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- Sat Oct 7 23:40:21 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
- -subjid 0050340 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050340/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
- subjid 0050340
- 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-593 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 60506144 5487704 1778476 0 56894828
- -/+ buffers/cache: 3611316 62382532
- Swap: 0 0 0
- ########################################
- program versions used
- $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
- $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
- mri_convert.bin -all-info
- ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
- mri_convert.bin --version
- stable6
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
- ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-21:40:21-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-593 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-6.0.0/0050340
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050340/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig/001.mgz
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050340/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig/001.mgz
- $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
- reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050340/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-6.0.0/0050340/mri/orig/001.mgz...
- #--------------------------------------------
- #@# MotionCor Sat Oct 7 23:40:23 CEST 2017
- Found 1 runs
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig.mgz --conform
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/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-6.0.0/0050340/mri/orig.mgz...
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Sat Oct 7 23:40:31 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/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-593 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
- Sat Oct 7 23:40:31 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.9103
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9103/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9103/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.9103/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 23:40:34 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.9103/nu0.mnc ./tmp.mri_nu_correct.mni.9103/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9103/0/ -iterations 1000 -distance 50
- [ntraut@tars-593:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/] [2017-10-07 23:40:34] 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.9103/0/ ./tmp.mri_nu_correct.mni.9103/nu0.mnc ./tmp.mri_nu_correct.mni.9103/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
- Number of iterations: 21
- CV of field change: 0.000980026
-
-
-
- mri_convert ./tmp.mri_nu_correct.mni.9103/nu1.mnc orig_nu.mgz --like orig.mgz --conform
- mri_convert.bin ./tmp.mri_nu_correct.mni.9103/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.9103/nu1.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -1)
- k_ras = (0, 1, 0)
- INFO: transform src into the like-volume: orig.mgz
- changing data type from float to uchar (noscale = 0)...
- MRIchangeType: Building histogram
- writing to orig_nu.mgz...
-
-
- Sat Oct 7 23:41:29 CEST 2017
- mri_nu_correct.mni done
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- talairach_avi log file is transforms/talairach_avi.log...
- Started at Sat Oct 7 23:41:29 CEST 2017
- Ended at Sat Oct 7 23:42:04 CEST 2017
- talairach_avi done
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Sat Oct 7 23:42:06 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7747, pval=0.6675 >= threshold=0.0050)
- awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/transforms/talairach_avi.log
- tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/transforms/talairach_avi.log
- TalAviQA: 0.97921
- z-score: 0
- #--------------------------------------------
- #@# Nu Intensity Correction Sat Oct 7 23:42:06 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-6.0.0/0050340/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-593 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
- Sat Oct 7 23:42:06 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.9640
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9640/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9640/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.9640/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 23:42:09 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.9640/nu0.mnc ./tmp.mri_nu_correct.mni.9640/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9640/0/
- [ntraut@tars-593:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/] [2017-10-07 23:42:09] running:
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9640/0/ ./tmp.mri_nu_correct.mni.9640/nu0.mnc ./tmp.mri_nu_correct.mni.9640/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 18
- CV of field change: 0.000970051
-
-
- --------------------------------------------------------
- Iteration 2 Sat Oct 7 23:42:50 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.9640/nu1.mnc ./tmp.mri_nu_correct.mni.9640/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9640/1/
- [ntraut@tars-593:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/] [2017-10-07 23:42:50] 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.9640/1/ ./tmp.mri_nu_correct.mni.9640/nu1.mnc ./tmp.mri_nu_correct.mni.9640/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 10
- CV of field change: 0.000990587
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.9640/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9640/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-6.0.0/0050340/mri
- cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.9640/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9640/ones.mgz
- sysname Linux
- hostname tars-593
- machine x86_64
- user ntraut
- input ./tmp.mri_nu_correct.mni.9640/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.9640/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.9640/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9640/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9640/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.9640/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9640/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9640/input.mean.dat
- sysname Linux
- hostname tars-593
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.9640/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.9640/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9640/ones.mgz --i ./tmp.mri_nu_correct.mni.9640/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9640/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9640/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.9640/ones.mgz --i ./tmp.mri_nu_correct.mni.9640/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9640/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9640/output.mean.dat
- sysname Linux
- hostname tars-593
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.9640/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.9640/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.9640/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.9640/nu2.mnc ./tmp.mri_nu_correct.mni.9640/nu2.mnc mul 1.00513163083385285011
- Saving result to './tmp.mri_nu_correct.mni.9640/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.9640/nu2.mnc nu.mgz --like orig.mgz
- mri_convert.bin ./tmp.mri_nu_correct.mni.9640/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.9640/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -1)
- k_ras = (0, 1, 0)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 8 seconds.
- mapping (10, 109) to ( 3, 110)
-
-
- Sat Oct 7 23:44:11 CEST 2017
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Sat Oct 7 23:44:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- mri_normalize -g 1 -mprage nu.mgz T1.mgz
- using max gradient = 1.000
- assuming input volume is MGH (Van der Kouwe) MP-RAGE
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.09368 0.03463 0.03277 -153.56221;
- -0.01305 1.02303 0.08753 -155.63049;
- -0.06859 -0.07832 1.19643 -60.15010;
- 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 = 19
- Starting OpenSpline(): npoints = 19
- 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 67 (67), valley at 10 (10)
- csf peak at 34, setting threshold to 56
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 110
- white matter peak found at 110
- gm peak at 67 (67), valley at 23 (23)
- csf peak at 34, setting threshold to 56
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 1 minutes and 50 seconds.
- #--------------------------------------------
- #@# Skull Stripping Sat Oct 7 23:46:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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=16.0
- skull bounding box = (41, 55, 28) --> (202, 187, 226)
- using (95, 99, 127) as brain centroid...
- mean wm in atlas = 108, using box (75,83,103) --> (114, 115,151) to find MRI wm
- before smoothing, mri peak at 105
- robust fit to distribution - 105 +- 4.6
- after smoothing, mri peak at 105, scaling input intensities by 1.029
- scaling channel 0 by 1.02857
- initial log_p = -4.552
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.433717 @ (9.091, -9.091, -9.091)
- max log p = -4.336064 @ (-4.545, 4.545, -4.545)
- max log p = -4.336064 @ (0.000, 0.000, 0.000)
- max log p = -4.294858 @ (-3.409, 1.136, -1.136)
- max log p = -4.294858 @ (0.000, 0.000, 0.000)
- max log p = -4.294858 @ (0.000, 0.000, 0.000)
- Found translation: (1.1, -3.4, -14.8): log p = -4.295
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.058, old_max_log_p =-4.295 (thresh=-4.3)
- 1.06375 0.00000 0.00000 -6.75199;
- 0.00000 1.22567 0.14032 -53.90052;
- 0.00000 -0.16136 1.06580 -7.05218;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.049, old_max_log_p =-4.058 (thresh=-4.1)
- 1.14353 0.00000 0.00000 -16.62404;
- 0.00000 1.22567 0.14032 -53.90052;
- 0.00000 -0.14926 0.98587 1.79597;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.045, old_max_log_p =-4.049 (thresh=-4.0)
- 1.05777 0.00000 0.00000 -6.01159;
- 0.00000 1.23467 0.01043 -37.97911;
- 0.00000 0.01290 1.07043 -25.39732;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.045, old_max_log_p =-4.045 (thresh=-4.0)
- 1.05777 0.00000 0.00000 -6.01159;
- 0.00000 1.23467 0.01043 -37.97911;
- 0.00000 0.01290 1.07043 -25.39732;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.943, old_max_log_p =-4.045 (thresh=-4.0)
- 1.05536 0.00158 -0.07148 5.15466;
- -0.00265 1.30313 0.07503 -55.66413;
- 0.07234 -0.06454 1.00600 -20.33563;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.932, old_max_log_p =-3.943 (thresh=-3.9)
- 1.05635 0.04494 -0.03812 -5.60182;
- -0.04118 1.27934 0.01013 -39.02319;
- 0.03744 0.02076 1.01055 -28.99963;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.932, old_max_log_p =-3.932 (thresh=-3.9)
- 1.05635 0.04494 -0.03812 -5.60182;
- -0.04118 1.27934 0.01013 -39.02319;
- 0.03744 0.02076 1.01055 -28.99963;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.917, old_max_log_p =-3.932 (thresh=-3.9)
- 1.05477 0.04472 -0.04635 -4.76688;
- -0.04122 1.28084 0.01014 -39.23503;
- 0.04611 0.02115 1.01139 -29.75636;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.916, old_max_log_p =-3.917 (thresh=-3.9)
- 1.05724 0.04482 -0.04646 -5.07073;
- -0.04122 1.28084 0.01014 -39.23503;
- 0.04606 0.02113 1.01020 -29.59150;
- 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
- 1.05724 0.04482 -0.04646 -5.07073;
- -0.04122 1.28084 0.01014 -39.23503;
- 0.04606 0.02113 1.01020 -29.59150;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3243
- Quasinewton: input matrix
- 1.05724 0.04482 -0.04646 -5.07073;
- -0.04122 1.28084 0.01014 -39.23503;
- 0.04606 0.02113 1.01020 -29.59150;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.05724 0.04482 -0.04646 -5.07073;
- -0.04122 1.28084 0.01014 -39.23503;
- 0.04606 0.02113 1.01020 -29.59150;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.916 (old=-4.552)
- transform before final EM align:
- 1.05724 0.04482 -0.04646 -5.07073;
- -0.04122 1.28084 0.01014 -39.23503;
- 0.04606 0.02113 1.01020 -29.59150;
- 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
- 1.05724 0.04482 -0.04646 -5.07073;
- -0.04122 1.28084 0.01014 -39.23503;
- 0.04606 0.02113 1.01020 -29.59150;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 364799
- Quasinewton: input matrix
- 1.05724 0.04482 -0.04646 -5.07073;
- -0.04122 1.28084 0.01014 -39.23503;
- 0.04606 0.02113 1.01020 -29.59150;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 013: -log(p) = 4.3 tol 0.000000
- final transform:
- 1.05724 0.04482 -0.04646 -5.07073;
- -0.04122 1.28084 0.01014 -39.23503;
- 0.04606 0.02113 1.01020 -29.59150;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach_with_skull.lta...
- mri_em_register utimesec 1773.889327
- mri_em_register stimesec 1.775730
- 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 157573
- mri_em_register ru_majflt 0
- mri_em_register ru_nswap 0
- mri_em_register ru_inblock 0
- mri_em_register ru_oublock 32
- mri_em_register ru_msgsnd 0
- mri_em_register ru_msgrcv 0
- mri_em_register ru_nsignals 0
- mri_em_register ru_nvcsw 440
- mri_em_register ru_nivcsw 24920
- registration took 15 minutes and 15 seconds.
- mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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=124 y=124 z=129 r=67
- first estimation of the main basin volume: 1284889 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 16 found in the rest of the brain
- global maximum in x=103, y=108, z=98, Imax=255
- CSF=19, WM_intensity=110, WM_VARIANCE=5
- WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
- preflooding height equal to 10 percent
- done.
- Analyze...
- main basin size=8891946141 voxels, voxel volume =1.000
- = 8891946141 mmm3 = 8891945.984 cm3
- done.
- PostAnalyze...Basin Prior
- 66 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=122,y=125, z=122, r=9558 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45440
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1101112322
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1123318834
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1124457339
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1074691960
- OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1074042714
- Problem with the least square interpolation in GM_MIN calculation.
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 4, 6, 39, 62
- after analyzing : 4, 28, 39, 36
- RIGHT_CER
- before analyzing : 3, 4, 41, 72
- after analyzing : 3, 28, 41, 39
- LEFT_CER
- before analyzing : 3, 3, 35, 73
- after analyzing : 3, 24, 35, 36
- RIGHT_BRAIN
- before analyzing : 4, 6, 38, 62
- after analyzing : 4, 27, 38, 35
- LEFT_BRAIN
- before analyzing : 4, 6, 40, 63
- after analyzing : 4, 28, 40, 36
- OTHER
- before analyzing : 3, 3, 8, 63
- after analyzing : 3, 17, 25, 28
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...67 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.010
- curvature mean = 69.123, std = 8.188
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 3.07, sigma = 4.42
- after rotation: sse = 3.07, sigma = 4.42
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 3.22, its var is 3.96
- before Erosion-Dilatation 0.35% 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...37 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1516099 voxels, voxel volume = 1.000 mm3
- = 1516099 mmm3 = 1516.099 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- mri_watershed utimesec 24.747237
- mri_watershed stimesec 0.453930
- mri_watershed ru_maxrss 818272
- mri_watershed ru_ixrss 0
- mri_watershed ru_idrss 0
- mri_watershed ru_isrss 0
- mri_watershed ru_minflt 211536
- mri_watershed ru_majflt 0
- mri_watershed ru_nswap 0
- mri_watershed ru_inblock 0
- mri_watershed ru_oublock 2344
- mri_watershed ru_msgsnd 0
- mri_watershed ru_msgrcv 0
- mri_watershed ru_nsignals 0
- mri_watershed ru_nvcsw 3134
- mri_watershed ru_nivcsw 87
- mri_watershed done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Sun Oct 8 00:01:41 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta
- setting unknown_nbr_spacing = 3
- using MR volume brainmask.mgz to mask input volume...
- == Number of threads available to mri_em_register for OpenMP = 2 ==
- reading 1 input volumes...
- logging results to talairach.log
- reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
- average std = 7.3 using min determinant for regularization = 5.3
- 0 singular and 841 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- accounting for voxel sizes in initial transform
- bounding unknown intensity as < 6.3 or > 503.7
- total sample mean = 78.8 (1011 zeros)
- ************************************************
- spacing=8, using 2830 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 2830, passno 0, spacing 8
- resetting wm mean[0]: 98 --> 107
- resetting gm mean[0]: 61 --> 61
- input volume #1 is the most T1-like
- using real data threshold=25.0
- skull bounding box = (56, 69, 46) --> (184, 176, 212)
- using (99, 105, 129) as brain centroid...
