_post
- 3508 2325 5494 2.449 0.391 0.110 0.021 30 2.8 S_front_inf
- 3429 2384 5164 2.418 0.376 0.115 0.022 26 3.1 S_front_middle
- 3020 2046 5229 2.741 0.440 0.099 0.021 16 2.6 S_front_sup
- 341 236 542 2.744 0.486 0.129 0.031 3 0.4 S_interm_prim-Jensen
- 2972 1983 4085 2.335 0.366 0.111 0.018 24 2.3 S_intrapariet&P_trans
- 1211 832 1578 2.236 0.323 0.119 0.022 9 1.1 S_oc_middle&Lunatus
- 1813 1196 2369 2.266 0.388 0.123 0.021 18 1.5 S_oc_sup&transversal
- 1193 787 1579 2.392 0.372 0.132 0.029 15 1.2 S_occipital_ant
- 1435 1004 2373 2.640 0.464 0.120 0.024 13 1.3 S_oc-temp_lat
- 2076 1455 3228 2.342 0.452 0.109 0.018 15 1.6 S_oc-temp_med&Lingual
- 799 536 1131 2.507 0.471 0.111 0.033 9 1.3 S_orbital_lateral
- 725 507 1164 2.624 0.707 0.112 0.016 5 0.5 S_orbital_med-olfact
- 1816 1201 3090 2.667 0.513 0.115 0.026 15 2.0 S_orbital-H_Shaped
- 2687 1771 3729 2.367 0.475 0.125 0.027 25 3.2 S_parieto_occipital
- 1826 1106 1474 1.718 0.642 0.119 0.029 26 2.1 S_pericallosal
- 3441 2268 4621 2.355 0.374 0.114 0.023 28 3.3 S_postcentral
- 1958 1347 3095 2.606 0.318 0.106 0.017 13 1.6 S_precentral-inf-part
- 2308 1462 3047 2.397 0.502 0.109 0.023 19 2.0 S_precentral-sup-part
- 392 281 589 2.595 0.463 0.128 0.016 3 0.3 S_suborbital
- 1606 1116 2364 2.288 0.350 0.132 0.026 16 1.7 S_subparietal
- 2269 1578 3202 2.501 0.517 0.111 0.019 14 1.9 S_temporal_inf
- 7442 5091 11781 2.562 0.383 0.103 0.019 46 5.7 S_temporal_sup
- 304 225 489 2.774 0.321 0.129 0.019 2 0.3 S_temporal_transverse
- PIDs (2179 2182) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 3 lh Sun Oct 8 03:25:56 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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 03:25:56 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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 2254 of (2254 2257) to complete...
- Waiting for PID 2257 of (2254 2257) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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...
- 1807 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2308 changed, 170760 examined...
- 001: 548 changed, 10607 examined...
- 002: 152 changed, 3018 examined...
- 003: 71 changed, 869 examined...
- 004: 32 changed, 416 examined...
- 005: 18 changed, 176 examined...
- 006: 13 changed, 98 examined...
- 007: 11 changed, 72 examined...
- 008: 7 changed, 57 examined...
- 009: 7 changed, 49 examined...
- 010: 6 changed, 36 examined...
- 011: 5 changed, 29 examined...
- 012: 4 changed, 25 examined...
- 013: 4 changed, 23 examined...
- 014: 7 changed, 22 examined...
- 015: 6 changed, 33 examined...
- 016: 6 changed, 37 examined...
- 017: 5 changed, 39 examined...
- 018: 4 changed, 33 examined...
- 019: 3 changed, 20 examined...
- 020: 1 changed, 21 examined...
- 021: 1 changed, 7 examined...
- 022: 0 changed, 8 examined...
- 298 labels changed using aseg
- 000: 55 total segments, 22 labels (402 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 11 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 919 vertices marked for relabeling...
- 919 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas.annot...
- classification took 0 minutes and 20 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051492 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...
- 1657 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2307 changed, 170973 examined...
- 001: 513 changed, 10693 examined...
- 002: 146 changed, 2941 examined...
- 003: 69 changed, 893 examined...
- 004: 31 changed, 385 examined...
- 005: 20 changed, 184 examined...
- 006: 9 changed, 111 examined...
- 007: 8 changed, 55 examined...
- 008: 5 changed, 41 examined...
- 009: 3 changed, 26 examined...
- 010: 3 changed, 16 examined...
- 011: 4 changed, 14 examined...
- 012: 2 changed, 16 examined...
- 013: 1 changed, 10 examined...
- 014: 2 changed, 7 examined...
- 015: 3 changed, 12 examined...
- 016: 3 changed, 17 examined...
- 017: 2 changed, 17 examined...
- 018: 0 changed, 11 examined...
- 169 labels changed using aseg
- 000: 53 total segments, 20 labels (169 vertices) changed
- 001: 35 total segments, 2 labels (4 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...
- 1119 vertices marked for relabeling...
- 1119 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas.annot...
- classification took 0 minutes and 20 seconds.
- PIDs (2254 2257) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Sun Oct 8 03:26:16 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0051492 lh white
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Sun Oct 8 03:26:16 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0051492 rh white
- Waiting for PID 2331 of (2331 2334) to complete...
- Waiting for PID 2334 of (2331 2334) 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 0051492 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 305147
- Total vertex volume 301436 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 2083 1378 4279 2.850 0.753 0.137 0.030 32 2.3 caudalanteriorcingulate
- 5043 3312 9859 2.761 0.471 0.120 0.027 54 5.2 caudalmiddlefrontal
- 3734 2423 5131 1.996 0.460 0.137 0.037 50 5.4 cuneus
- 871 606 2557 3.159 0.925 0.123 0.033 8 1.1 entorhinal
- 5509 3782 11567 2.685 0.590 0.127 0.031 68 6.9 fusiform
- 7840 5067 14072 2.596 0.380 0.122 0.026 95 8.2 inferiorparietal
- 6222 4112 14301 2.877 0.665 0.129 0.038 94 9.5 inferiortemporal
- 1707 1128 2714 2.219 0.774 0.138 0.033 24 2.2 isthmuscingulate
- 10142 6233 13671 2.074 0.601 0.137 0.037 138 15.7 lateraloccipital
- 5441 3614 11015 2.788 0.740 0.132 0.038 80 8.3 lateralorbitofrontal
- 6127 3920 9386 2.157 0.561 0.143 0.044 91 10.9 lingual
- 2795 1881 5697 2.501 0.706 0.128 0.040 48 5.0 medialorbitofrontal
- 7727 5242 17712 2.812 0.612 0.115 0.024 83 7.7 middletemporal
- 1371 902 2971 2.943 0.753 0.124 0.035 19 1.8 parahippocampal
- 2981 1825 4806 2.463 0.482 0.109 0.029 27 3.4 paracentral
- 2363 1566 4593 2.737 0.402 0.110 0.023 23 2.1 parsopercularis
- 1213 751 2511 2.870 0.577 0.120 0.032 15 1.5 parsorbitalis
- 3041 1977 5363 2.526 0.580 0.117 0.030 40 3.5 parstriangularis
- 2676 1798 2886 1.786 0.521 0.138 0.037 34 4.4 pericalcarine
- 9373 5652 13644 2.238 0.617 0.110 0.026 92 10.3 postcentral
- 2147 1440 3501 2.340 0.668 0.135 0.032 32 2.8 posteriorcingulate
- 9815 6066 15326 2.416 0.613 0.116 0.032 129 13.3 precentral
- 6175 4075 11131 2.492 0.440 0.129 0.029 74 7.5 precuneus
- 2164 1436 4692 3.071 0.684 0.122 0.027 27 2.3 rostralanteriorcingulate
- 8170 5358 16387 2.693 0.497 0.131 0.031 111 10.6 rostralmiddlefrontal
- 15739 10312 33490 2.840 0.539 0.129 0.034 212 22.4 superiorfrontal
- 7305 4659 11405 2.316 0.459 0.123 0.027 84 8.1 superiorparietal
- 9738 6599 22131 2.892 0.721 0.112 0.023 90 9.3 superiortemporal
- 8187 5432 15651 2.667 0.459 0.128 0.029 103 10.0 supramarginal
- 838 501 1447 2.522 0.343 0.109 0.029 10 0.8 transversetemporal
- 3558 2342 7541 3.108 0.639 0.124 0.039 57 5.5 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 0051492 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 313446
- Total vertex volume 309132 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 1504 1004 2952 2.583 0.712 0.123 0.021 22 1.2 caudalanteriorcingulate
- 4186 2601 7660 2.722 0.483 0.114 0.034 47 6.0 caudalmiddlefrontal
- 3468 2212 4758 2.009 0.508 0.141 0.040 48 5.8 cuneus
- 669 471 2239 3.390 0.816 0.130 0.036 8 0.8 entorhinal
- 5175 3590 11394 2.782 0.554 0.129 0.029 63 6.2 fusiform
- 8832 5697 16354 2.635 0.419 0.123 0.027 107 9.3 inferiorparietal
- 7609 5124 18102 2.857 0.696 0.128 0.034 113 10.0 inferiortemporal
- 1585 1007 2747 2.339 0.823 0.139 0.046 26 2.9 isthmuscingulate
- 10400 6712 15182 2.136 0.581 0.139 0.034 141 15.0 lateraloccipital
- 5325 3541 11494 2.838 0.698 0.142 0.042 91 9.5 lateralorbitofrontal
- 5125 3373 8193 2.174 0.622 0.142 0.038 77 8.0 lingual
- 2488 1732 5399 2.655 0.667 0.126 0.030 43 2.9 medialorbitofrontal
- 8301 5762 18922 2.830 0.645 0.126 0.029 103 9.7 middletemporal
- 1222 791 2288 2.544 0.724 0.102 0.026 10 1.3 parahippocampal
- 2904 1804 4916 2.523 0.486 0.106 0.026 25 3.0 paracentral
- 2638 1768 5446 2.776 0.394 0.123 0.026 34 2.7 parsopercularis
- 1442 947 3258 2.892 0.601 0.127 0.031 17 1.8 parsorbitalis
- 2968 1935 5868 2.707 0.457 0.122 0.029 32 3.8 parstriangularis
- 2721 1723 3244 1.938 0.521 0.124 0.036 33 3.7 pericalcarine
- 8988 5384 13233 2.262 0.594 0.111 0.028 92 9.8 postcentral
- 2426 1641 4207 2.390 0.734 0.144 0.037 38 3.9 posteriorcingulate
- 9101 5460 14126 2.460 0.596 0.106 0.026 72 10.1 precentral
- 7362 4934 13088 2.481 0.438 0.135 0.032 105 10.1 precuneus
- 1203 804 2541 2.989 0.607 0.126 0.030 15 1.3 rostralanteriorcingulate
- 10268 6612 18824 2.592 0.512 0.125 0.031 131 13.0 rostralmiddlefrontal
- 17684 11514 37533 2.903 0.545 0.120 0.029 228 21.0 superiorfrontal
- 7714 4934 13115 2.419 0.465 0.122 0.024 86 7.2 superiorparietal
- 8732 5972 21106 3.052 0.699 0.115 0.026 85 9.8 superiortemporal
- 6178 4113 12095 2.729 0.471 0.131 0.032 81 7.8 supramarginal
- 560 341 974 2.703 0.372 0.129 0.029 7 0.6 transversetemporal
- 3572 2380 7873 3.221 0.714 0.118 0.032 38 4.3 insula
- PIDs (2331 2334) completed and logs appended.