- mean wm in atlas = 107, using box (83,92,109) --> (114, 118,149) to find MRI wm
- before smoothing, mri peak at 104
- robust fit to distribution - 104 +- 4.7
- after smoothing, mri peak at 104, scaling input intensities by 1.029
- scaling channel 0 by 1.02885
- initial log_p = -4.162
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.072098 @ (9.091, -9.091, -9.091)
- max log p = -3.843884 @ (-4.545, 4.545, -4.545)
- max log p = -3.788487 @ (-2.273, -2.273, -2.273)
- max log p = -3.786718 @ (1.136, 1.136, 1.136)
- max log p = -3.786718 @ (0.000, 0.000, 0.000)
- max log p = -3.777655 @ (-1.420, -2.557, -1.420)
- Found translation: (2.0, -8.2, -16.2): log p = -3.778
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.620, old_max_log_p =-3.778 (thresh=-3.8)
- 1.07500 0.00000 0.00000 -7.36751;
- 0.00000 1.14016 0.13053 -41.99015;
- 0.00000 -0.15011 0.99144 3.99015;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.620, old_max_log_p =-3.620 (thresh=-3.6)
- 1.07500 0.00000 0.00000 -7.36751;
- 0.00000 1.14016 0.13053 -41.99015;
- 0.00000 -0.15011 0.99144 3.99015;
- 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=-3.512, old_max_log_p =-3.620 (thresh=-3.6)
- 1.05380 -0.00166 -0.03693 1.61059;
- -0.00526 1.18727 0.09939 -41.68822;
- 0.03549 -0.11229 1.01274 -7.96986;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.495, old_max_log_p =-3.512 (thresh=-3.5)
- 1.07355 -0.00169 -0.03762 -0.73553;
- -0.00526 1.18727 0.09939 -41.68822;
- 0.03549 -0.11229 1.01274 -7.96986;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.495, old_max_log_p =-3.495 (thresh=-3.5)
- 1.07355 -0.00169 -0.03762 -0.73553;
- -0.00526 1.18727 0.09939 -41.68822;
- 0.03549 -0.11229 1.01274 -7.96986;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.480, old_max_log_p =-3.495 (thresh=-3.5)
- 1.07082 0.01766 -0.03563 -3.07738;
- -0.02230 1.18792 0.11682 -40.85401;
- 0.03549 -0.13139 1.00861 -4.12369;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.467, old_max_log_p =-3.480 (thresh=-3.5)
- 1.07230 -0.00181 -0.03731 -0.61851;
- -0.00533 1.18586 0.09935 -41.51546;
- 0.03499 -0.11155 1.00684 -7.27160;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.462, old_max_log_p =-3.467 (thresh=-3.5)
- 1.07230 -0.00181 -0.03731 -0.61851;
- -0.00532 1.18308 0.09912 -41.13857;
- 0.03495 -0.11142 1.00566 -7.13952;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.462, old_max_log_p =-3.462 (thresh=-3.5)
- 1.07230 -0.00181 -0.03731 -0.61851;
- -0.00532 1.18308 0.09912 -41.13857;
- 0.03495 -0.11142 1.00566 -7.13952;
- 0.00000 0.00000 0.00000 1.00000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 2830 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.07230 -0.00181 -0.03731 -0.61851;
- -0.00532 1.18308 0.09912 -41.13857;
- 0.03495 -0.11142 1.00566 -7.13952;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2830
- Quasinewton: input matrix
- 1.07230 -0.00181 -0.03731 -0.61851;
- -0.00532 1.18308 0.09912 -41.13857;
- 0.03495 -0.11142 1.00566 -7.13952;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.07230 -0.00181 -0.03731 -0.61851;
- -0.00532 1.18308 0.09912 -41.13857;
- 0.03495 -0.11142 1.00566 -7.13952;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.462 (old=-4.162)
- transform before final EM align:
- 1.07230 -0.00181 -0.03731 -0.61851;
- -0.00532 1.18308 0.09912 -41.13857;
- 0.03495 -0.11142 1.00566 -7.13952;
- 0.00000 0.00000 0.00000 1.00000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 315557 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.07230 -0.00181 -0.03731 -0.61851;
- -0.00532 1.18308 0.09912 -41.13857;
- 0.03495 -0.11142 1.00566 -7.13952;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 315557
- Quasinewton: input matrix
- 1.07230 -0.00181 -0.03731 -0.61851;
- -0.00532 1.18308 0.09912 -41.13857;
- 0.03495 -0.11142 1.00566 -7.13952;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 013: -log(p) = 3.9 tol 0.000000
- final transform:
- 1.07230 -0.00181 -0.03731 -0.61851;
- -0.00532 1.18308 0.09912 -41.13857;
- 0.03495 -0.11142 1.00566 -7.13952;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach.lta...
- mri_em_register utimesec 1435.782727
- mri_em_register stimesec 1.599756
- mri_em_register ru_maxrss 600920
- mri_em_register ru_ixrss 0
- mri_em_register ru_idrss 0
- mri_em_register ru_isrss 0
- mri_em_register ru_minflt 158949
- 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 177
- mri_em_register ru_nivcsw 14307
- registration took 12 minutes and 15 seconds.
- #--------------------------------------
- #@# CA Normalize Sun Oct 8 00:13:56 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz
- writing control point volume to ctrl_pts.mgz
- using MR volume brainmask.mgz to mask input volume...
- reading 1 input volume
- reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
- reading transform from 'transforms/talairach.lta'...
- reading input volume from nu.mgz...
- resetting wm mean[0]: 98 --> 107
- resetting gm mean[0]: 61 --> 61
- input volume #1 is the most T1-like
- using real data threshold=25.0
- skull bounding box = (56, 69, 46) --> (184, 176, 212)
- using (99, 105, 129) as brain centroid...
- mean wm in atlas = 107, using box (83,92,109) --> (114, 118,149) to find MRI wm
- before smoothing, mri peak at 104
- robust fit to distribution - 104 +- 4.7
- after smoothing, mri peak at 104, scaling input intensities by 1.029
- scaling channel 0 by 1.02885
- using 246344 sample points...
- INFO: compute sample coordinates transform
- 1.07230 -0.00181 -0.03731 -0.61851;
- -0.00532 1.18308 0.09912 -41.13857;
- 0.03495 -0.11142 1.00566 -7.13952;
- 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 (120, 69, 44) --> (184, 169, 209)
- Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0
- 0 of 3097 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (63, 70, 44) --> (125, 168, 210)
- Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
- 0 of 2973 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (123, 144, 68) --> (168, 180, 122)
- Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0
- 0 of 65 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (81, 144, 67) --> (122, 179, 125)
- Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0
- 0 of 26 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (108, 135, 105) --> (139, 195, 134)
- Brain_Stem: limiting intensities to 97.0 --> 132.0
- 8 of 96 (8.3%) samples deleted
- using 6257 total control points for intensity normalization...
- bias field = 0.942 +- 0.050
- 34 of 6249 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (120, 69, 44) --> (184, 169, 209)
- Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
- 0 of 3857 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (63, 70, 44) --> (125, 168, 210)
- Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 0 of 3774 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (123, 144, 68) --> (168, 180, 122)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 9 of 169 (5.3%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (81, 144, 67) --> (122, 179, 125)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 47 of 104 (45.2%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (108, 135, 105) --> (139, 195, 134)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 29 of 177 (16.4%) samples deleted
- using 8081 total control points for intensity normalization...
- bias field = 1.034 +- 0.053
- 35 of 7920 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (120, 69, 44) --> (184, 169, 209)
- Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
- 3 of 3897 (0.1%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (63, 70, 44) --> (125, 168, 210)
- Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 5 of 3884 (0.1%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (123, 144, 68) --> (168, 180, 122)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 49 of 217 (22.6%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (81, 144, 67) --> (122, 179, 125)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 60 of 129 (46.5%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (108, 135, 105) --> (139, 195, 134)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 65 of 256 (25.4%) samples deleted
- using 8383 total control points for intensity normalization...
- bias field = 1.032 +- 0.052
- 21 of 8049 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 1 minutes and 39 seconds.
- #--------------------------------------
- #@# CA Reg Sun Oct 8 00:15:35 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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) = 1.29 (predicted orig area = 6.2)
- 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=0.799, neg=0, invalid=762
- 0001: dt=205.538462, rms=0.723 (9.536%), neg=0, invalid=762
- 0002: dt=156.123515, rms=0.703 (2.656%), neg=0, invalid=762
- 0003: dt=221.952000, rms=0.694 (1.413%), neg=0, invalid=762
- 0004: dt=134.620690, rms=0.688 (0.768%), neg=0, invalid=762
- 0005: dt=369.920000, rms=0.683 (0.744%), neg=0, invalid=762
- 0006: dt=110.976000, rms=0.680 (0.503%), neg=0, invalid=762
- 0007: dt=517.888000, rms=0.676 (0.600%), neg=0, invalid=762
- 0008: dt=129.472000, rms=0.674 (0.245%), neg=0, invalid=762
- 0009: dt=129.472000, rms=0.673 (0.130%), neg=0, invalid=762
- 0010: dt=129.472000, rms=0.672 (0.184%), neg=0, invalid=762
- 0011: dt=129.472000, rms=0.670 (0.283%), neg=0, invalid=762
- 0012: dt=129.472000, rms=0.668 (0.262%), neg=0, invalid=762
- 0013: dt=129.472000, rms=0.666 (0.269%), neg=0, invalid=762
- 0014: dt=129.472000, rms=0.665 (0.251%), neg=0, invalid=762
- 0015: dt=129.472000, rms=0.663 (0.200%), neg=0, invalid=762
- 0016: dt=129.472000, rms=0.662 (0.188%), neg=0, invalid=762
- 0017: dt=129.472000, rms=0.661 (0.151%), neg=0, invalid=762
- 0018: dt=129.472000, rms=0.660 (0.163%), neg=0, invalid=762
- 0019: dt=129.472000, rms=0.659 (0.132%), neg=0, invalid=762
- 0020: dt=129.472000, rms=0.658 (0.105%), neg=0, invalid=762
- 0021: dt=129.472000, rms=0.658 (0.100%), neg=0, invalid=762
- 0022: dt=1479.680000, rms=0.657 (0.179%), neg=0, invalid=762
- 0023: dt=92.480000, rms=0.656 (0.083%), neg=0, invalid=762
- 0024: dt=92.480000, rms=0.656 (0.007%), neg=0, invalid=762
- 0025: dt=92.480000, rms=0.656 (0.015%), neg=0, invalid=762
- 0026: dt=92.480000, rms=0.656 (0.018%), neg=0, invalid=762
- 0027: dt=92.480000, rms=0.656 (0.024%), neg=0, invalid=762
- 0028: dt=92.480000, rms=0.655 (0.033%), neg=0, invalid=762
- 0029: dt=92.480000, rms=0.655 (0.047%), neg=0, invalid=762
- 0030: dt=92.480000, rms=0.655 (0.053%), neg=0, invalid=762
- 0031: dt=92.480000, rms=0.654 (0.052%), neg=0, invalid=762
- 0032: dt=92.480000, rms=0.654 (0.046%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.655, neg=0, invalid=762
- 0033: dt=295.936000, rms=0.653 (0.230%), neg=0, invalid=762
- 0034: dt=129.472000, rms=0.653 (0.045%), neg=0, invalid=762
- 0035: dt=129.472000, rms=0.652 (0.033%), neg=0, invalid=762
- 0036: dt=129.472000, rms=0.652 (0.048%), neg=0, invalid=762
- 0037: dt=129.472000, rms=0.652 (0.052%), neg=0, invalid=762
- 0038: dt=129.472000, rms=0.652 (0.053%), neg=0, invalid=762
- 0039: dt=129.472000, rms=0.651 (0.062%), neg=0, invalid=762
- 0040: dt=129.472000, rms=0.651 (0.074%), neg=0, invalid=762
- 0041: dt=129.472000, rms=0.650 (0.074%), neg=0, invalid=762
- 0042: dt=129.472000, rms=0.650 (0.071%), neg=0, invalid=762
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.653, neg=0, invalid=762
- 0043: dt=113.053892, rms=0.649 (0.700%), neg=0, invalid=762
- 0044: dt=248.832000, rms=0.640 (1.396%), neg=0, invalid=762
- 0045: dt=80.372093, rms=0.637 (0.495%), neg=0, invalid=762
- 0046: dt=145.152000, rms=0.633 (0.630%), neg=0, invalid=762
- 0047: dt=36.288000, rms=0.632 (0.174%), neg=0, invalid=762
- 0048: dt=36.288000, rms=0.631 (0.118%), neg=0, invalid=762
- 0049: dt=36.288000, rms=0.630 (0.184%), neg=0, invalid=762
- 0050: dt=36.288000, rms=0.628 (0.283%), neg=0, invalid=762
- 0051: dt=36.288000, rms=0.626 (0.368%), neg=0, invalid=762
- 0052: dt=36.288000, rms=0.623 (0.414%), neg=0, invalid=762
- 0053: dt=36.288000, rms=0.620 (0.409%), neg=0, invalid=762
- 0054: dt=36.288000, rms=0.618 (0.391%), neg=0, invalid=762
- 0055: dt=36.288000, rms=0.616 (0.374%), neg=0, invalid=762
- 0056: dt=36.288000, rms=0.614 (0.338%), neg=0, invalid=762
- 0057: dt=36.288000, rms=0.612 (0.306%), neg=0, invalid=762
- 0058: dt=36.288000, rms=0.610 (0.310%), neg=0, invalid=762
- 0059: dt=36.288000, rms=0.608 (0.296%), neg=0, invalid=762
- 0060: dt=36.288000, rms=0.606 (0.264%), neg=0, invalid=762
- 0061: dt=36.288000, rms=0.605 (0.231%), neg=0, invalid=762
- 0062: dt=36.288000, rms=0.604 (0.199%), neg=0, invalid=762
- 0063: dt=36.288000, rms=0.603 (0.172%), neg=0, invalid=762
- 0064: dt=36.288000, rms=0.602 (0.157%), neg=0, invalid=762
- 0065: dt=36.288000, rms=0.601 (0.152%), neg=0, invalid=762
- 0066: dt=36.288000, rms=0.600 (0.146%), neg=0, invalid=762
- 0067: dt=36.288000, rms=0.599 (0.129%), neg=0, invalid=762
- 0068: dt=36.288000, rms=0.599 (0.117%), neg=0, invalid=762
- 0069: dt=36.288000, rms=0.598 (0.108%), neg=0, invalid=762
- 0070: dt=145.152000, rms=0.598 (0.007%), neg=0, invalid=762
- 0071: dt=145.152000, rms=0.597 (0.102%), neg=0, invalid=762
- 0072: dt=145.152000, rms=0.597 (-0.067%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.598, neg=0, invalid=762
- 0073: dt=95.000000, rms=0.596 (0.288%), neg=0, invalid=762
- 0074: dt=103.680000, rms=0.595 (0.167%), neg=0, invalid=762
- 0075: dt=103.680000, rms=0.595 (-0.165%), neg=0, invalid=762
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.616, neg=0, invalid=762
- 0076: dt=9.600000, rms=0.615 (0.201%), neg=0, invalid=762
- 0077: dt=2.800000, rms=0.615 (0.018%), neg=0, invalid=762
- 0078: dt=2.800000, rms=0.615 (0.004%), neg=0, invalid=762
- 0079: dt=2.800000, rms=0.615 (-0.015%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.616, neg=0, invalid=762
- 0080: dt=2.800000, rms=0.615 (0.093%), neg=0, invalid=762
- 0081: dt=1.600000, rms=0.615 (0.004%), neg=0, invalid=762
- 0082: dt=1.600000, rms=0.615 (-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=0.665, neg=0, invalid=762
- 0083: dt=5.788945, rms=0.652 (1.998%), neg=0, invalid=762
- 0084: dt=2.785714, rms=0.651 (0.063%), neg=0, invalid=762
- 0085: dt=2.785714, rms=0.651 (-0.023%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.652, neg=0, invalid=762
- 0086: dt=0.000000, rms=0.651 (0.070%), neg=0, invalid=762
- 0087: dt=0.000000, rms=0.651 (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=0.701, neg=0, invalid=762
- 0088: dt=0.448000, rms=0.700 (0.203%), neg=0, invalid=762
- 0089: dt=1.024000, rms=0.699 (0.168%), neg=0, invalid=762
- 0090: dt=1.024000, rms=0.697 (0.274%), neg=0, invalid=762
- 0091: dt=1.024000, rms=0.696 (0.127%), neg=0, invalid=762
- 0092: dt=1.024000, rms=0.696 (-0.283%), neg=0, invalid=762
- 0093: dt=1.792000, rms=0.695 (0.093%), neg=0, invalid=762
- 0094: dt=1.792000, rms=0.694 (0.160%), neg=0, invalid=762
- 0095: dt=0.000000, rms=0.694 (-0.002%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.695, neg=0, invalid=762
- 0096: dt=0.768000, rms=0.694 (0.126%), neg=0, invalid=762
- 0097: dt=1.792000, rms=0.693 (0.056%), neg=0, invalid=762
- 0098: dt=1.792000, rms=0.693 (-0.032%), neg=0, invalid=762
- resetting metric properties...