- #-----------------------------------------
- #@# WM/GM Contrast lh Sun Oct 8 03:27:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- pctsurfcon --s 0051492 --lh-only
- #-----------------------------------------
- #@# WM/GM Contrast rh Sun Oct 8 03:27:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts
- pctsurfcon --s 0051492 --rh-only
- Waiting for PID 2399 of (2399 2410) to complete...
- Waiting for PID 2410 of (2399 2410) to complete...
- pctsurfcon --s 0051492 --lh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts/pctsurfcon.log
- Sun Oct 8 03:27:10 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-6.0.0/0051492/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-582 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-6.0.0/0051492/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2399/lh.wm.mgh --regheader 0051492 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00001;
- 0.00000 0.00000 1.00000 0.00000;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 = 92044
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2399/lh.wm.mgh
- Dim: 170760 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2399/lh.gm.mgh --projfrac 0.3 --regheader 0051492 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00001;
- 0.00000 0.00000 1.00000 0.00000;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 = 110882
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2399/lh.gm.mgh
- Dim: 170760 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2399/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2399/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/surf/lh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.w-g.pct.mgh --annot 0051492 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/surf/lh.w-g.pct.mgh --annot 0051492 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-582
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/surf/lh.w-g.pct.mgh
- Vertex Area is 0.651262 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 0051492 --rh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/scripts/pctsurfcon.log
- Sun Oct 8 03:27:10 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-6.0.0/0051492/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-582 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-6.0.0/0051492/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2410/rh.wm.mgh --regheader 0051492 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00001;
- 0.00000 0.00000 1.00000 0.00000;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 = 93063
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2410/rh.wm.mgh
- Dim: 170973 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2410/rh.gm.mgh --projfrac 0.3 --regheader 0051492 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00001;
- 0.00000 0.00000 1.00000 0.00000;
- 0.00000 -1.00000 0.00000 0.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 = 110956
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2410/rh.gm.mgh
- Dim: 170973 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2410/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/tmp.pctsurfcon.2410/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/surf/rh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.w-g.pct.mgh --annot 0051492 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/surf/rh.w-g.pct.mgh --annot 0051492 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-582
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/surf/rh.w-g.pct.mgh
- Vertex Area is 0.652511 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 (2399 2410) completed and logs appended.
- #-----------------------------------------
- #@# Relabel Hypointensities Sun Oct 8 03:27:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri
- mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
- reading input surface ../surf/lh.white...
- relabeling lh hypointensities...
- 7942 voxels changed to hypointensity...
- reading input surface ../surf/rh.white...
- relabeling rh hypointensities...
- 8527 voxels changed to hypointensity...
- 15996 hypointense voxels neighboring cortex changed
- #-----------------------------------------
- #@# AParc-to-ASeg aparc Sun Oct 8 03:27:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492
- mri_aparc2aseg --s 0051492 --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 03:27:46 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492
- mri_aparc2aseg --s 0051492 --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 03:27:46 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492
- mri_aparc2aseg --s 0051492 --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 2558 of (2558 2561 2564) to complete...
- Waiting for PID 2561 of (2558 2561 2564) to complete...
- Waiting for PID 2564 of (2558 2561 2564) to complete...
- mri_aparc2aseg --s 0051492 --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 0051492
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/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-6.0.0/0051492/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 7.97
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 103
- rescaling Left_Cerebral_Cortex from 61 --> 81
- rescaling Left_Lateral_Ventricle from 13 --> 32
- rescaling Left_Inf_Lat_Vent from 34 --> 42
- rescaling Left_Cerebellum_White_Matter from 86 --> 88
- rescaling Left_Cerebellum_Cortex from 60 --> 75
- rescaling Left_Thalamus from 94 --> 102
- rescaling Left_Thalamus_Proper from 84 --> 94
- rescaling Left_Caudate from 75 --> 87
- rescaling Left_Putamen from 80 --> 91
- rescaling Left_Pallidum from 98 --> 97
- rescaling Third_Ventricle from 25 --> 47
- rescaling Fourth_Ventricle from 22 --> 29
- rescaling Brain_Stem from 81 --> 85
- rescaling Left_Hippocampus from 57 --> 70
- rescaling Left_Amygdala from 56 --> 75
- rescaling CSF from 32 --> 67
- rescaling Left_Accumbens_area from 62 --> 70
- rescaling Left_VentralDC from 87 --> 91
- rescaling Right_Cerebral_White_Matter from 105 --> 101
- rescaling Right_Cerebral_Cortex from 58 --> 79
- rescaling Right_Lateral_Ventricle from 13 --> 27
- rescaling Right_Inf_Lat_Vent from 25 --> 29
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 70
- rescaling Right_Thalamus_Proper from 85 --> 88
- rescaling Right_Caudate from 62 --> 82
- rescaling Right_Putamen from 80 --> 84
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 70
- rescaling Right_Amygdala from 55 --> 73
- rescaling Right_Accumbens_area from 65 --> 81
- rescaling Right_VentralDC from 86 --> 90
- rescaling Fifth_Ventricle from 40 --> 56
- rescaling WM_hypointensities from 78 --> 75
- rescaling non_WM_hypointensities from 40 --> 54
- 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 = 606104
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 160 changed.
- pass 2: 13 changed.
- pass 3: 7 changed.
- pass 4: 6 changed.
- pass 5: 6 changed.
- pass 6: 6 changed.
- pass 7: 6 changed.
- pass 8: 6 changed.
- pass 9: 6 changed.
- pass 10: 6 changed.
- pass 11: 6 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/aparc+aseg.mgz
- mri_aparc2aseg --s 0051492 --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 0051492
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/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-6.0.0/0051492/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 7.97
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 103
- rescaling Left_Cerebral_Cortex from 61 --> 81
- rescaling Left_Lateral_Ventricle from 13 --> 32
- rescaling Left_Inf_Lat_Vent from 34 --> 42
- rescaling Left_Cerebellum_White_Matter from 86 --> 88
- rescaling Left_Cerebellum_Cortex from 60 --> 75
- rescaling Left_Thalamus from 94 --> 102
- rescaling Left_Thalamus_Proper from 84 --> 94
- rescaling Left_Caudate from 75 --> 87
- rescaling Left_Putamen from 80 --> 91
- rescaling Left_Pallidum from 98 --> 97
- rescaling Third_Ventricle from 25 --> 47
- rescaling Fourth_Ventricle from 22 --> 29
- rescaling Brain_Stem from 81 --> 85
- rescaling Left_Hippocampus from 57 --> 70
- rescaling Left_Amygdala from 56 --> 75
- rescaling CSF from 32 --> 67
- rescaling Left_Accumbens_area from 62 --> 70
- rescaling Left_VentralDC from 87 --> 91
- rescaling Right_Cerebral_White_Matter from 105 --> 101
- rescaling Right_Cerebral_Cortex from 58 --> 79
- rescaling Right_Lateral_Ventricle from 13 --> 27
- rescaling Right_Inf_Lat_Vent from 25 --> 29
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 70
- rescaling Right_Thalamus_Proper from 85 --> 88
- rescaling Right_Caudate from 62 --> 82
- rescaling Right_Putamen from 80 --> 84
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 70
- rescaling Right_Amygdala from 55 --> 73
- rescaling Right_Accumbens_area from 65 --> 81
- rescaling Right_VentralDC from 86 --> 90
- rescaling Fifth_Ventricle from 40 --> 56
- rescaling WM_hypointensities from 78 --> 75
- rescaling non_WM_hypointensities from 40 --> 54
- 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 = 606209
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 160 changed.
- pass 2: 13 changed.
- pass 3: 7 changed.
- pass 4: 6 changed.
- pass 5: 6 changed.
- pass 6: 6 changed.
- pass 7: 6 changed.
- pass 8: 6 changed.
- pass 9: 6 changed.
- pass 10: 6 changed.