- setting smoothness coefficient to 10.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.663, neg=0, invalid=762
- 0099: dt=0.823858, rms=0.646 (2.579%), neg=0, invalid=762
- 0100: dt=0.080000, rms=0.645 (0.132%), neg=0, invalid=762
- 0101: dt=0.080000, rms=0.645 (-0.091%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.645, neg=0, invalid=762
- 0102: dt=0.028000, rms=0.645 (0.094%), neg=0, invalid=762
- 0103: dt=0.001750, rms=0.645 (-0.002%), neg=0, invalid=762
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.10027 (20)
- mri peak = 0.06482 (18)
- Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (757 voxels, overlap=0.571)
- Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (757 voxels, peak = 21), gca=21.3
- gca peak = 0.15565 (16)
- mri peak = 0.04843 (17)
- Right_Lateral_Ventricle (43): linear fit = 2.71 x + 0.0 (722 voxels, overlap=0.432)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (722 voxels, peak = 43), gca=24.0
- gca peak = 0.26829 (96)
- mri peak = 0.08830 (90)
- Right_Pallidum (52): linear fit = 0.93 x + 0.0 (970 voxels, overlap=0.759)
- Right_Pallidum (52): linear fit = 0.93 x + 0.0 (970 voxels, peak = 89), gca=88.8
- gca peak = 0.20183 (93)
- mri peak = 0.10163 (93)
- Left_Pallidum (13): linear fit = 0.96 x + 0.0 (798 voxels, overlap=0.931)
- Left_Pallidum (13): linear fit = 0.96 x + 0.0 (798 voxels, peak = 90), gca=89.7
- gca peak = 0.21683 (55)
- mri peak = 0.05795 (68)
- Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (946 voxels, overlap=0.033)
- Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (946 voxels, peak = 64), gca=63.5
- gca peak = 0.30730 (58)
- mri peak = 0.07831 (67)
- Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (956 voxels, overlap=0.591)
- Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (956 voxels, peak = 65), gca=64.7
- gca peak = 0.11430 (101)
- mri peak = 0.09138 (101)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (61113 voxels, overlap=0.902)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (61113 voxels, peak = 104), gca=103.5
- gca peak = 0.12076 (102)
- mri peak = 0.08975 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (60832 voxels, overlap=0.779)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (60832 voxels, peak = 106), gca=105.6
- gca peak = 0.14995 (59)
- mri peak = 0.03681 (65)
- Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (26709 voxels, overlap=0.905)
- Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (26709 voxels, peak = 63), gca=63.4
- gca peak = 0.15082 (58)
- mri peak = 0.03710 (61)
- Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (27500 voxels, overlap=0.919)
- Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (27500 voxels, peak = 61), gca=60.6
- gca peak = 0.14161 (67)
- mri peak = 0.07219 (74)
- Right_Caudate (50): linear fit = 1.09 x + 0.0 (980 voxels, overlap=0.863)
- Right_Caudate (50): linear fit = 1.09 x + 0.0 (980 voxels, peak = 73), gca=72.7
- gca peak = 0.15243 (71)
- mri peak = 0.09621 (79)
- Left_Caudate (11): linear fit = 1.03 x + 0.0 (972 voxels, overlap=0.887)
- Left_Caudate (11): linear fit = 1.03 x + 0.0 (972 voxels, peak = 73), gca=73.5
- gca peak = 0.13336 (57)
- mri peak = 0.03916 (56)
- Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (26710 voxels, overlap=0.936)
- Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (26710 voxels, peak = 64), gca=63.6
- gca peak = 0.13252 (56)
- mri peak = 0.03977 (59)
- Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (25021 voxels, overlap=0.886)
- Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (25021 voxels, peak = 62), gca=62.4
- gca peak = 0.18181 (84)
- mri peak = 0.07474 (89)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9145 voxels, overlap=0.784)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9145 voxels, peak = 89), gca=89.5
- gca peak = 0.20573 (83)
- mri peak = 0.05118 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7406 voxels, overlap=0.924)
- Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7406 voxels, peak = 87), gca=86.7
- gca peak = 0.21969 (57)
- mri peak = 0.08525 (75)
- Left_Amygdala (18): linear fit = 1.29 x + 0.0 (435 voxels, overlap=0.053)
- Left_Amygdala (18): linear fit = 1.29 x + 0.0 (435 voxels, peak = 74), gca=73.8
- gca peak = 0.39313 (56)
- mri peak = 0.09650 (73)
- Right_Amygdala (54): linear fit = 1.27 x + 0.0 (516 voxels, overlap=0.021)
- Right_Amygdala (54): linear fit = 1.27 x + 0.0 (516 voxels, peak = 71), gca=71.4
- gca peak = 0.14181 (85)
- mri peak = 0.06866 (88)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5295 voxels, overlap=0.958)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5295 voxels, peak = 86), gca=86.3
- gca peak = 0.11978 (83)
- mri peak = 0.07183 (87)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4485 voxels, overlap=0.928)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4485 voxels, peak = 85), gca=85.1
- gca peak = 0.13399 (79)
- mri peak = 0.06704 (82)
- Left_Putamen (12): linear fit = 1.04 x + 0.0 (2313 voxels, overlap=0.919)
- Left_Putamen (12): linear fit = 1.04 x + 0.0 (2313 voxels, peak = 83), gca=82.6
- gca peak = 0.14159 (79)
- mri peak = 0.07093 (75)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (2220 voxels, overlap=1.000)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (2220 voxels, peak = 79), gca=78.6
- gca peak = 0.10025 (80)
- mri peak = 0.07865 (88)
- Brain_Stem (16): linear fit = 1.14 x + 0.0 (10306 voxels, overlap=0.402)
- Brain_Stem (16): linear fit = 1.14 x + 0.0 (10306 voxels, peak = 92), gca=91.6
- gca peak = 0.13281 (86)
- mri peak = 0.07487 (95)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1132 voxels, overlap=0.417)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1132 voxels, peak = 93), gca=93.3
- gca peak = 0.12801 (89)
- mri peak = 0.07379 (95)
- Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1420 voxels, overlap=0.502)
- Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1420 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 = 0.21881 (14)
- Fourth_Ventricle (15): linear fit = 0.73 x + 0.0 (305 voxels, overlap=0.458)
- Fourth_Ventricle (15): linear fit = 0.73 x + 0.0 (305 voxels, peak = 15), gca=15.2
- 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 1.16 x + 0.0
- estimating mean wm scale to be 1.03 x + 0.0
- estimating mean csf scale to be 1.10 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=0.645, neg=0, invalid=762
- 0104: dt=111.325670, rms=0.638 (1.105%), neg=0, invalid=762
- 0105: dt=221.952000, rms=0.635 (0.511%), neg=0, invalid=762
- 0106: dt=295.936000, rms=0.632 (0.426%), neg=0, invalid=762
- 0107: dt=92.480000, rms=0.631 (0.191%), neg=0, invalid=762
- 0108: dt=517.888000, rms=0.629 (0.247%), neg=0, invalid=762
- 0109: dt=73.984000, rms=0.629 (0.126%), neg=0, invalid=762
- 0110: dt=517.888000, rms=0.628 (0.167%), neg=0, invalid=762
- 0111: dt=129.472000, rms=0.627 (0.123%), neg=0, invalid=762
- 0112: dt=73.984000, rms=0.627 (0.007%), neg=0, invalid=762
- 0113: dt=73.984000, rms=0.627 (0.022%), neg=0, invalid=762
- 0114: dt=73.984000, rms=0.626 (0.038%), neg=0, invalid=762
- 0115: dt=73.984000, rms=0.626 (0.055%), neg=0, invalid=762
- 0116: dt=73.984000, rms=0.626 (0.071%), neg=0, invalid=762
- 0117: dt=73.984000, rms=0.625 (0.078%), neg=0, invalid=762
- 0118: dt=73.984000, rms=0.625 (0.080%), neg=0, invalid=762
- 0119: dt=73.984000, rms=0.624 (0.079%), neg=0, invalid=762
- 0120: dt=73.984000, rms=0.624 (0.075%), neg=0, invalid=762
- 0121: dt=73.984000, rms=0.623 (0.063%), neg=0, invalid=762
- 0122: dt=73.984000, rms=0.623 (0.062%), neg=0, invalid=762
- 0123: dt=73.984000, rms=0.623 (0.056%), neg=0, invalid=762
- 0124: dt=73.984000, rms=0.622 (0.047%), neg=0, invalid=762
- 0125: dt=73.984000, rms=0.622 (0.036%), neg=0, invalid=762
- 0126: dt=73.984000, rms=0.622 (0.031%), neg=0, invalid=762
- 0127: dt=73.984000, rms=0.622 (0.038%), neg=0, invalid=762
- 0128: dt=73.984000, rms=0.621 (0.042%), neg=0, invalid=762
- 0129: dt=73.984000, rms=0.621 (0.041%), neg=0, invalid=762
- 0130: dt=73.984000, rms=0.621 (0.039%), neg=0, invalid=762
- 0131: dt=73.984000, rms=0.621 (0.035%), neg=0, invalid=762
- 0132: dt=73.984000, rms=0.620 (0.032%), neg=0, invalid=762
- 0133: dt=73.984000, rms=0.620 (0.037%), neg=0, invalid=762
- 0134: dt=73.984000, rms=0.620 (0.039%), neg=0, invalid=762
- 0135: dt=73.984000, rms=0.620 (0.039%), neg=0, invalid=762
- 0136: dt=73.984000, rms=0.620 (0.038%), neg=0, invalid=762
- 0137: dt=73.984000, rms=0.619 (0.035%), neg=0, invalid=762
- 0138: dt=73.984000, rms=0.619 (0.036%), neg=0, invalid=762
- 0139: dt=73.984000, rms=0.619 (0.037%), neg=0, invalid=762
- 0140: dt=73.984000, rms=0.619 (0.038%), neg=0, invalid=762
- 0141: dt=73.984000, rms=0.618 (0.037%), neg=0, invalid=762
- 0142: dt=73.984000, rms=0.618 (0.035%), neg=0, invalid=762
- 0143: dt=73.984000, rms=0.618 (0.035%), neg=0, invalid=762
- 0144: dt=73.984000, rms=0.618 (0.033%), neg=0, invalid=762
- 0145: dt=73.984000, rms=0.618 (0.036%), neg=0, invalid=762
- 0146: dt=73.984000, rms=0.617 (0.035%), neg=0, invalid=762
- 0147: dt=73.984000, rms=0.617 (0.035%), neg=0, invalid=762
- 0148: dt=73.984000, rms=0.617 (0.030%), neg=0, invalid=762
- 0149: dt=73.984000, rms=0.617 (0.028%), neg=0, invalid=762
- 0150: dt=73.984000, rms=0.617 (0.028%), neg=0, invalid=762
- 0151: dt=73.984000, rms=0.616 (0.029%), neg=0, invalid=762
- 0152: dt=73.984000, rms=0.616 (0.027%), neg=0, invalid=762
- 0153: dt=73.984000, rms=0.616 (0.025%), neg=0, invalid=762
- 0154: dt=73.984000, rms=0.616 (0.023%), neg=0, invalid=762
- 0155: dt=7102.464000, rms=0.615 (0.097%), neg=0, invalid=762
- 0156: dt=129.472000, rms=0.615 (0.123%), neg=0, invalid=762
- 0157: dt=0.005645, rms=0.615 (-0.002%), neg=0, invalid=762
- 0158: dt=0.005645, rms=0.615 (0.000%), neg=0, invalid=762
- 0159: dt=0.005645, rms=0.615 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.615, neg=0, invalid=762
- 0160: dt=221.952000, rms=0.613 (0.249%), neg=0, invalid=762
- 0161: dt=129.472000, rms=0.613 (0.052%), neg=0, invalid=762
- 0162: dt=369.920000, rms=0.613 (0.046%), neg=0, invalid=762
- 0163: dt=369.920000, rms=0.613 (-0.142%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.614, neg=0, invalid=762
- 0164: dt=102.603175, rms=0.610 (0.541%), neg=0, invalid=762
- 0165: dt=181.020921, rms=0.603 (1.186%), neg=0, invalid=762
- 0166: dt=57.043478, rms=0.600 (0.505%), neg=0, invalid=762
- 0167: dt=414.720000, rms=0.594 (1.079%), neg=0, invalid=762
- 0168: dt=55.752577, rms=0.590 (0.657%), neg=0, invalid=762
- 0169: dt=145.152000, rms=0.587 (0.486%), neg=0, invalid=762
- 0170: dt=36.288000, rms=0.586 (0.079%), neg=0, invalid=762
- 0171: dt=497.664000, rms=0.584 (0.487%), neg=0, invalid=762
- 0172: dt=64.260516, rms=0.580 (0.570%), neg=0, invalid=762
- 0173: dt=36.288000, rms=0.580 (0.048%), neg=0, invalid=762
- 0174: dt=36.288000, rms=0.580 (0.052%), neg=0, invalid=762
- 0175: dt=36.288000, rms=0.579 (0.094%), neg=0, invalid=762
- 0176: dt=36.288000, rms=0.578 (0.130%), neg=0, invalid=762
- 0177: dt=36.288000, rms=0.577 (0.161%), neg=0, invalid=762
- 0178: dt=36.288000, rms=0.576 (0.182%), neg=0, invalid=762
- 0179: dt=36.288000, rms=0.575 (0.191%), neg=0, invalid=762
- 0180: dt=36.288000, rms=0.574 (0.198%), neg=0, invalid=762
- 0181: dt=36.288000, rms=0.573 (0.192%), neg=0, invalid=762
- 0182: dt=36.288000, rms=0.572 (0.193%), neg=0, invalid=762
- 0183: dt=36.288000, rms=0.571 (0.195%), neg=0, invalid=762
- 0184: dt=36.288000, rms=0.570 (0.193%), neg=0, invalid=762
- 0185: dt=36.288000, rms=0.569 (0.188%), neg=0, invalid=762
- 0186: dt=36.288000, rms=0.568 (0.180%), neg=0, invalid=762
- 0187: dt=36.288000, rms=0.568 (0.017%), neg=0, invalid=762
- 0188: dt=36.288000, rms=0.567 (0.032%), neg=0, invalid=762
- 0189: dt=36.288000, rms=0.567 (0.056%), neg=0, invalid=762
- 0190: dt=36.288000, rms=0.567 (0.075%), neg=0, invalid=762
- 0191: dt=36.288000, rms=0.566 (0.081%), neg=0, invalid=762
- 0192: dt=36.288000, rms=0.566 (0.094%), neg=0, invalid=762
- 0193: dt=36.288000, rms=0.565 (0.095%), neg=0, invalid=762
- 0194: dt=36.288000, rms=0.565 (0.097%), neg=0, invalid=762
- 0195: dt=36.288000, rms=0.564 (0.100%), neg=0, invalid=762
- 0196: dt=36.288000, rms=0.564 (0.013%), neg=0, invalid=762
- 0197: dt=36.288000, rms=0.564 (0.029%), neg=0, invalid=762
- 0198: dt=18.144000, rms=0.564 (0.006%), neg=0, invalid=762
- 0199: dt=9.072000, rms=0.564 (0.004%), neg=0, invalid=762
- 0200: dt=1.620000, rms=0.564 (0.001%), neg=0, invalid=762
- 0201: dt=0.050625, rms=0.564 (0.000%), neg=0, invalid=762
- 0202: dt=0.003164, rms=0.564 (0.000%), neg=0, invalid=762
- 0203: dt=0.000791, rms=0.564 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.564, neg=0, invalid=762
- 0204: dt=119.560440, rms=0.561 (0.526%), neg=0, invalid=762
- 0205: dt=68.682927, rms=0.560 (0.168%), neg=0, invalid=762
- 0206: dt=145.152000, rms=0.560 (0.123%), neg=0, invalid=762
- 0207: dt=62.208000, rms=0.559 (0.121%), neg=0, invalid=762
- 0208: dt=82.944000, rms=0.559 (0.050%), neg=0, invalid=762
- 0209: dt=82.944000, rms=0.558 (0.077%), neg=0, invalid=762
- 0210: dt=82.944000, rms=0.558 (0.130%), neg=0, invalid=762
- 0211: dt=82.944000, rms=0.557 (0.104%), neg=0, invalid=762
- 0212: dt=82.944000, rms=0.556 (0.211%), neg=0, invalid=762
- 0213: dt=82.944000, rms=0.555 (0.166%), neg=0, invalid=762
- 0214: dt=82.944000, rms=0.554 (0.151%), neg=0, invalid=762
- 0215: dt=20.736000, rms=0.554 (0.029%), neg=0, invalid=762
- 0216: dt=20.736000, rms=0.554 (0.014%), neg=0, invalid=762
- 0217: dt=10.368000, rms=0.554 (0.004%), neg=0, invalid=762
- 0218: dt=2.268000, rms=0.554 (0.002%), neg=0, invalid=762
- 0219: dt=1.134000, rms=0.554 (0.000%), neg=0, invalid=762
- 0220: dt=0.567000, rms=0.554 (0.000%), neg=0, invalid=762
- 0221: dt=0.141750, rms=0.554 (0.000%), neg=0, invalid=762
- 0222: dt=0.002215, rms=0.554 (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=0.560, neg=0, invalid=762
- 0223: dt=53.806452, rms=0.554 (0.991%), neg=0, invalid=762
- 0224: dt=54.914573, rms=0.546 (1.497%), neg=0, invalid=762
- 0225: dt=22.826667, rms=0.542 (0.649%), neg=0, invalid=762
- 0226: dt=179.200000, rms=0.532 (1.940%), neg=0, invalid=762
- 0227: dt=32.000000, rms=0.529 (0.593%), neg=0, invalid=762
- 0228: dt=38.400000, rms=0.527 (0.321%), neg=0, invalid=762
- 0229: dt=25.600000, rms=0.526 (0.177%), neg=0, invalid=762
- 0230: dt=44.800000, rms=0.525 (0.252%), neg=0, invalid=762
- 0231: dt=25.600000, rms=0.524 (0.109%), neg=0, invalid=762
- 0232: dt=44.800000, rms=0.523 (0.215%), neg=0, invalid=762
- 0233: dt=8.000000, rms=0.523 (0.049%), neg=0, invalid=762
- 0234: dt=0.062500, rms=0.523 (0.016%), neg=0, invalid=762
- 0235: dt=0.031250, rms=0.523 (0.000%), neg=0, invalid=762
- 0236: dt=0.003906, rms=0.523 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.523, neg=0, invalid=762
- 0237: dt=38.400000, rms=0.520 (0.619%), neg=0, invalid=762
- 0238: dt=32.000000, rms=0.518 (0.326%), neg=0, invalid=762
- 0239: dt=25.600000, rms=0.517 (0.176%), neg=0, invalid=762
- 0240: dt=44.800000, rms=0.516 (0.213%), neg=0, invalid=762
- 0241: dt=24.041451, rms=0.516 (0.126%), neg=0, invalid=762
- 0242: dt=44.800000, rms=0.515 (0.175%), neg=0, invalid=762
- 0243: dt=11.200000, rms=0.514 (0.077%), neg=0, invalid=762
- 0244: dt=44.800000, rms=0.514 (0.119%), neg=0, invalid=762
- 0245: dt=32.000000, rms=0.513 (0.124%), neg=0, invalid=762
- 0246: dt=19.200000, rms=0.513 (0.071%), neg=0, invalid=762
- 0247: dt=102.400000, rms=0.512 (0.233%), neg=0, invalid=762
- 0248: dt=11.200000, rms=0.511 (0.082%), neg=0, invalid=762
- 0249: dt=25.600000, rms=0.511 (0.069%), neg=0, invalid=762
- 0250: dt=32.000000, rms=0.510 (0.095%), neg=0, invalid=762
- 0251: dt=19.200000, rms=0.510 (0.036%), neg=0, invalid=762
- 0252: dt=19.200000, rms=0.510 (0.069%), neg=0, invalid=762