- pass 11: 6 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/aparc.a2009s+aseg.mgz
- mri_aparc2aseg --s 0051492 --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 0051492
- outvol mri/aparc.DKTatlas+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/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-6.0.0/0051492/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 7.97
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 103
- rescaling Left_Cerebral_Cortex from 61 --> 81
- rescaling Left_Lateral_Ventricle from 13 --> 32
- rescaling Left_Inf_Lat_Vent from 34 --> 42
- rescaling Left_Cerebellum_White_Matter from 86 --> 88
- rescaling Left_Cerebellum_Cortex from 60 --> 75
- rescaling Left_Thalamus from 94 --> 102
- rescaling Left_Thalamus_Proper from 84 --> 94
- rescaling Left_Caudate from 75 --> 87
- rescaling Left_Putamen from 80 --> 91
- rescaling Left_Pallidum from 98 --> 97
- rescaling Third_Ventricle from 25 --> 47
- rescaling Fourth_Ventricle from 22 --> 29
- rescaling Brain_Stem from 81 --> 85
- rescaling Left_Hippocampus from 57 --> 70
- rescaling Left_Amygdala from 56 --> 75
- rescaling CSF from 32 --> 67
- rescaling Left_Accumbens_area from 62 --> 70
- rescaling Left_VentralDC from 87 --> 91
- rescaling Right_Cerebral_White_Matter from 105 --> 101
- rescaling Right_Cerebral_Cortex from 58 --> 79
- rescaling Right_Lateral_Ventricle from 13 --> 27
- rescaling Right_Inf_Lat_Vent from 25 --> 29
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 70
- rescaling Right_Thalamus_Proper from 85 --> 88
- rescaling Right_Caudate from 62 --> 82
- rescaling Right_Putamen from 80 --> 84
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 70
- rescaling Right_Amygdala from 55 --> 73
- rescaling Right_Accumbens_area from 65 --> 81
- rescaling Right_VentralDC from 86 --> 90
- rescaling Fifth_Ventricle from 40 --> 56
- rescaling WM_hypointensities from 78 --> 75
- rescaling non_WM_hypointensities from 40 --> 54
- 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 = 606209
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 160 changed.
- pass 2: 13 changed.
- pass 3: 7 changed.
- pass 4: 6 changed.
- pass 5: 6 changed.
- pass 6: 6 changed.
- pass 7: 6 changed.
- pass 8: 6 changed.
- pass 9: 6 changed.
- pass 10: 6 changed.
- pass 11: 6 changed.
- nchanged = 0
- Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
- PIDs (2558 2561 2564) completed and logs appended.
- #-----------------------------------------
- #@# APas-to-ASeg Sun Oct 8 03:39:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri
- apas2aseg --i aparc+aseg.mgz --o aseg.mgz
- Sun Oct 8 03:39:19 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-6.0.0/0051492/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-582 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-6.0.0/0051492/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-582
- 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 03:39:19 CEST 2017
- Ended at Sun Oct 8 03:39:25 CEST 2017
- Apas2aseg-Run-Time-Sec 6
-
- apas2aseg Done
- #--------------------------------------------
- #@# ASeg Stats Sun Oct 8 03:39:25 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492
- 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 0051492
- $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 0051492
- sysname Linux
- hostname tars-582
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1873742 mm^3 (det: 1.039687 )
- Computing euler number
- orig.nofix lheno = -122, rheno = -122
- orig.nofix lhholes = 62, rhholes = 62
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 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 03:41:52 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492
- mri_aparc2aseg --s 0051492 --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 0051492
- 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-6.0.0/0051492/mri/aparc+aseg.mgz
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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-6.0.0/0051492/mri/ribbon.mgz
- Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/ribbon.mgz
- Ripping vertices labeled as unkown
- Ripped 8676 vertices from left hemi
- Ripped 8643 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-6.0.0/0051492/mri/aseg.mgz
- Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 = 1184828
- Used brute-force search on 321 voxels
- Fixing Parahip LH WM
- Found 15 clusters
- 0 k 1.000000
- 1 k 2.000000
- 2 k 1.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 53.000000
- 7 k 1.000000
- 8 k 1.000000
- 9 k 1.000000
- 10 k 1.000000
- 11 k 1.000000
- 12 k 1938.000000
- 13 k 1.000000
- 14 k 1.000000
- Fixing Parahip RH WM
- Found 12 clusters
- 0 k 2.000000
- 1 k 1.000000
- 2 k 1.000000
- 3 k 2.000000
- 4 k 2.000000
- 5 k 1758.000000
- 6 k 1.000000
- 7 k 1.000000
- 8 k 18.000000
- 9 k 2.000000
- 10 k 1.000000
- 11 k 1.000000
- Writing output aseg to mri/wmparc.mgz
- mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0051492 --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 0051492 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname tars-582
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1873742 mm^3 (det: 1.039687 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 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-6.0.0/0051492/label
- #--------------------------------------------
- #@# BA_exvivo Labels lh Sun Oct 8 03:52:27 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 0051492 --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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 4722 of (4722 4728 4734 4740 4746) to complete...
- Waiting for PID 4728 of (4722 4728 4734 4740 4746) to complete...
- Waiting for PID 4734 of (4722 4728 4734 4740 4746) to complete...
- Waiting for PID 4740 of (4722 4728 4734 4740 4746) to complete...
- Waiting for PID 4746 of (4722 4728 4734 4740 4746) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 848
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.label 4977
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 1323
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.label 9232
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 299
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.label 4376
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 827
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.label 6810
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 1020
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.label 6804
- mri_label2label: Done
- PIDs (4722 4728 4734 4740 4746) 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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 4813 of (4813 4819 4824 4827) to complete...
- Waiting for PID 4819 of (4813 4819 4824 4827) to complete...
- Waiting for PID 4824 of (4813 4819 4824 4827) to complete...