- 0253: dt=19.200000, rms=0.509 (0.082%), neg=0, invalid=762
- 0254: dt=19.200000, rms=0.509 (0.112%), neg=0, invalid=762
- 0255: dt=19.200000, rms=0.508 (0.141%), neg=0, invalid=762
- 0256: dt=19.200000, rms=0.507 (0.164%), neg=0, invalid=762
- 0257: dt=19.200000, rms=0.506 (0.171%), neg=0, invalid=762
- 0258: dt=19.200000, rms=0.506 (0.175%), neg=0, invalid=762
- 0259: dt=19.200000, rms=0.505 (0.174%), neg=0, invalid=762
- 0260: dt=19.200000, rms=0.504 (0.176%), neg=0, invalid=762
- 0261: dt=19.200000, rms=0.504 (0.022%), neg=0, invalid=762
- 0262: dt=19.200000, rms=0.503 (0.039%), neg=0, invalid=762
- 0263: dt=9.600000, rms=0.503 (0.011%), neg=0, invalid=762
- 0264: dt=4.800000, rms=0.503 (0.003%), neg=0, invalid=762
- 0265: dt=0.043750, rms=0.503 (0.001%), neg=0, invalid=762
- 0266: dt=0.043750, rms=0.503 (0.000%), neg=0, invalid=762
- 0267: dt=0.021875, rms=0.503 (0.000%), neg=0, invalid=762
- 0268: dt=0.001367, rms=0.503 (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=0.521, neg=0, invalid=762
- 0269: dt=0.000000, rms=0.521 (0.103%), neg=0, invalid=762
- 0270: dt=0.000000, rms=0.521 (0.000%), neg=0, invalid=762
- 0271: dt=0.150000, rms=0.521 (-0.010%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.521, neg=0, invalid=762
- 0272: dt=0.000000, rms=0.521 (0.103%), neg=0, invalid=762
- 0273: dt=0.000000, rms=0.521 (0.000%), neg=0, invalid=762
- 0274: dt=0.150000, rms=0.521 (-0.010%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.556, neg=0, invalid=762
- 0275: dt=1.536000, rms=0.553 (0.575%), neg=0, invalid=762
- 0276: dt=0.112000, rms=0.553 (0.002%), neg=0, invalid=762
- 0277: dt=0.112000, rms=0.553 (0.000%), neg=0, invalid=762
- 0278: dt=0.112000, rms=0.553 (-0.008%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.553, neg=0, invalid=762
- 0279: dt=1.024000, rms=0.552 (0.185%), neg=0, invalid=762
- 0280: dt=0.112000, rms=0.552 (0.001%), neg=0, invalid=762
- 0281: dt=0.112000, rms=0.552 (-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=0.514, neg=0, invalid=762
- 0282: dt=0.448000, rms=0.501 (2.580%), neg=0, invalid=762
- 0283: dt=0.448000, rms=0.498 (0.602%), neg=0, invalid=762
- 0284: dt=0.448000, rms=0.496 (0.338%), neg=0, invalid=762
- 0285: dt=0.448000, rms=0.495 (0.209%), neg=0, invalid=762
- 0286: dt=0.466667, rms=0.494 (0.163%), neg=0, invalid=762
- 0287: dt=0.448000, rms=0.494 (0.106%), neg=0, invalid=762
- 0288: dt=0.448000, rms=0.493 (0.092%), neg=0, invalid=762
- 0289: dt=0.448000, rms=0.493 (0.064%), neg=0, invalid=762
- 0290: dt=0.448000, rms=0.493 (0.061%), neg=0, invalid=762
- 0291: dt=0.448000, rms=0.492 (0.042%), neg=0, invalid=762
- 0292: dt=0.448000, rms=0.492 (0.042%), neg=0, invalid=762
- 0293: dt=0.448000, rms=0.492 (0.068%), neg=0, invalid=762
- 0294: dt=0.448000, rms=0.491 (0.075%), neg=0, invalid=762
- 0295: dt=0.448000, rms=0.491 (0.079%), neg=0, invalid=762
- 0296: dt=0.448000, rms=0.491 (0.007%), neg=0, invalid=762
- 0297: dt=0.448000, rms=0.491 (0.003%), neg=0, invalid=762
- 0298: dt=0.384000, rms=0.491 (0.004%), neg=0, invalid=762
- 0299: dt=0.448000, rms=0.491 (0.005%), neg=0, invalid=762
- 0300: dt=0.112000, rms=0.491 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.492, neg=0, invalid=762
- 0301: dt=0.448000, rms=0.487 (1.014%), neg=0, invalid=762
- 0302: dt=0.448000, rms=0.486 (0.125%), neg=0, invalid=762
- 0303: dt=0.448000, rms=0.486 (0.034%), neg=0, invalid=762
- 0304: dt=0.448000, rms=0.486 (0.018%), neg=0, invalid=762
- 0305: dt=0.448000, rms=0.486 (0.012%), neg=0, invalid=762
- 0306: dt=0.448000, rms=0.486 (-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=0.484, neg=0, invalid=762
- 0307: dt=0.000000, rms=0.483 (0.119%), neg=0, invalid=762
- 0308: dt=0.000000, rms=0.483 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.484, neg=0, invalid=762
- 0309: dt=129.472000, rms=0.483 (0.147%), neg=0, invalid=762
- 0310: dt=110.976000, rms=0.483 (0.010%), neg=0, invalid=762
- 0311: dt=110.976000, rms=0.483 (0.011%), neg=0, invalid=762
- 0312: dt=110.976000, rms=0.483 (0.018%), neg=0, invalid=762
- 0313: dt=110.976000, rms=0.483 (0.013%), neg=0, invalid=762
- 0314: dt=110.976000, rms=0.483 (0.025%), neg=0, invalid=762
- 0315: dt=110.976000, rms=0.483 (0.013%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.483, neg=0, invalid=762
- 0316: dt=9.072000, rms=0.483 (0.127%), neg=0, invalid=762
- 0317: dt=9.072000, rms=0.483 (0.004%), neg=0, invalid=762
- 0318: dt=9.072000, rms=0.483 (0.001%), neg=0, invalid=762
- 0319: dt=9.072000, rms=0.483 (-0.011%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.483, neg=0, invalid=762
- 0320: dt=145.152000, rms=0.481 (0.434%), neg=0, invalid=762
- 0321: dt=36.288000, rms=0.481 (0.123%), neg=0, invalid=762
- 0322: dt=36.288000, rms=0.480 (0.038%), neg=0, invalid=762
- 0323: dt=36.288000, rms=0.480 (0.069%), neg=0, invalid=762
- 0324: dt=36.288000, rms=0.480 (0.085%), neg=0, invalid=762
- 0325: dt=36.288000, rms=0.479 (0.102%), neg=0, invalid=762
- 0326: dt=36.288000, rms=0.479 (0.102%), neg=0, invalid=762
- 0327: dt=36.288000, rms=0.478 (0.099%), neg=0, invalid=762
- 0328: dt=124.416000, rms=0.478 (0.034%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.479, neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0329: dt=25.456869, rms=0.477 (0.432%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0330: dt=44.800000, rms=0.475 (0.438%), neg=0, invalid=762
- 0331: dt=25.600000, rms=0.474 (0.211%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0332: dt=25.600000, rms=0.472 (0.287%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 7 iterations, nbhd size=1, neg = 0
- 0333: dt=25.600000, rms=0.471 (0.281%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 11 iterations, nbhd size=1, neg = 0
- 0334: dt=25.600000, rms=0.470 (0.250%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 10 iterations, nbhd size=1, neg = 0
- 0335: dt=25.600000, rms=0.469 (0.237%), neg=0, invalid=762
- iter 0, gcam->neg = 6
- after 10 iterations, nbhd size=1, neg = 0
- 0336: dt=25.600000, rms=0.468 (0.165%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 2 iterations, nbhd size=0, neg = 0
- 0337: dt=25.600000, rms=0.467 (0.158%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 12 iterations, nbhd size=1, neg = 0
- 0338: dt=25.600000, rms=0.467 (0.127%), neg=0, invalid=762
- iter 0, gcam->neg = 11
- after 9 iterations, nbhd size=1, neg = 0
- 0339: dt=25.600000, rms=0.466 (0.164%), neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 2 iterations, nbhd size=0, neg = 0
- 0340: dt=25.600000, rms=0.465 (0.133%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 2 iterations, nbhd size=0, neg = 0
- 0341: dt=25.600000, rms=0.465 (0.153%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0342: dt=25.600000, rms=0.464 (0.128%), neg=0, invalid=762
- iter 0, gcam->neg = 8
- after 11 iterations, nbhd size=1, neg = 0
- 0343: dt=25.600000, rms=0.463 (0.137%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 0 iterations, nbhd size=0, neg = 0
- 0344: dt=25.600000, rms=0.463 (0.125%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 3 iterations, nbhd size=0, neg = 0
- 0345: dt=25.600000, rms=0.462 (0.115%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 3 iterations, nbhd size=0, neg = 0
- 0346: dt=38.400000, rms=0.462 (0.077%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0347: dt=38.400000, rms=0.462 (-0.004%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.463, neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 11 iterations, nbhd size=1, neg = 0
- 0348: dt=38.400000, rms=0.459 (0.828%), neg=0, invalid=762
- 0349: dt=25.600000, rms=0.457 (0.287%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0350: dt=32.000000, rms=0.456 (0.265%), neg=0, invalid=762
- 0351: dt=19.200000, rms=0.456 (0.099%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0352: dt=19.200000, rms=0.455 (0.138%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 2 iterations, nbhd size=0, neg = 0
- 0353: dt=19.200000, rms=0.455 (0.140%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 2 iterations, nbhd size=0, neg = 0
- 0354: dt=19.200000, rms=0.454 (0.148%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 4 iterations, nbhd size=0, neg = 0
- 0355: dt=19.200000, rms=0.453 (0.161%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0356: dt=19.200000, rms=0.453 (0.132%), neg=0, invalid=762
- 0357: dt=19.200000, rms=0.452 (0.087%), neg=0, invalid=762
- 0358: dt=19.200000, rms=0.452 (0.060%), neg=0, invalid=762
- 0359: dt=25.600000, rms=0.452 (0.030%), neg=0, invalid=762
- 0360: dt=25.600000, rms=0.452 (-0.022%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.459, neg=0, invalid=762
- 0361: dt=1.008000, rms=0.458 (0.113%), neg=0, invalid=762
- 0362: dt=0.720000, rms=0.458 (0.011%), neg=0, invalid=762
- 0363: dt=0.720000, rms=0.458 (0.002%), neg=0, invalid=762
- 0364: dt=0.720000, rms=0.458 (-0.009%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.459, neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0365: dt=4.210526, rms=0.458 (0.180%), neg=0, invalid=762
- 0366: dt=4.000000, rms=0.458 (0.030%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0367: dt=4.000000, rms=0.458 (0.018%), neg=0, invalid=762
- 0368: dt=4.000000, rms=0.458 (-0.031%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.467, neg=0, invalid=762
- 0369: dt=0.000050, rms=0.466 (0.128%), neg=0, invalid=762
- 0370: dt=0.000000, rms=0.466 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.467, neg=0, invalid=762
- 0371: dt=1.024000, rms=0.466 (0.209%), neg=0, invalid=762
- 0372: dt=0.448000, rms=0.466 (0.013%), neg=0, invalid=762
- 0373: dt=0.448000, rms=0.466 (-0.002%), 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=0.456, neg=0, invalid=762
- iter 0, gcam->neg = 696
- after 11 iterations, nbhd size=1, neg = 0
- 0374: dt=2.078525, rms=0.428 (6.124%), neg=0, invalid=762
- 0375: dt=0.028000, rms=0.428 (0.014%), neg=0, invalid=762
- 0376: dt=0.028000, rms=0.428 (-0.005%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.429, neg=0, invalid=762
- 0377: dt=0.080000, rms=0.428 (0.218%), neg=0, invalid=762
- 0378: dt=0.000000, rms=0.428 (0.002%), neg=0, invalid=762
- 0379: dt=0.050000, rms=0.428 (-0.019%), 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=0.415, neg=0, invalid=762
- 0380: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.415, neg=0, invalid=762
- 0381: dt=32.368000, rms=0.415 (0.006%), neg=0, invalid=762
- 0382: dt=32.368000, rms=0.415 (0.001%), neg=0, invalid=762
- 0383: dt=32.368000, rms=0.415 (0.000%), neg=0, invalid=762
- 0384: dt=32.368000, rms=0.415 (-0.002%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.415, neg=0, invalid=762
- 0385: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.415, neg=0, invalid=762
- 0386: dt=36.288000, rms=0.415 (0.025%), neg=0, invalid=762
- 0387: dt=124.416000, rms=0.414 (0.027%), neg=0, invalid=762
- 0388: dt=248.832000, rms=0.414 (0.071%), neg=0, invalid=762
- 0389: dt=31.104000, rms=0.414 (0.007%), neg=0, invalid=762
- 0390: dt=31.104000, rms=0.414 (0.002%), neg=0, invalid=762
- 0391: dt=31.104000, rms=0.414 (0.001%), neg=0, invalid=762
- 0392: dt=31.104000, rms=0.414 (0.004%), neg=0, invalid=762
- 0393: dt=31.104000, rms=0.414 (0.012%), neg=0, invalid=762
- 0394: dt=31.104000, rms=0.414 (0.019%), neg=0, invalid=762
- 0395: dt=31.104000, rms=0.414 (0.020%), neg=0, invalid=762
- 0396: dt=31.104000, rms=0.414 (0.016%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.414, neg=0, invalid=762
- 0397: dt=2.800000, rms=0.414 (0.009%), neg=0, invalid=762
- 0398: dt=2.800000, rms=0.414 (0.003%), neg=0, invalid=762
- 0399: dt=2.800000, rms=0.414 (-0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.414, neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0400: dt=102.400000, rms=0.412 (0.642%), neg=0, invalid=762
- 0401: dt=25.600000, rms=0.411 (0.241%), neg=0, invalid=762
- 0402: dt=25.600000, rms=0.411 (0.071%), neg=0, invalid=762
- 0403: dt=25.600000, rms=0.410 (0.100%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 2 iterations, nbhd size=0, neg = 0
- 0404: dt=25.600000, rms=0.409 (0.163%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 7 iterations, nbhd size=1, neg = 0
- 0405: dt=25.600000, rms=0.409 (0.153%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 10 iterations, nbhd size=1, neg = 0
- 0406: dt=25.600000, rms=0.408 (0.167%), neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 2 iterations, nbhd size=0, neg = 0
- 0407: dt=25.600000, rms=0.407 (0.151%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 2 iterations, nbhd size=0, neg = 0
- 0408: dt=25.600000, rms=0.407 (0.135%), neg=0, invalid=762
- iter 0, gcam->neg = 11
- after 15 iterations, nbhd size=1, neg = 0
- 0409: dt=25.600000, rms=0.406 (0.110%), neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 11 iterations, nbhd size=1, neg = 0
- 0410: dt=25.600000, rms=0.406 (0.092%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0411: dt=19.200000, rms=0.406 (0.010%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0412: dt=19.200000, rms=0.406 (0.006%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0413: dt=19.200000, rms=0.406 (0.007%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0414: dt=19.200000, rms=0.406 (0.004%), neg=0, invalid=762
- 0415: dt=19.200000, rms=0.406 (0.002%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.410, neg=0, invalid=762
- 0416: dt=0.252000, rms=0.410 (0.000%), neg=0, invalid=762
- 0417: dt=0.027000, rms=0.410 (0.000%), neg=0, invalid=762
- 0418: dt=0.027000, rms=0.410 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.410, neg=0, invalid=762
- 0419: dt=7.142857, rms=0.410 (0.065%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0420: dt=11.076923, rms=0.409 (0.065%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 3 iterations, nbhd size=0, neg = 0
- 0421: dt=11.076923, rms=0.409 (0.086%), neg=0, invalid=762
- iter 0, gcam->neg = 22
- after 5 iterations, nbhd size=0, neg = 0
- 0422: dt=11.076923, rms=0.409 (0.097%), neg=0, invalid=762
- iter 0, gcam->neg = 30
- after 6 iterations, nbhd size=0, neg = 0
- 0423: dt=11.076923, rms=0.408 (0.101%), neg=0, invalid=762
- iter 0, gcam->neg = 13
- after 6 iterations, nbhd size=0, neg = 0
- 0424: dt=11.076923, rms=0.408 (0.165%), neg=0, invalid=762
- iter 0, gcam->neg = 11
- after 12 iterations, nbhd size=1, neg = 0
- 0425: dt=11.076923, rms=0.407 (0.208%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 10 iterations, nbhd size=0, neg = 0
- 0426: dt=11.076923, rms=0.406 (0.205%), neg=0, invalid=762
- iter 0, gcam->neg = 15
- after 18 iterations, nbhd size=1, neg = 0
- 0427: dt=11.076923, rms=0.405 (0.099%), neg=0, invalid=762
- iter 0, gcam->neg = 13
- after 14 iterations, nbhd size=1, neg = 0
- 0428: dt=11.076923, rms=0.405 (-0.007%), neg=0, invalid=762
- 0429: dt=0.001688, rms=0.405 (0.000%), neg=0, invalid=762
- 0430: dt=0.000000, rms=0.405 (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=0.412, neg=0, invalid=762
- 0431: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.412, neg=0, invalid=762
- 0432: dt=0.000000, rms=0.412 (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=0.401, neg=0, invalid=762
- iter 0, gcam->neg = 558
- after 15 iterations, nbhd size=1, neg = 0
- 0433: dt=1.280000, rms=0.392 (2.245%), neg=0, invalid=762
- 0434: dt=0.000023, rms=0.392 (0.000%), neg=0, invalid=762
- 0435: dt=0.000023, rms=0.392 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.392, neg=0, invalid=762
- 0436: dt=0.080000, rms=0.392 (0.032%), neg=0, invalid=762
- 0437: dt=0.028000, rms=0.392 (0.006%), neg=0, invalid=762
- 0438: dt=0.028000, rms=0.392 (0.003%), neg=0, invalid=762
- 0439: dt=0.028000, rms=0.392 (-0.004%), neg=0, invalid=762
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- mri_ca_register took 2 hours, 16 minutes and 44 seconds.
- mri_ca_register utimesec 9065.639813
- mri_ca_register stimesec 8.306737
- mri_ca_register ru_maxrss 1334100
- mri_ca_register ru_ixrss 0
- mri_ca_register ru_idrss 0
- mri_ca_register ru_isrss 0
- mri_ca_register ru_minflt 4297014
- mri_ca_register ru_majflt 0
- mri_ca_register ru_nswap 0
- mri_ca_register ru_inblock 0
- mri_ca_register ru_oublock 62752
- mri_ca_register ru_msgsnd 0
- mri_ca_register ru_msgrcv 0
- mri_ca_register ru_nsignals 0
- mri_ca_register ru_nvcsw 4035
- mri_ca_register ru_nivcsw 17829
- FSRUNTIME@ mri_ca_register 2.2788 hours 2 threads
- #--------------------------------------
- #@# SubCort Seg Sun Oct 8 02:32:19 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-593
- 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-6.0.0/0050340/mri
- mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz
- == Number of threads available to mri_ca_label for OpenMP = 2 ==
- relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
- using Gibbs prior factor = 0.500
- renormalizing sequences with structure alignment, equivalent to:
- -renormalize
- -renormalize_mean 0.500
- -regularize 0.500
- reading 1 input volumes
- reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
- reading input volume from norm.mgz
- average std[0] = 7.3
- reading transform from transforms/talairach.m3z
- setting orig areas to linear transform determinant scaled 6.21
- 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 = 0.06061 (22)
- Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (179 voxels, overlap=0.669)
- Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (179 voxels, peak = 19), gca=19.3
- gca peak = 0.17677 (13)
- mri peak = 0.08093 (43)
- Right_Lateral_Ventricle (43): linear fit = 3.04 x + 0.0 (173 voxels, overlap=0.325)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (173 voxels, peak = 39), gca=19.5
- gca peak = 0.28129 (95)
- mri peak = 0.11229 (90)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (511 voxels, overlap=0.730)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (511 voxels, peak = 91), gca=90.7
- gca peak = 0.16930 (96)
- mri peak = 0.10454 (91)
- Left_Pallidum (13): linear fit = 0.96 x + 0.0 (504 voxels, overlap=0.870)
- Left_Pallidum (13): linear fit = 0.96 x + 0.0 (504 voxels, peak = 93), gca=92.6
- gca peak = 0.24553 (55)
- mri peak = 0.09619 (66)
- Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (995 voxels, overlap=0.440)
- Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (995 voxels, peak = 64), gca=63.5
- gca peak = 0.30264 (59)
- mri peak = 0.09011 (67)
- Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (905 voxels, overlap=0.133)
- Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (905 voxels, peak = 67), gca=67.0
- gca peak = 0.07580 (103)
- mri peak = 0.09097 (101)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36647 voxels, overlap=0.824)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36647 voxels, peak = 102), gca=102.5
- gca peak = 0.07714 (104)
- mri peak = 0.09083 (104)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38403 voxels, overlap=0.704)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38403 voxels, peak = 105), gca=104.5
- gca peak = 0.09712 (58)
- mri peak = 0.04402 (62)
- Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (32425 voxels, overlap=0.913)
- Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (32425 voxels, peak = 62), gca=62.4
- gca peak = 0.11620 (58)
- mri peak = 0.04639 (62)
- Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (31653 voxels, overlap=0.944)
- Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (31653 voxels, peak = 61), gca=60.6
- gca peak = 0.30970 (66)
- mri peak = 0.09662 (72)
- Right_Caudate (50): linear fit = 1.10 x + 0.0 (908 voxels, overlap=0.915)
- Right_Caudate (50): linear fit = 1.10 x + 0.0 (908 voxels, peak = 72), gca=72.3
- gca peak = 0.15280 (69)
- mri peak = 0.10964 (75)
- Left_Caudate (11): linear fit = 1.01 x + 0.0 (785 voxels, overlap=1.001)
- Left_Caudate (11): linear fit = 1.01 x + 0.0 (785 voxels, peak = 70), gca=70.0
- gca peak = 0.13902 (56)
- mri peak = 0.04659 (64)
- Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (27072 voxels, overlap=0.864)
- Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (27072 voxels, peak = 64), gca=63.6
- gca peak = 0.14777 (55)
- mri peak = 0.04750 (63)
- Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (27323 voxels, overlap=0.940)
- Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (27323 voxels, peak = 62), gca=62.4
- gca peak = 0.16765 (84)
- mri peak = 0.10334 (89)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5858 voxels, overlap=0.729)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5858 voxels, peak = 89), gca=89.5
- gca peak = 0.18739 (84)
- mri peak = 0.08722 (83)
- Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5855 voxels, overlap=0.910)
- Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5855 voxels, peak = 86), gca=86.1
- gca peak = 0.29869 (57)
- mri peak = 0.09622 (75)
- Left_Amygdala (18): linear fit = 1.29 x + 0.0 (575 voxels, overlap=0.057)
- Left_Amygdala (18): linear fit = 1.29 x + 0.0 (575 voxels, peak = 74), gca=73.8
- gca peak = 0.33601 (57)
- mri peak = 0.09966 (72)
- Right_Amygdala (54): linear fit = 1.24 x + 0.0 (582 voxels, overlap=0.046)
- Right_Amygdala (54): linear fit = 1.24 x + 0.0 (582 voxels, peak = 70), gca=70.4
- gca peak = 0.11131 (90)
- mri peak = 0.07930 (88)
- Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4616 voxels, overlap=0.995)
- Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4616 voxels, peak = 88), gca=87.8
- gca peak = 0.11793 (83)
- mri peak = 0.07779 (87)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4518 voxels, overlap=0.978)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4518 voxels, peak = 84), gca=84.2
- gca peak = 0.08324 (81)
- mri peak = 0.07834 (79)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2071 voxels, overlap=0.905)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2071 voxels, peak = 81), gca=81.0
- gca peak = 0.10360 (77)
- mri peak = 0.07224 (78)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (1842 voxels, overlap=0.950)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (1842 voxels, peak = 76), gca=75.8
- gca peak = 0.08424 (78)
- mri peak = 0.07832 (87)
- Brain_Stem (16): linear fit = 1.11 x + 0.0 (11209 voxels, overlap=0.476)
- Brain_Stem (16): linear fit = 1.11 x + 0.0 (11209 voxels, peak = 86), gca=86.2
- gca peak = 0.12631 (89)
- mri peak = 0.08616 (91)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1526 voxels, overlap=0.568)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1526 voxels, peak = 97), gca=96.6
- gca peak = 0.14500 (87)
- mri peak = 0.08124 (92)
- Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1663 voxels, overlap=0.583)
- Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1663 voxels, peak = 94), gca=93.5
- gca peak = 0.14975 (24)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.19357 (14)
- mri peak = 0.21461 (14)
- Fourth_Ventricle (15): linear fit = 0.83 x + 0.0 (323 voxels, overlap=0.642)
- Fourth_Ventricle (15): linear fit = 0.83 x + 0.0 (323 voxels, peak = 12), gca=11.7
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.16825 (27)
- gca peak Left_Thalamus = 1.00000 (94)
- gca peak Third_Ventricle = 0.14975 (24)
- gca peak CSF = 0.23379 (36)
- gca peak Left_Accumbens_area = 0.70037 (62)
- gca peak Left_undetermined = 1.00000 (26)
- gca peak Left_vessel = 0.75997 (52)
- gca peak Left_choroid_plexus = 0.12089 (35)
- gca peak Right_Inf_Lat_Vent = 0.24655 (23)
- gca peak Right_Accumbens_area = 0.45042 (65)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14516 (37)
- gca peak Fifth_Ventricle = 0.65475 (32)
- gca peak WM_hypointensities = 0.07854 (76)
- gca peak non_WM_hypointensities = 0.08491 (43)
- gca peak Optic_Chiasm = 0.71127 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.16 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 1.10 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.14846 (20)
- mri peak = 0.06061 (22)
- Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (179 voxels, overlap=0.708)
- Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (179 voxels, peak = 20), gca=20.5
- gca peak = 0.13423 (19)
- mri peak = 0.08093 (43)
- Right_Lateral_Ventricle (43): linear fit = 1.82 x + 0.0 (173 voxels, overlap=0.337)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (173 voxels, peak = 34), gca=28.5
- gca peak = 0.25462 (90)
- mri peak = 0.11229 (90)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (511 voxels, overlap=1.005)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (511 voxels, peak = 90), gca=89.6
- gca peak = 0.20088 (93)
- mri peak = 0.10454 (91)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (504 voxels, overlap=1.004)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (504 voxels, peak = 93), gca=92.5
- gca peak = 0.24791 (64)
- mri peak = 0.09619 (66)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (995 voxels, overlap=1.005)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (995 voxels, peak = 64), gca=64.0
- gca peak = 0.28088 (67)
- mri peak = 0.09011 (67)
- Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (905 voxels, overlap=1.003)
- Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (905 voxels, peak = 66), gca=66.0
- gca peak = 0.07831 (102)
- mri peak = 0.09097 (101)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (36647 voxels, overlap=0.804)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (36647 voxels, peak = 104), gca=103.5
- gca peak = 0.07908 (105)
- mri peak = 0.09083 (104)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38403 voxels, overlap=0.724)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38403 voxels, peak = 105), gca=105.0
- gca peak = 0.09089 (62)
- mri peak = 0.04402 (62)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (32425 voxels, overlap=0.984)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (32425 voxels, peak = 64), gca=63.5
- gca peak = 0.11303 (61)
- mri peak = 0.04639 (62)
- Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (31653 voxels, overlap=0.972)
- Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (31653 voxels, peak = 63), gca=62.5
- gca peak = 0.25723 (73)
- mri peak = 0.09662 (72)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (908 voxels, overlap=1.008)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (908 voxels, peak = 72), gca=71.9
- gca peak = 0.15451 (70)
- mri peak = 0.10964 (75)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (785 voxels, overlap=1.002)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (785 voxels, peak = 70), gca=70.0
- gca peak = 0.12644 (63)
- mri peak = 0.04659 (64)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (27072 voxels, overlap=1.000)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (27072 voxels, peak = 62), gca=62.1
- gca peak = 0.13587 (62)
- mri peak = 0.04750 (63)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27323 voxels, overlap=0.982)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27323 voxels, peak = 61), gca=61.1
- gca peak = 0.15888 (90)
- mri peak = 0.10334 (89)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5858 voxels, overlap=0.959)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5858 voxels, peak = 90), gca=89.6
- gca peak = 0.15827 (86)
- mri peak = 0.08722 (83)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5855 voxels, overlap=0.966)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5855 voxels, peak = 86), gca=85.6
- gca peak = 0.24884 (74)
- mri peak = 0.09622 (75)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (575 voxels, overlap=0.981)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (575 voxels, peak = 74), gca=74.0
- gca peak = 0.29264 (70)
- mri peak = 0.09966 (72)
- Right_Amygdala (54): linear fit = 1.03 x + 0.0 (582 voxels, overlap=1.000)
- Right_Amygdala (54): linear fit = 1.03 x + 0.0 (582 voxels, peak = 72), gca=72.4
- gca peak = 0.11017 (86)
- mri peak = 0.07930 (88)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4616 voxels, overlap=0.995)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4616 voxels, peak = 86), gca=86.0
- gca peak = 0.11084 (82)
- mri peak = 0.07779 (87)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4518 voxels, overlap=0.993)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4518 voxels, peak = 82), gca=81.6
- gca peak = 0.08324 (81)
- mri peak = 0.07834 (79)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2071 voxels, overlap=0.906)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2071 voxels, peak = 81), gca=81.0
- gca peak = 0.09873 (76)
- mri peak = 0.07224 (78)
- Right_Putamen (51): linear fit = 1.01 x + 0.0 (1842 voxels, overlap=0.939)
- Right_Putamen (51): linear fit = 1.01 x + 0.0 (1842 voxels, peak = 77), gca=77.1
- gca peak = 0.07464 (89)
- mri peak = 0.07832 (87)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (11209 voxels, overlap=0.847)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (11209 voxels, peak = 89), gca=88.6
- gca peak = 0.11849 (95)
- mri peak = 0.08616 (91)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1526 voxels, overlap=0.772)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1526 voxels, peak = 95), gca=94.5
- gca peak = 0.17000 (92)
- mri peak = 0.08124 (92)
- Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1663 voxels, overlap=0.888)
- Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1663 voxels, peak = 90), gca=89.7
- gca peak = 0.16787 (28)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.24326 (13)
- mri peak = 0.21461 (14)
- Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (323 voxels, overlap=0.795)
- Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (323 voxels, peak = 14), gca=14.5
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.15127 (30)
- gca peak Left_Thalamus = 0.36646 (102)
- gca peak Third_Ventricle = 0.16787 (28)
- gca peak CSF = 0.24269 (40)
- gca peak Left_Accumbens_area = 0.76968 (63)
- gca peak Left_undetermined = 1.00000 (26)
- gca peak Left_vessel = 0.75997 (52)
- gca peak Left_choroid_plexus = 0.11917 (35)
- gca peak Right_Inf_Lat_Vent = 0.18678 (27)
- gca peak Right_Accumbens_area = 0.29943 (71)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14511 (37)
- gca peak Fifth_Ventricle = 0.65358 (35)
- gca peak WM_hypointensities = 0.07957 (76)
- gca peak non_WM_hypointensities = 0.08491 (43)
- gca peak Optic_Chiasm = 0.71063 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.01 x + 0.0
- estimating mean wm scale to be 1.01 x + 0.0
- estimating mean csf scale to be 1.21 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
- 54951 voxels changed in iteration 0 of unlikely voxel relabeling
- 272 voxels changed in iteration 1 of unlikely voxel relabeling
- 23 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 34476 gm and wm labels changed (%32 to gray, %68 to white out of all changed labels)
- 278 hippocampal voxels changed.