- Waiting for PID 4827 of (4813 4819 4824 4827) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 501
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.label 4571
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 3477
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.label 17066
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 642
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.label 4823
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 1171
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.label 4593
- mri_label2label: Done
- PIDs (4813 4819 4824 4827) 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 0051492 --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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 4871 of (4871 4877 4882 4886 4892) to complete...
- Waiting for PID 4877 of (4871 4877 4882 4886 4892) to complete...
- Waiting for PID 4882 of (4871 4877 4882 4886 4892) to complete...
- Waiting for PID 4886 of (4871 4877 4882 4886 4892) to complete...
- Waiting for PID 4892 of (4871 4877 4882 4886 4892) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 2883
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.label 7524
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 5787
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.label 13901
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 700
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.label 2718
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 379
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.label 1669
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 381
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.label 1580
- mri_label2label: Done
- PIDs (4871 4877 4882 4886 4892) 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 0051492 --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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 4960 of (4960 4966 4970 4975 4984) to complete...
- Waiting for PID 4966 of (4960 4966 4970 4975 4984) to complete...
- Waiting for PID 4970 of (4960 4966 4970 4975 4984) to complete...
- Waiting for PID 4975 of (4960 4966 4970 4975 4984) to complete...
- Waiting for PID 4984 of (4960 4966 4970 4975 4984) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 255
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.thresh.label 1269
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 388
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.thresh.label 2480
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 88
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.thresh.label 1592
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 181
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.thresh.label 2177
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 325
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.thresh.label 2644
- mri_label2label: Done
- PIDs (4960 4966 4970 4975 4984) 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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 5027 of (5027 5033 5037 5042) to complete...
- Waiting for PID 5033 of (5027 5033 5037 5042) to complete...
- Waiting for PID 5037 of (5027 5033 5037 5042) to complete...
- Waiting for PID 5042 of (5027 5033 5037 5042) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 143
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.thresh.label 1692
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 1983
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.thresh.label 9018
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 212
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.thresh.label 2124
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 488
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.thresh.label 1639
- mri_label2label: Done
- PIDs (5027 5033 5037 5042) 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 0051492 --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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 5102 of (5102 5109 5116 5119 5128) to complete...
- Waiting for PID 5109 of (5102 5109 5116 5119 5128) to complete...
- Waiting for PID 5116 of (5102 5109 5116 5119 5128) to complete...
- Waiting for PID 5119 of (5102 5109 5116 5119 5128) to complete...
- Waiting for PID 5128 of (5102 5109 5116 5119 5128) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 2032
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.thresh.label 5437
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 2723
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.thresh.label 6057
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 144
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.thresh.label 657
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 148
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.thresh.label 618
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170760
- Number of reverse mapping hits = 167
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.thresh.label 617
- mri_label2label: Done
- PIDs (5102 5109 5116 5119 5128) completed and logs appended.
- mris_label2annot --s 0051492 --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-6.0.0/0051492/label
- cmdline mris_label2annot --s 0051492 --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-582
- machine x86_64
- user ntraut
- subject 0051492
- 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-6.0.0/0051492/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 116457 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/lh.BA_exvivo.annot
- mris_label2annot --s 0051492 --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-6.0.0/0051492/label
- cmdline mris_label2annot --s 0051492 --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-582
- machine x86_64
- user ntraut
- subject 0051492
- 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-6.0.0/0051492/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 138466 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0051492 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 305147
- Total vertex volume 301436 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 1608 791 2089 2.178 0.493 0.104 0.031 15 2.0 BA1_exvivo
- 4849 3078 7486 2.446 0.479 0.116 0.027 49 5.3 BA2_exvivo
- 1258 812 1136 1.808 0.422 0.135 0.033 12 1.7 BA3a_exvivo
- 3008 1928 4545 2.081 0.779 0.114 0.026 29 3.4 BA3b_exvivo
- 2059 1213 3008 2.320 0.547 0.109 0.032 48 3.1 BA4a_exvivo
- 1448 968 2007 2.207 0.531 0.105 0.026 8 1.6 BA4p_exvivo
- 13329 8202 25487 2.738 0.591 0.119 0.036 165 19.6 BA6_exvivo
- 2650 1740 5259 2.692 0.372 0.112 0.023 30 2.3 BA44_exvivo
- 3763 2471 7048 2.579 0.542 0.122 0.031 50 4.7 BA45_exvivo
- 4773 3185 5731 1.786 0.576 0.143 0.041 66 8.7 V1_exvivo
- 11307 7022 14617 1.972 0.551 0.143 0.043 163 19.8 V2_exvivo
- 2340 1400 4004 2.556 0.435 0.129 0.032 33 3.0 MT_exvivo
- 879 583 2194 3.135 0.763 0.111 0.028 6 0.9 perirhinal_exvivo
- 1032 711 3160 3.246 0.710 0.139 0.038 16 1.5 entorhinal_exvivo
- mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0051492 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 305147
- Total vertex volume 301436 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 1043 484 1373 2.121 0.488 0.113 0.035 12 1.6 BA1_exvivo
- 2007 1165 2927 2.371 0.433 0.095 0.023 18 1.8 BA2_exvivo
- 1012 662 847 1.739 0.363 0.144 0.035 11 1.5 BA3a_exvivo
- 1578 1043 1707 1.609 0.478 0.091 0.018 8 1.4 BA3b_exvivo
- 1956 1178 2751 2.276 0.565 0.105 0.032 45 3.0 BA4a_exvivo
- 1210 809 1599 2.189 0.519 0.106 0.026 7 1.3 BA4p_exvivo
- 7811 4606 13627 2.635 0.628 0.114 0.037 90 11.9 BA6_exvivo
- 1640 1058 3288 2.738 0.354 0.112 0.025 20 1.5 BA44_exvivo
- 1529 979 3144 2.651 0.592 0.122 0.032 25 2.0 BA45_exvivo
- 5087 3384 6188 1.787 0.580 0.142 0.041 69 9.2 V1_exvivo
- 5825 3555 6888 1.858 0.529 0.152 0.048 93 11.6 V2_exvivo
- 569 347 941 2.479 0.484 0.128 0.027 8 0.6 MT_exvivo
- 460 310 921 2.840 0.735 0.118 0.026 3 0.5 perirhinal_exvivo
- 567 376 1632 3.189 0.649 0.139 0.036 9 0.9 entorhinal_exvivo
- #--------------------------------------------
- #@# BA_exvivo Labels rh Sun Oct 8 03:56:18 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 0051492 --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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 5242 of (5242 5248 5253 5260 5265) to complete...