- 0 amygdala voxels changed.
- pass 1: 61412 changed. image ll: -2.087, PF=0.500
- pass 2: 17272 changed. image ll: -2.086, PF=0.500
- pass 3: 5205 changed.
- pass 4: 1884 changed.
- 38058 voxels changed in iteration 0 of unlikely voxel relabeling
- 281 voxels changed in iteration 1 of unlikely voxel relabeling
- 11 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 5954 voxels changed in iteration 0 of unlikely voxel relabeling
- 91 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
- 5152 voxels changed in iteration 0 of unlikely voxel relabeling
- 60 voxels changed in iteration 1 of unlikely voxel relabeling
- 6 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 4246 voxels changed in iteration 0 of unlikely voxel relabeling
- 32 voxels changed in iteration 1 of unlikely voxel relabeling
- 3 voxels changed in iteration 2 of unlikely voxel relabeling
- 1 voxels changed in iteration 3 of unlikely voxel relabeling
- 0 voxels changed in iteration 4 of unlikely voxel relabeling
- MRItoUCHAR: min=0, max=85
- MRItoUCHAR: converting to UCHAR
- writing labeled volume to aseg.auto_noCCseg.mgz
- mri_ca_label utimesec 3294.989085
- mri_ca_label stimesec 2.100680
- mri_ca_label ru_maxrss 2097412
- mri_ca_label ru_ixrss 0
- mri_ca_label ru_idrss 0
- mri_ca_label ru_isrss 0
- mri_ca_label ru_minflt 682051
- mri_ca_label ru_majflt 0
- mri_ca_label ru_nswap 0
- mri_ca_label ru_inblock 62744
- mri_ca_label ru_oublock 448
- mri_ca_label ru_msgsnd 0
- mri_ca_label ru_msgrcv 0
- mri_ca_label ru_nsignals 0
- mri_ca_label ru_nvcsw 256
- mri_ca_label ru_nivcsw 4136
- auto-labeling took 54 minutes and 10 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/transforms/cc_up.lta 0050340
- 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-6.0.0/0050340/mri/transforms/cc_up.lta
- reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aseg.auto_noCCseg.mgz
- reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/norm.mgz
- 30148 voxels in left wm, 84415 in right wm, xrange [114, 127]
- searching rotation angles z=[-9 5], y=[-9 5]
-
searching scale 1 Z rot -9.5
searching scale 1 Z rot -9.2
searching scale 1 Z rot -9.0
searching scale 1 Z rot -8.7
searching scale 1 Z rot -8.5
searching scale 1 Z rot -8.2
searching scale 1 Z rot -8.0
searching scale 1 Z rot -7.7
searching scale 1 Z rot -7.5
searching scale 1 Z rot -7.2
searching scale 1 Z rot -7.0
searching scale 1 Z rot -6.7
searching scale 1 Z rot -6.5
searching scale 1 Z rot -6.2
searching scale 1 Z rot -6.0
searching scale 1 Z rot -5.7
searching scale 1 Z rot -5.5
searching scale 1 Z rot -5.2
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.7
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.2
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.7
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.2
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.2
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.7
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.2
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.7
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.0
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.8
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.3
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.8
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.3
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.8
searching scale 1 Z rot 4.0
searching scale 1 Z rot 4.3 global minimum found at slice 123.2, rotations (-2.09, -2.47)
- final transformation (x=123.2, yr=-2.091, zr=-2.470):
- 0.99841 0.04310 -0.03646 4.95386;
- -0.04307 0.99907 0.00157 27.20911;
- 0.03649 -0.00000 0.99933 0.58773;
- 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 128 106 123
- eigenvectors:
- -0.00241 -0.01237 0.99992;
- 0.05919 -0.99817 -0.01220;
- 0.99824 0.05916 0.00314;
- writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aseg.auto.mgz...
- corpus callosum segmentation took 1.2 minutes
- #--------------------------------------
- #@# Merge ASeg Sun Oct 8 03:27:42 CEST 2017
- cp aseg.auto.mgz aseg.presurf.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Sun Oct 8 03:27:42 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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...
- 1012 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 110
- white matter peak found at 109
- gm peak at 65 (65), valley at 33 (33)
- csf peak at 33, setting threshold to 54
- 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 65 (65), valley at 32 (32)
- csf peak at 33, setting threshold to 54
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 2 minutes and 55 seconds.
- #--------------------------------------------
- #@# Mask BFS Sun Oct 8 03:30:39 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1434058 voxels in mask (pct= 8.55)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Sun Oct 8 03:30:40 CEST 2017
- mri_segment -mprage brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (103.0): 103.0 +- 6.4 [79.0 --> 125.0]
- GM (73.0) : 71.2 +- 10.0 [30.0 --> 95.0]
- setting bottom of white matter range to 81.1
- setting top of gray matter range to 91.1
- 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...
- 4187 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 3135 filled
- 1864 bright non-wm voxels segmented.
- 2164 diagonally connected voxels added...
- white matter segmentation took 1.5 minutes
- writing output to wm.seg.mgz...
- assuming input volume is MGH (Van der Kouwe) MP-RAGE
- mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz
- preserving editing changes in input volume...
- auto filling took 0.53 minutes
- reading wm segmentation from wm.seg.mgz...
- 599 voxels added to wm to prevent paths from MTL structures to cortex
- 2371 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 29829 voxels turned on, 41852 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+): 15 found - 15 modified | TOTAL: 15
- pass 2 (xy+): 0 found - 15 modified | TOTAL: 15
- pass 1 (xy-): 17 found - 17 modified | TOTAL: 32
- pass 2 (xy-): 0 found - 17 modified | TOTAL: 32
- pass 1 (yz+): 14 found - 14 modified | TOTAL: 46
- pass 2 (yz+): 0 found - 14 modified | TOTAL: 46
- pass 1 (yz-): 22 found - 22 modified | TOTAL: 68
- pass 2 (yz-): 0 found - 22 modified | TOTAL: 68
- pass 1 (xz+): 17 found - 17 modified | TOTAL: 85
- pass 2 (xz+): 0 found - 17 modified | TOTAL: 85
- pass 1 (xz-): 15 found - 15 modified | TOTAL: 100
- pass 2 (xz-): 0 found - 15 modified | TOTAL: 100
- Iteration Number : 1
- pass 1 (+++): 23 found - 23 modified | TOTAL: 23
- pass 2 (+++): 0 found - 23 modified | TOTAL: 23
- pass 1 (+++): 22 found - 22 modified | TOTAL: 45
- pass 2 (+++): 0 found - 22 modified | TOTAL: 45
- pass 1 (+++): 19 found - 19 modified | TOTAL: 64
- pass 2 (+++): 0 found - 19 modified | TOTAL: 64
- pass 1 (+++): 20 found - 20 modified | TOTAL: 84
- pass 2 (+++): 0 found - 20 modified | TOTAL: 84
- Iteration Number : 1
- pass 1 (++): 47 found - 47 modified | TOTAL: 47
- pass 2 (++): 0 found - 47 modified | TOTAL: 47
- pass 1 (+-): 49 found - 49 modified | TOTAL: 96
- pass 2 (+-): 0 found - 49 modified | TOTAL: 96
- pass 1 (--): 62 found - 62 modified | TOTAL: 158
- pass 2 (--): 0 found - 62 modified | TOTAL: 158
- pass 1 (-+): 43 found - 43 modified | TOTAL: 201
- pass 2 (-+): 0 found - 43 modified | TOTAL: 201
- Iteration Number : 2
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 2 found - 2 modified | TOTAL: 5
- pass 2 (xy-): 0 found - 2 modified | TOTAL: 5
- pass 1 (yz+): 4 found - 4 modified | TOTAL: 9
- pass 2 (yz+): 0 found - 4 modified | TOTAL: 9
- pass 1 (yz-): 8 found - 8 modified | TOTAL: 17
- pass 2 (yz-): 0 found - 8 modified | TOTAL: 17
- pass 1 (xz+): 3 found - 3 modified | TOTAL: 20
- pass 2 (xz+): 0 found - 3 modified | TOTAL: 20
- pass 1 (xz-): 3 found - 3 modified | TOTAL: 23
- pass 2 (xz-): 0 found - 3 modified | TOTAL: 23
- 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 (+++): 2 found - 2 modified | TOTAL: 6
- pass 2 (+++): 0 found - 2 modified | TOTAL: 6
- pass 1 (+++): 0 found - 0 modified | TOTAL: 6
- Iteration Number : 2
- pass 1 (++): 3 found - 3 modified | TOTAL: 3
- pass 2 (++): 0 found - 3 modified | TOTAL: 3
- pass 1 (+-): 0 found - 0 modified | TOTAL: 3
- pass 1 (--): 1 found - 1 modified | TOTAL: 4
- pass 2 (--): 0 found - 1 modified | TOTAL: 4
- pass 1 (-+): 2 found - 2 modified | TOTAL: 6
- pass 2 (-+): 0 found - 2 modified | TOTAL: 6
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 1 found - 1 modified | TOTAL: 1
- pass 2 (-+): 0 found - 1 modified | TOTAL: 1
- Iteration Number : 4
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 422 (out of 494954: 0.085260)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Sun Oct 8 03:32:47 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
- logging cutting plane coordinates to ../scripts/ponscc.cut.log...
- INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
- using segmentation aseg.auto_noCCseg.mgz...
- reading input volume...done.
- searching for cutting planes...voxel to talairach voxel transform
- 1.07230 -0.00181 -0.03731 -0.61850;
- -0.00532 1.18308 0.09912 -41.13858;
- 0.03495 -0.11142 1.00566 -7.13951;
- 0.00000 0.00000 0.00000 1.00000;
- voxel to talairach voxel transform
- 1.07230 -0.00181 -0.03731 -0.61850;
- -0.00532 1.18308 0.09912 -41.13858;
- 0.03495 -0.11142 1.00566 -7.13951;
- 0.00000 0.00000 0.00000 1.00000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1025 (min = 350, max = 1400), aspect = 0.59 (min = 0.10, max = 0.75)
- no need to search
- using seed (126, 124, 150), TAL = (2.0, 22.0, 4.0)
- talairach voxel to voxel transform
- 0.93148 0.00464 0.03410 1.01048;
- 0.00684 0.83751 -0.08230 33.87076;
- -0.03162 0.09263 0.98407 10.81677;
- 0.00000 0.00000 0.00000 1.00000;
- segmentation indicates cc at (126, 124, 150) --> (2.0, 22.0, 4.0)
- done.
- writing output to filled.mgz...
- filling took 0.6 minutes
- talairach cc position changed to (2.00, 22.00, 4.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, 22.00, 4.00) SRC: (107.30, 126.12, 166.50)
- search lh wm seed point around talairach space (-16.00, 22.00, 4.00), SRC: (140.83, 126.36, 165.36)
- compute mri_fill using aseg
- Erasing Brain Stem and Cerebellum ...
- Define left and right masks using aseg:
- Building Voronoi diagram ...
- Using the Voronoi diagram to separate WM into two hemispheres ...
- Find the largest connected component for each hemisphere ...
- #--------------------------------------------
- #@# Tessellate lh Sun Oct 8 03:33:25 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 4 found - 4 modified | TOTAL: 4
- pass 2 (xy-): 0 found - 4 modified | TOTAL: 4
- pass 1 (yz+): 7 found - 7 modified | TOTAL: 11
- pass 2 (yz+): 0 found - 7 modified | TOTAL: 11
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 11
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 13
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 13
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 14
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 14
- 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 (+-): 1 found - 1 modified | TOTAL: 2
- pass 2 (+-): 0 found - 1 modified | TOTAL: 2
- pass 1 (--): 0 found - 0 modified | TOTAL: 2
- pass 1 (-+): 0 found - 0 modified | TOTAL: 2
- 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 = 16 (out of 239828: 0.006671)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- slice 50: 787 vertices, 890 faces
- slice 60: 5514 vertices, 5712 faces
- slice 70: 12242 vertices, 12482 faces
- slice 80: 19881 vertices, 20184 faces
- slice 90: 28648 vertices, 29000 faces
- slice 100: 38060 vertices, 38398 faces
- slice 110: 48321 vertices, 48696 faces
- slice 120: 59435 vertices, 59822 faces
- slice 130: 70342 vertices, 70738 faces
- slice 140: 81018 vertices, 81449 faces
- slice 150: 91371 vertices, 91757 faces
- slice 160: 99522 vertices, 99874 faces
- slice 170: 106595 vertices, 106935 faces
- slice 180: 113091 vertices, 113384 faces
- slice 190: 118535 vertices, 118781 faces
- slice 200: 122980 vertices, 123192 faces
- slice 210: 124943 vertices, 125045 faces
- slice 220: 124968 vertices, 125060 faces
- slice 230: 124968 vertices, 125060 faces
- slice 240: 124968 vertices, 125060 faces
- slice 250: 124968 vertices, 125060 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...
- 124968 voxel in cpt #1: X=-92 [v=124968,e=375180,f=250120] located at (-20.971233, -5.387883, 5.483764)
- For the whole surface: X=-92 [v=124968,e=375180,f=250120]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Tessellate rh Sun Oct 8 03:33:30 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 2
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 2
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 1 found - 1 modified | TOTAL: 1
- pass 2 (-+): 0 found - 1 modified | TOTAL: 1
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 3 (out of 235717: 0.001273)
- 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 50: 581 vertices, 641 faces
- slice 60: 3873 vertices, 4036 faces
- slice 70: 10230 vertices, 10471 faces
- slice 80: 18138 vertices, 18446 faces
- slice 90: 26579 vertices, 26906 faces
- slice 100: 36547 vertices, 36887 faces
- slice 110: 46973 vertices, 47374 faces
- slice 120: 57882 vertices, 58267 faces
- slice 130: 68735 vertices, 69131 faces
- slice 140: 79728 vertices, 80161 faces
- slice 150: 90023 vertices, 90416 faces
- slice 160: 98279 vertices, 98641 faces
- slice 170: 105186 vertices, 105520 faces
- slice 180: 111657 vertices, 111972 faces
- slice 190: 117191 vertices, 117462 faces
- slice 200: 121583 vertices, 121815 faces
- slice 210: 123462 vertices, 123566 faces
- slice 220: 123462 vertices, 123566 faces
- slice 230: 123462 vertices, 123566 faces
- slice 240: 123462 vertices, 123566 faces
- slice 250: 123462 vertices, 123566 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...
- 123462 voxel in cpt #1: X=-104 [v=123462,e=370698,f=247132] located at (31.876286, -4.478074, 9.574388)
- For the whole surface: X=-104 [v=123462,e=370698,f=247132]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Sun Oct 8 03:33:35 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- #--------------------------------------------
- #@# Smooth1 rh Sun Oct 8 03:33:35 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- Waiting for PID 24419 of (24419 24422) to complete...
- Waiting for PID 24422 of (24419 24422) 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 (24419 24422) completed and logs appended.
- #--------------------------------------------
- #@# Inflation1 lh Sun Oct 8 03:33:40 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- #--------------------------------------------
- #@# Inflation1 rh Sun Oct 8 03:33:40 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Waiting for PID 24467 of (24467 24470) to complete...
- Waiting for PID 24470 of (24467 24470) to complete...
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- Not saving sulc
- Reading ../surf/lh.smoothwm.nofix
- avg radius = 45.7 mm, total surface area = 66573 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.7 minutes
-
step 000: RMS=0.160 (target=0.015)
step 005: RMS=0.123 (target=0.015)
step 010: RMS=0.096 (target=0.015)
step 015: RMS=0.084 (target=0.015)
step 020: RMS=0.074 (target=0.015)
step 025: RMS=0.069 (target=0.015)
step 030: RMS=0.063 (target=0.015)
step 035: RMS=0.059 (target=0.015)
step 040: RMS=0.057 (target=0.015)
step 045: RMS=0.055 (target=0.015)
step 050: RMS=0.055 (target=0.015)
step 055: RMS=0.054 (target=0.015)
step 060: RMS=0.054 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 39.250033
- mris_inflate stimesec 0.101984
- mris_inflate ru_maxrss 183332
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 26862
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 8816
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2141
- mris_inflate ru_nivcsw 3069
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Not saving sulc
- Reading ../surf/rh.smoothwm.nofix
- avg radius = 44.8 mm, total surface area = 65650 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.7 minutes
-
step 000: RMS=0.160 (target=0.015)
step 005: RMS=0.124 (target=0.015)
step 010: RMS=0.097 (target=0.015)
step 015: RMS=0.084 (target=0.015)
step 020: RMS=0.075 (target=0.015)
step 025: RMS=0.068 (target=0.015)
step 030: RMS=0.063 (target=0.015)
step 035: RMS=0.058 (target=0.015)
step 040: RMS=0.056 (target=0.015)
step 045: RMS=0.054 (target=0.015)
step 050: RMS=0.054 (target=0.015)
step 055: RMS=0.053 (target=0.015)
step 060: RMS=0.052 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 39.031066
- mris_inflate stimesec 0.088986
- mris_inflate ru_maxrss 181220
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 26333
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 8688
- mris_inflate ru_oublock 8712
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 1948
- mris_inflate ru_nivcsw 3063
- PIDs (24467 24470) completed and logs appended.
- #--------------------------------------------
- #@# QSphere lh Sun Oct 8 03:34:20 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- #--------------------------------------------
- #@# QSphere rh Sun Oct 8 03:34:20 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- Waiting for PID 24538 of (24538 24541) to complete...
- Waiting for PID 24541 of (24538 24541) to complete...
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 1.02 +- 0.60 (0.00-->6.41) (max @ vno 44761 --> 45743)
- face area 0.03 +- 0.03 (-0.14-->0.50)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.310...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=177.508, avgs=0
- 005/300: dt: 0.9000, rms radial error=177.247, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.686, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.949, avgs=0
- 020/300: dt: 0.9000, rms radial error=175.110, avgs=0
- 025/300: dt: 0.9000, rms radial error=174.217, avgs=0
- 030/300: dt: 0.9000, rms radial error=173.295, avgs=0
- 035/300: dt: 0.9000, rms radial error=172.355, avgs=0
- 040/300: dt: 0.9000, rms radial error=171.409, avgs=0
- 045/300: dt: 0.9000, rms radial error=170.460, avgs=0
- 050/300: dt: 0.9000, rms radial error=169.512, avgs=0
- 055/300: dt: 0.9000, rms radial error=168.566, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.624, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.686, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.753, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.824, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.900, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.980, avgs=0
- 090/300: dt: 0.9000, rms radial error=162.066, avgs=0
- 095/300: dt: 0.9000, rms radial error=161.156, avgs=0
- 100/300: dt: 0.9000, rms radial error=160.251, avgs=0
- 105/300: dt: 0.9000, rms radial error=159.351, avgs=0
- 110/300: dt: 0.9000, rms radial error=158.455, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.564, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.678, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.797, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.921, avgs=0
- 135/300: dt: 0.9000, rms radial error=154.050, avgs=0
- 140/300: dt: 0.9000, rms radial error=153.183, avgs=0
- 145/300: dt: 0.9000, rms radial error=152.321, avgs=0
- 150/300: dt: 0.9000, rms radial error=151.464, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.611, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.763, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.919, avgs=0
- 170/300: dt: 0.9000, rms radial error=148.081, avgs=0
- 175/300: dt: 0.9000, rms radial error=147.246, avgs=0
- 180/300: dt: 0.9000, rms radial error=146.417, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.592, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.771, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.955, avgs=0
- 200/300: dt: 0.9000, rms radial error=143.144, avgs=0
- 205/300: dt: 0.9000, rms radial error=142.337, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.534, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.736, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.942, avgs=0
- 225/300: dt: 0.9000, rms radial error=139.153, avgs=0
- 230/300: dt: 0.9000, rms radial error=138.368, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.587, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.811, avgs=0
- 245/300: dt: 0.9000, rms radial error=136.039, avgs=0
- 250/300: dt: 0.9000, rms radial error=135.271, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.508, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.749, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.994, avgs=0
- 270/300: dt: 0.9000, rms radial error=132.243, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.497, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.754, avgs=0
- 285/300: dt: 0.9000, rms radial error=130.016, avgs=0
- 290/300: dt: 0.9000, rms radial error=129.282, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.552, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.827, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 14622.98
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
- epoch 2 (K=40.0), pass 1, starting sse = 2458.43
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
- epoch 3 (K=160.0), pass 1, starting sse = 271.43
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.06/10 = 0.00624
- epoch 4 (K=640.0), pass 1, starting sse = 24.56
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.12/13 = 0.00931
- final distance error %27.23
- writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.06 hours
- mris_sphere utimesec 230.699928
- mris_sphere stimesec 0.170974
- mris_sphere ru_maxrss 183532
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 26916
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 8800
- mris_sphere ru_oublock 8840
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 8618
- mris_sphere ru_nivcsw 16609
- FSRUNTIME@ mris_sphere 0.0641 hours 1 threads
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 1.03 +- 0.59 (0.00-->7.14) (max @ vno 51164 --> 52368)
- face area 0.03 +- 0.03 (-0.32-->0.77)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.311...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=177.637, avgs=0
- 005/300: dt: 0.9000, rms radial error=177.376, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.817, avgs=0
- 015/300: dt: 0.9000, rms radial error=176.082, avgs=0
- 020/300: dt: 0.9000, rms radial error=175.244, avgs=0
- 025/300: dt: 0.9000, rms radial error=174.349, avgs=0
- 030/300: dt: 0.9000, rms radial error=173.420, avgs=0
- 035/300: dt: 0.9000, rms radial error=172.474, avgs=0
- 040/300: dt: 0.9000, rms radial error=171.524, avgs=0
- 045/300: dt: 0.9000, rms radial error=170.573, avgs=0
- 050/300: dt: 0.9000, rms radial error=169.621, avgs=0
- 055/300: dt: 0.9000, rms radial error=168.673, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.728, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.787, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.851, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.919, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.992, avgs=0
- 085/300: dt: 0.9000, rms radial error=163.070, avgs=0
- 090/300: dt: 0.9000, rms radial error=162.153, avgs=0
- 095/300: dt: 0.9000, rms radial error=161.241, avgs=0
- 100/300: dt: 0.9000, rms radial error=160.334, avgs=0
- 105/300: dt: 0.9000, rms radial error=159.432, avgs=0
- 110/300: dt: 0.9000, rms radial error=158.535, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.642, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.755, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.872, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.994, avgs=0
- 135/300: dt: 0.9000, rms radial error=154.121, avgs=0
- 140/300: dt: 0.9000, rms radial error=153.253, avgs=0
- 145/300: dt: 0.9000, rms radial error=152.389, avgs=0
- 150/300: dt: 0.9000, rms radial error=151.531, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.677, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.828, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.984, avgs=0
- 170/300: dt: 0.9000, rms radial error=148.144, avgs=0
- 175/300: dt: 0.9000, rms radial error=147.309, avgs=0
- 180/300: dt: 0.9000, rms radial error=146.479, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.653, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.832, avgs=0
- 195/300: dt: 0.9000, rms radial error=144.015, avgs=0
- 200/300: dt: 0.9000, rms radial error=143.203, avgs=0
- 205/300: dt: 0.9000, rms radial error=142.395, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.592, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.794, avgs=0
- 220/300: dt: 0.9000, rms radial error=140.000, avgs=0
- 225/300: dt: 0.9000, rms radial error=139.210, avgs=0
- 230/300: dt: 0.9000, rms radial error=138.424, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.644, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.867, avgs=0
- 245/300: dt: 0.9000, rms radial error=136.095, avgs=0
- 250/300: dt: 0.9000, rms radial error=135.327, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.563, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.804, avgs=0
- 265/300: dt: 0.9000, rms radial error=133.049, avgs=0
- 270/300: dt: 0.9000, rms radial error=132.298, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.551, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.809, avgs=0
- 285/300: dt: 0.9000, rms radial error=130.070, avgs=0
- 290/300: dt: 0.9000, rms radial error=129.336, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.606, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.880, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 14404.58
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00013
- epoch 2 (K=40.0), pass 1, starting sse = 2387.69
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00008
- epoch 3 (K=160.0), pass 1, starting sse = 253.66
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.05/10 = 0.00535
- epoch 4 (K=640.0), pass 1, starting sse = 23.20
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.13/14 = 0.00944
- final distance error %26.27
- writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.06 hours
- mris_sphere utimesec 231.958736
- mris_sphere stimesec 0.164974
- mris_sphere ru_maxrss 181424
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 26390
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 8696
- mris_sphere ru_oublock 8736
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 8905
- mris_sphere ru_nivcsw 16881
- FSRUNTIME@ mris_sphere 0.0644 hours 1 threads
- PIDs (24538 24541) completed and logs appended.
- #--------------------------------------------
- #@# Fix Topology Copy lh Sun Oct 8 03:38:12 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- #--------------------------------------------
- #@# Fix Topology Copy rh Sun Oct 8 03:38:12 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- #@# Fix Topology lh Sun Oct 8 03:38:12 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050340 lh
- #@# Fix Topology rh Sun Oct 8 03:38:12 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050340 rh
- Waiting for PID 24728 of (24728 24731) to complete...
- Waiting for PID 24731 of (24728 24731) to complete...
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050340 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=-92 (nv=124968, nf=250120, ne=375180, g=47)
- 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...
- 7832 ambiguous faces found in tessellation
- segmenting defects...
- 55 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 6 into 5
- -merging segment 7 into 5
- -merging segment 27 into 22
- 52 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.0920 (-4.5460)
- -vertex loglikelihood: -6.0931 (-3.0466)
- -normal dot loglikelihood: -3.6001 (-3.6001)
- -quad curv loglikelihood: -6.1614 (-3.0807)
- Total Loglikelihood : -24.9466
- CORRECTING DEFECT 0 (vertices=122, convex hull=159, v0=4)
- After retessellation of defect 0 (v0=4), euler #=-49 (120306,359259,238904) : difference with theory (-49) = 0
- CORRECTING DEFECT 1 (vertices=36, convex hull=60, v0=745)
- After retessellation of defect 1 (v0=745), euler #=-48 (120324,359336,238964) : difference with theory (-48) = 0
- CORRECTING DEFECT 2 (vertices=51, convex hull=52, v0=3297)
- After retessellation of defect 2 (v0=3297), euler #=-47 (120336,359393,239010) : difference with theory (-47) = 0
- CORRECTING DEFECT 3 (vertices=71, convex hull=107, v0=4039)
- After retessellation of defect 3 (v0=4039), euler #=-46 (120377,359566,239143) : difference with theory (-46) = 0
- CORRECTING DEFECT 4 (vertices=202, convex hull=181, v0=5987)
- After retessellation of defect 4 (v0=5987), euler #=-45 (120459,359892,239388) : difference with theory (-45) = 0
- CORRECTING DEFECT 5 (vertices=102, convex hull=95, v0=9623)
- After retessellation of defect 5 (v0=9623), euler #=-42 (120476,359986,239468) : difference with theory (-44) = -2
- CORRECTING DEFECT 6 (vertices=25, convex hull=20, v0=12249)
- After retessellation of defect 6 (v0=12249), euler #=-41 (120478,359997,239478) : difference with theory (-43) = -2
- CORRECTING DEFECT 7 (vertices=6, convex hull=20, v0=20649)
- After retessellation of defect 7 (v0=20649), euler #=-40 (120479,360006,239487) : difference with theory (-42) = -2
- CORRECTING DEFECT 8 (vertices=42, convex hull=80, v0=24189)
- After retessellation of defect 8 (v0=24189), euler #=-39 (120505,360116,239572) : difference with theory (-41) = -2
- CORRECTING DEFECT 9 (vertices=78, convex hull=89, v0=25556)
- After retessellation of defect 9 (v0=25556), euler #=-38 (120529,360224,239657) : difference with theory (-40) = -2
- CORRECTING DEFECT 10 (vertices=16, convex hull=49, v0=27582)
- After retessellation of defect 10 (v0=27582), euler #=-37 (120539,360272,239696) : difference with theory (-39) = -2
- CORRECTING DEFECT 11 (vertices=29, convex hull=34, v0=30291)
- After retessellation of defect 11 (v0=30291), euler #=-36 (120543,360293,239714) : difference with theory (-38) = -2
- CORRECTING DEFECT 12 (vertices=158, convex hull=135, v0=41134)
- After retessellation of defect 12 (v0=41134), euler #=-35 (120577,360467,239855) : difference with theory (-37) = -2
- CORRECTING DEFECT 13 (vertices=307, convex hull=180, v0=41862)
- After retessellation of defect 13 (v0=41862), euler #=-35 (120695,360908,240178) : difference with theory (-36) = -1
- CORRECTING DEFECT 14 (vertices=75, convex hull=104, v0=42564)
- After retessellation of defect 14 (v0=42564), euler #=-34 (120739,361087,240314) : difference with theory (-35) = -1
- CORRECTING DEFECT 15 (vertices=16, convex hull=32, v0=48028)
- After retessellation of defect 15 (v0=48028), euler #=-33 (120742,361111,240336) : difference with theory (-34) = -1
- CORRECTING DEFECT 16 (vertices=39, convex hull=31, v0=50635)
- After retessellation of defect 16 (v0=50635), euler #=-32 (120745,361131,240354) : difference with theory (-33) = -1
- CORRECTING DEFECT 17 (vertices=44, convex hull=60, v0=55166)
- After retessellation of defect 17 (v0=55166), euler #=-31 (120763,361209,240415) : difference with theory (-32) = -1
- CORRECTING DEFECT 18 (vertices=10, convex hull=22, v0=57249)
- After retessellation of defect 18 (v0=57249), euler #=-30 (120764,361222,240428) : difference with theory (-31) = -1
- CORRECTING DEFECT 19 (vertices=6, convex hull=25, v0=60336)
- After retessellation of defect 19 (v0=60336), euler #=-29 (120767,361240,240444) : difference with theory (-30) = -1
- CORRECTING DEFECT 20 (vertices=64, convex hull=125, v0=62696)
- After retessellation of defect 20 (v0=62696), euler #=-27 (120805,361410,240578) : difference with theory (-29) = -2
- CORRECTING DEFECT 21 (vertices=73, convex hull=37, v0=64923)
- After retessellation of defect 21 (v0=64923), euler #=-26 (120813,361446,240607) : difference with theory (-28) = -2
- CORRECTING DEFECT 22 (vertices=23, convex hull=43, v0=67088)
- After retessellation of defect 22 (v0=67088), euler #=-25 (120815,361467,240627) : difference with theory (-27) = -2
- CORRECTING DEFECT 23 (vertices=18, convex hull=58, v0=67435)
- After retessellation of defect 23 (v0=67435), euler #=-24 (120824,361516,240668) : difference with theory (-26) = -2
- CORRECTING DEFECT 24 (vertices=57, convex hull=57, v0=67848)
- After retessellation of defect 24 (v0=67848), euler #=-23 (120833,361567,240711) : difference with theory (-25) = -2
- CORRECTING DEFECT 25 (vertices=54, convex hull=98, v0=70710)
- After retessellation of defect 25 (v0=70710), euler #=-22 (120868,361712,240822) : difference with theory (-24) = -2
- CORRECTING DEFECT 26 (vertices=76, convex hull=49, v0=73412)
- After retessellation of defect 26 (v0=73412), euler #=-21 (120879,361765,240865) : difference with theory (-23) = -2
- CORRECTING DEFECT 27 (vertices=1168, convex hull=358, v0=75111)
- L defect detected...