- Waiting for PID 5248 of (5242 5248 5253 5260 5265) to complete...
- Waiting for PID 5253 of (5242 5248 5253 5260 5265) to complete...
- Waiting for PID 5260 of (5242 5248 5253 5260 5265) to complete...
- Waiting for PID 5265 of (5242 5248 5253 5260 5265) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 749
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.label 4711
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 1144
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.label 7831
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 276
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.label 4256
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 529
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.label 5051
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 1189
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.label 6936
- mri_label2label: Done
- PIDs (5242 5248 5253 5260 5265) 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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 5313 of (5313 5319 5325 5331) to complete...
- Waiting for PID 5319 of (5313 5319 5325 5331) to complete...
- Waiting for PID 5325 of (5313 5319 5325 5331) to complete...
- Waiting for PID 5331 of (5313 5319 5325 5331) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 520
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.label 4993
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 2586
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.label 14842
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 1499
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.label 8411
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 2359
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.label 7714
- mri_label2label: Done
- PIDs (5313 5319 5325 5331) 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 0051492 --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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 5381 of (5381 5387 5392 5399 5404) to complete...
- Waiting for PID 5387 of (5381 5387 5392 5399 5404) to complete...
- Waiting for PID 5392 of (5381 5387 5392 5399 5404) to complete...
- Waiting for PID 5399 of (5381 5387 5392 5399 5404) to complete...
- Waiting for PID 5404 of (5381 5387 5392 5399 5404) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 2707
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.label 7434
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 4652
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.label 12668
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 956
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.label 2888
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 236
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.label 1274
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 215
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.label 967
- mri_label2label: Done
- PIDs (5381 5387 5392 5399 5404) 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 0051492 --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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 5447 of (5447 5453 5458 5465 5469) to complete...
- Waiting for PID 5453 of (5447 5453 5458 5465 5469) to complete...
- Waiting for PID 5458 of (5447 5453 5458 5465 5469) to complete...
- Waiting for PID 5465 of (5447 5453 5458 5465 5469) to complete...
- Waiting for PID 5469 of (5447 5453 5458 5465 5469) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 184
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.thresh.label 1060
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 422
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.thresh.label 3110
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 74
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.thresh.label 1772
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 269
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.thresh.label 2452
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 184
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.thresh.label 1572
- mri_label2label: Done
- PIDs (5447 5453 5458 5465 5469) 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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 5526 of (5526 5532 5536 5544) to complete...
- Waiting for PID 5532 of (5526 5532 5536 5544) to complete...
- Waiting for PID 5536 of (5526 5532 5536 5544) to complete...
- Waiting for PID 5544 of (5526 5532 5536 5544) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 152
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.thresh.label 1641
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 1815
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.thresh.label 8774
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 139
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.thresh.label 1151
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 199
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.thresh.label 1377
- mri_label2label: Done
- PIDs (5526 5532 5536 5544) 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 0051492 --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 0051492 --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 0051492 --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 0051492 --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 0051492 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 5583 of (5583 5589 5594 5601 5606) to complete...
- Waiting for PID 5589 of (5583 5589 5594 5601 5606) to complete...
- Waiting for PID 5594 of (5583 5589 5594 5601 5606) to complete...
- Waiting for PID 5601 of (5583 5589 5594 5601 5606) to complete...
- Waiting for PID 5606 of (5583 5589 5594 5601 5606) 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 1826
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.thresh.label 5058
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 2176
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.thresh.label 5613
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 156
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.thresh.label 424
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 141
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.thresh.label 835
- 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 0051492 --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 = 0051492
- 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-6.0.0/0051492/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 170973
- Number of reverse mapping hits = 97
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.thresh.label 388
- mri_label2label: Done
- PIDs (5583 5589 5594 5601 5606) completed and logs appended.
- mris_label2annot --s 0051492 --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-6.0.0/0051492/label
- cmdline mris_label2annot --s 0051492 --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-582
- machine x86_64
- user ntraut
- subject 0051492
- 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-6.0.0/0051492/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 118133 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/label/rh.BA_exvivo.annot
- mris_label2annot --s 0051492 --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-6.0.0/0051492/label
- cmdline mris_label2annot --s 0051492 --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-582
- machine x86_64
- user ntraut
- subject 0051492
- 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-6.0.0/0051492/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 141300 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/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 0051492 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 313446
- Total vertex volume 309132 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 1242 627 1789 2.244 0.525 0.115 0.038 15 1.9 BA1_exvivo
- 4513 2774 6997 2.442 0.454 0.116 0.027 50 4.8 BA2_exvivo
- 1261 820 1155 1.857 0.414 0.126 0.026 11 1.4 BA3a_exvivo
- 2424 1477 3078 1.861 0.537 0.101 0.026 20 2.5 BA3b_exvivo
- 2035 1162 3100 2.452 0.602 0.105 0.031 16 2.6 BA4a_exvivo
- 1551 936 2247 2.468 0.417 0.097 0.025 11 1.5 BA4p_exvivo
- 10836 6382 19044 2.655 0.596 0.108 0.031 109 13.5 BA6_exvivo
- 4026 2709 7864 2.729 0.394 0.118 0.024 44 4.0 BA44_exvivo
- 6028 3912 12103 2.693 0.523 0.126 0.030 73 7.5 BA45_exvivo
- 4926 3104 5953 1.850 0.556 0.128 0.035 59 7.1 V1_exvivo
- 9952 6406 14045 2.038 0.588 0.147 0.040 150 16.6 V2_exvivo
- 2768 1847 4719 2.517 0.402 0.131 0.028 34 3.2 MT_exvivo
- 752 516 2299 3.248 0.739 0.123 0.037 8 1.1 perirhinal_exvivo
- 526 342 1456 3.124 0.735 0.128 0.032 8 0.6 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 0051492 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051492/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 313446
- Total vertex volume 309132 (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) = 1873742 mm^3 (det: 1.039687 )
- lhCtxGM: 299884.264 299156.000 diff= 728.3 pctdiff= 0.243
- rhCtxGM: 307992.314 307226.000 diff= 766.3 pctdiff= 0.249
- lhCtxWM: 290159.708 289931.500 diff= 228.2 pctdiff= 0.079
- rhCtxWM: 291189.791 292710.500 diff=-1520.7 pctdiff=-0.522
- SubCortGMVol 70633.000
- SupraTentVol 1271675.077 (1268016.000) diff=3659.077 pctdiff=0.288
- SupraTentVolNotVent 1263321.077 (1259662.000) diff=3659.077 pctdiff=0.290
- BrainSegVol 1421067.000 (1418809.000) diff=2258.000 pctdiff=0.159
- BrainSegVolNotVent 1409562.000 (1409557.077) diff= 4.923 pctdiff=0.000
- BrainSegVolNotVent 1409562.000
- CerebellumVol 149693.000
- VentChorVol 8354.000
- 3rd4th5thCSF 3151.000
- CSFVol 893.000, OptChiasmVol 207.000
- MaskVol 1893438.000
- 890 439 1208 2.140 0.564 0.107 0.034 10 1.3 BA1_exvivo
- 2505 1501 3946 2.453 0.453 0.107 0.023 24 2.1 BA2_exvivo
- 1135 741 940 1.839 0.413 0.132 0.028 10 1.3 BA3a_exvivo
- 1914 1183 2122 1.742 0.422 0.091 0.022 13 1.8 BA3b_exvivo
- 1208 684 1799 2.396 0.682 0.115 0.034 13 1.7 BA4a_exvivo
- 1232 768 1817 2.500 0.397 0.084 0.021 6 1.0 BA4p_exvivo
- 7527 4290 12315 2.588 0.624 0.107 0.032 74 9.7 BA6_exvivo
- 941 621 2091 2.855 0.420 0.117 0.026 11 0.9 BA44_exvivo
- 1147 764 2867 2.914 0.395 0.127 0.033 15 1.4 BA45_exvivo
- 4649 2935 5573 1.854 0.558 0.125 0.035 53 6.7 V1_exvivo
- 5318 3453 6778 1.852 0.575 0.154 0.042 87 9.2 V2_exvivo
- 415 276 773 2.444 0.385 0.139 0.025 6 0.5 MT_exvivo
- 434 304 1393 3.216 0.754 0.100 0.020 3 0.4 perirhinal_exvivo
- 358 244 856 3.191 0.587 0.142 0.035 4 0.5 entorhinal_exvivo
- Started at Sat Oct 7 16:21:56 CEST 2017
- Ended at Sun Oct 8 04:00:07 CEST 2017
- #@#%# recon-all-run-time-hours 11.636
- recon-all -s 0051492 finished without error at Sun Oct 8 04:00:07 CEST 2017
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