- After retessellation of defect 27 (v0=75111), euler #=-22 (121120,362692,241550) : difference with theory (-22) = 0
- CORRECTING DEFECT 28 (vertices=15, convex hull=28, v0=75460)
- After retessellation of defect 28 (v0=75460), euler #=-21 (121122,362711,241568) : difference with theory (-21) = 0
- CORRECTING DEFECT 29 (vertices=37, convex hull=58, v0=75477)
- After retessellation of defect 29 (v0=75477), euler #=-20 (121136,362778,241622) : difference with theory (-20) = 0
- CORRECTING DEFECT 30 (vertices=59, convex hull=44, v0=76462)
- After retessellation of defect 30 (v0=76462), euler #=-19 (121144,362818,241655) : difference with theory (-19) = 0
- CORRECTING DEFECT 31 (vertices=32, convex hull=69, v0=79845)
- After retessellation of defect 31 (v0=79845), euler #=-18 (121160,362897,241719) : difference with theory (-18) = 0
- CORRECTING DEFECT 32 (vertices=34, convex hull=27, v0=79857)
- After retessellation of defect 32 (v0=79857), euler #=-17 (121165,362922,241740) : difference with theory (-17) = 0
- CORRECTING DEFECT 33 (vertices=51, convex hull=60, v0=81033)
- After retessellation of defect 33 (v0=81033), euler #=-16 (121193,363030,241821) : difference with theory (-16) = 0
- CORRECTING DEFECT 34 (vertices=40, convex hull=60, v0=81921)
- After retessellation of defect 34 (v0=81921), euler #=-15 (121207,363092,241870) : difference with theory (-15) = 0
- CORRECTING DEFECT 35 (vertices=50, convex hull=33, v0=84494)
- After retessellation of defect 35 (v0=84494), euler #=-14 (121217,363137,241906) : difference with theory (-14) = 0
- CORRECTING DEFECT 36 (vertices=87, convex hull=89, v0=88513)
- After retessellation of defect 36 (v0=88513), euler #=-13 (121257,363296,242026) : difference with theory (-13) = 0
- CORRECTING DEFECT 37 (vertices=149, convex hull=79, v0=89545)
- After retessellation of defect 37 (v0=89545), euler #=-12 (121293,363448,242143) : difference with theory (-12) = 0
- CORRECTING DEFECT 38 (vertices=59, convex hull=73, v0=89949)
- After retessellation of defect 38 (v0=89949), euler #=-11 (121307,363524,242206) : difference with theory (-11) = 0
- CORRECTING DEFECT 39 (vertices=69, convex hull=52, v0=90096)
- After retessellation of defect 39 (v0=90096), euler #=-10 (121314,363564,242240) : difference with theory (-10) = 0
- CORRECTING DEFECT 40 (vertices=26, convex hull=37, v0=90120)
- After retessellation of defect 40 (v0=90120), euler #=-9 (121317,363582,242256) : difference with theory (-9) = 0
- CORRECTING DEFECT 41 (vertices=98, convex hull=108, v0=90982)
- After retessellation of defect 41 (v0=90982), euler #=-8 (121347,363718,242363) : difference with theory (-8) = 0
- CORRECTING DEFECT 42 (vertices=72, convex hull=86, v0=95506)
- After retessellation of defect 42 (v0=95506), euler #=-7 (121376,363842,242459) : difference with theory (-7) = 0
- CORRECTING DEFECT 43 (vertices=478, convex hull=206, v0=97016)
- After retessellation of defect 43 (v0=97016), euler #=-6 (121519,364376,242851) : difference with theory (-6) = 0
- CORRECTING DEFECT 44 (vertices=159, convex hull=118, v0=97136)
- After retessellation of defect 44 (v0=97136), euler #=-5 (121572,364595,243018) : difference with theory (-5) = 0
- CORRECTING DEFECT 45 (vertices=25, convex hull=37, v0=100921)
- After retessellation of defect 45 (v0=100921), euler #=-4 (121578,364626,243044) : difference with theory (-4) = 0
- CORRECTING DEFECT 46 (vertices=39, convex hull=41, v0=105880)
- After retessellation of defect 46 (v0=105880), euler #=-3 (121585,364661,243073) : difference with theory (-3) = 0
- CORRECTING DEFECT 47 (vertices=25, convex hull=23, v0=108565)
- After retessellation of defect 47 (v0=108565), euler #=-2 (121586,364672,243084) : difference with theory (-2) = 0
- CORRECTING DEFECT 48 (vertices=38, convex hull=85, v0=116217)
- After retessellation of defect 48 (v0=116217), euler #=-1 (121609,364779,243169) : difference with theory (-1) = 0
- CORRECTING DEFECT 49 (vertices=36, convex hull=81, v0=121942)
- After retessellation of defect 49 (v0=121942), euler #=0 (121620,364845,243225) : difference with theory (0) = 0
- CORRECTING DEFECT 50 (vertices=6, convex hull=13, v0=124753)
- After retessellation of defect 50 (v0=124753), euler #=1 (121620,364848,243229) : difference with theory (1) = 0
- CORRECTING DEFECT 51 (vertices=56, convex hull=22, v0=124828)
- After retessellation of defect 51 (v0=124828), euler #=2 (121622,364860,243240) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.89 +- 0.24 (0.07-->8.69) (max @ vno 6316 --> 10975)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.89 +- 0.24 (0.07-->8.69) (max @ vno 6316 --> 10975)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 179 mutations (35.0%), 333 crossovers (65.0%), 127 vertices were eliminated
- building final representation...
- 3346 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=121622, nf=243240, ne=364860, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 26.9 minutes
- 0 defective edges
- removing intersecting faces
- 000: 413 intersecting
- 001: 5 intersecting
- mris_fix_topology utimesec 1615.864351
- mris_fix_topology stimesec 0.318951
- mris_fix_topology ru_maxrss 404520
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 54583
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 24160
- mris_fix_topology ru_oublock 11784
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 415
- mris_fix_topology ru_nivcsw 3476
- FSRUNTIME@ mris_fix_topology lh 0.4488 hours 1 threads
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050340 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=-104 (nv=123462, nf=247132, ne=370698, g=53)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 7258 ambiguous faces found in tessellation
- segmenting defects...
- 55 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 6 into 5
- -merging segment 32 into 26
- -merging segment 42 into 40
- 52 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.0936 (-4.5468)
- -vertex loglikelihood: -6.0727 (-3.0363)
- -normal dot loglikelihood: -3.5928 (-3.5928)
- -quad curv loglikelihood: -6.1123 (-3.0562)
- Total Loglikelihood : -24.8713
- CORRECTING DEFECT 0 (vertices=191, convex hull=97, v0=0)
- After retessellation of defect 0 (v0=0), euler #=-49 (119160,355975,236766) : difference with theory (-49) = 0
- CORRECTING DEFECT 1 (vertices=140, convex hull=147, v0=231)
- After retessellation of defect 1 (v0=231), euler #=-49 (119206,356192,236937) : difference with theory (-48) = 1
- CORRECTING DEFECT 2 (vertices=6, convex hull=35, v0=349)
- After retessellation of defect 2 (v0=349), euler #=-48 (119208,356208,236952) : difference with theory (-47) = 1
- CORRECTING DEFECT 3 (vertices=32, convex hull=44, v0=509)
- After retessellation of defect 3 (v0=509), euler #=-47 (119213,356244,236984) : difference with theory (-46) = 1
- CORRECTING DEFECT 4 (vertices=77, convex hull=126, v0=1062)
- After retessellation of defect 4 (v0=1062), euler #=-46 (119261,356445,237138) : difference with theory (-45) = 1
- CORRECTING DEFECT 5 (vertices=65, convex hull=111, v0=6450)
- After retessellation of defect 5 (v0=6450), euler #=-44 (119279,356539,237216) : difference with theory (-44) = 0
- CORRECTING DEFECT 6 (vertices=55, convex hull=87, v0=10951)
- After retessellation of defect 6 (v0=10951), euler #=-43 (119294,356623,237286) : difference with theory (-43) = 0
- CORRECTING DEFECT 7 (vertices=24, convex hull=52, v0=12493)
- After retessellation of defect 7 (v0=12493), euler #=-42 (119309,356690,237339) : difference with theory (-42) = 0
- CORRECTING DEFECT 8 (vertices=131, convex hull=134, v0=14566)
- After retessellation of defect 8 (v0=14566), euler #=-41 (119344,356857,237472) : difference with theory (-41) = 0
- CORRECTING DEFECT 9 (vertices=35, convex hull=74, v0=17414)
- After retessellation of defect 9 (v0=17414), euler #=-40 (119368,356955,237547) : difference with theory (-40) = 0
- CORRECTING DEFECT 10 (vertices=36, convex hull=64, v0=20478)
- After retessellation of defect 10 (v0=20478), euler #=-39 (119391,357049,237619) : difference with theory (-39) = 0
- CORRECTING DEFECT 11 (vertices=29, convex hull=61, v0=22052)
- After retessellation of defect 11 (v0=22052), euler #=-38 (119400,357101,237663) : difference with theory (-38) = 0
- CORRECTING DEFECT 12 (vertices=36, convex hull=79, v0=27589)
- After retessellation of defect 12 (v0=27589), euler #=-37 (119411,357164,237716) : difference with theory (-37) = 0
- CORRECTING DEFECT 13 (vertices=441, convex hull=224, v0=41063)
- normal vector of length zero at vertex 120259 with 3 faces
- After retessellation of defect 13 (v0=41063), euler #=-36 (119434,357344,237874) : difference with theory (-36) = 0
- CORRECTING DEFECT 14 (vertices=22, convex hull=63, v0=41688)
- After retessellation of defect 14 (v0=41688), euler #=-35 (119443,357397,237919) : difference with theory (-35) = 0
- CORRECTING DEFECT 15 (vertices=26, convex hull=20, v0=43681)
- After retessellation of defect 15 (v0=43681), euler #=-34 (119444,357402,237924) : difference with theory (-34) = 0
- CORRECTING DEFECT 16 (vertices=30, convex hull=58, v0=51313)
- After retessellation of defect 16 (v0=51313), euler #=-33 (119453,357449,237963) : difference with theory (-33) = 0
- CORRECTING DEFECT 17 (vertices=33, convex hull=27, v0=56426)
- After retessellation of defect 17 (v0=56426), euler #=-32 (119454,357462,237976) : difference with theory (-32) = 0
- CORRECTING DEFECT 18 (vertices=32, convex hull=49, v0=57780)
- After retessellation of defect 18 (v0=57780), euler #=-31 (119464,357508,238013) : difference with theory (-31) = 0
- CORRECTING DEFECT 19 (vertices=23, convex hull=52, v0=57915)
- After retessellation of defect 19 (v0=57915), euler #=-30 (119473,357555,238052) : difference with theory (-30) = 0
- CORRECTING DEFECT 20 (vertices=15, convex hull=36, v0=58898)
- After retessellation of defect 20 (v0=58898), euler #=-29 (119476,357578,238073) : difference with theory (-29) = 0
- CORRECTING DEFECT 21 (vertices=14, convex hull=34, v0=60079)
- After retessellation of defect 21 (v0=60079), euler #=-28 (119478,357592,238086) : difference with theory (-28) = 0
- CORRECTING DEFECT 22 (vertices=64, convex hull=105, v0=63718)
- After retessellation of defect 22 (v0=63718), euler #=-27 (119501,357710,238182) : difference with theory (-27) = 0
- CORRECTING DEFECT 23 (vertices=11, convex hull=32, v0=65605)
- After retessellation of defect 23 (v0=65605), euler #=-26 (119502,357723,238195) : difference with theory (-26) = 0
- CORRECTING DEFECT 24 (vertices=54, convex hull=38, v0=67771)
- After retessellation of defect 24 (v0=67771), euler #=-25 (119506,357749,238218) : difference with theory (-25) = 0
- CORRECTING DEFECT 25 (vertices=128, convex hull=141, v0=70958)
- After retessellation of defect 25 (v0=70958), euler #=-23 (119576,358033,238434) : difference with theory (-24) = -1
- CORRECTING DEFECT 26 (vertices=15, convex hull=25, v0=70962)
- After retessellation of defect 26 (v0=70962), euler #=-22 (119578,358047,238447) : difference with theory (-23) = -1
- CORRECTING DEFECT 27 (vertices=56, convex hull=55, v0=73069)
- After retessellation of defect 27 (v0=73069), euler #=-21 (119585,358088,238482) : difference with theory (-22) = -1
- CORRECTING DEFECT 28 (vertices=34, convex hull=70, v0=73739)
- After retessellation of defect 28 (v0=73739), euler #=-20 (119599,358158,238539) : difference with theory (-21) = -1
- CORRECTING DEFECT 29 (vertices=1386, convex hull=428, v0=74973)
- L defect detected...
- After retessellation of defect 29 (v0=74973), euler #=-21 (119682,358647,238944) : difference with theory (-20) = 1
- CORRECTING DEFECT 30 (vertices=46, convex hull=24, v0=75296)
- After retessellation of defect 30 (v0=75296), euler #=-20 (119688,358672,238964) : difference with theory (-19) = 1
- CORRECTING DEFECT 31 (vertices=24, convex hull=32, v0=79165)
- After retessellation of defect 31 (v0=79165), euler #=-19 (119692,358695,238984) : difference with theory (-18) = 1
- CORRECTING DEFECT 32 (vertices=18, convex hull=45, v0=85108)
- After retessellation of defect 32 (v0=85108), euler #=-18 (119702,358737,239017) : difference with theory (-17) = 1
- CORRECTING DEFECT 33 (vertices=30, convex hull=30, v0=89829)
- After retessellation of defect 33 (v0=89829), euler #=-17 (119707,358763,239039) : difference with theory (-16) = 1
- CORRECTING DEFECT 34 (vertices=10, convex hull=17, v0=90543)
- After retessellation of defect 34 (v0=90543), euler #=-16 (119709,358774,239049) : difference with theory (-15) = 1
- CORRECTING DEFECT 35 (vertices=20, convex hull=23, v0=92414)
- After retessellation of defect 35 (v0=92414), euler #=-15 (119713,358792,239064) : difference with theory (-14) = 1
- CORRECTING DEFECT 36 (vertices=45, convex hull=65, v0=93547)
- After retessellation of defect 36 (v0=93547), euler #=-14 (119731,358869,239124) : difference with theory (-13) = 1
- CORRECTING DEFECT 37 (vertices=269, convex hull=73, v0=95882)
- After retessellation of defect 37 (v0=95882), euler #=-13 (119750,358958,239195) : difference with theory (-12) = 1
- CORRECTING DEFECT 38 (vertices=120, convex hull=102, v0=96542)
- After retessellation of defect 38 (v0=96542), euler #=-11 (119795,359143,239337) : difference with theory (-11) = 0
- CORRECTING DEFECT 39 (vertices=5, convex hull=22, v0=96568)
- After retessellation of defect 39 (v0=96568), euler #=-10 (119795,359154,239349) : difference with theory (-10) = 0
- CORRECTING DEFECT 40 (vertices=30, convex hull=76, v0=98999)
- After retessellation of defect 40 (v0=98999), euler #=-9 (119811,359231,239411) : difference with theory (-9) = 0
- CORRECTING DEFECT 41 (vertices=17, convex hull=50, v0=101119)
- After retessellation of defect 41 (v0=101119), euler #=-8 (119819,359271,239444) : difference with theory (-8) = 0
- CORRECTING DEFECT 42 (vertices=10, convex hull=20, v0=103651)
- After retessellation of defect 42 (v0=103651), euler #=-7 (119819,359276,239450) : difference with theory (-7) = 0
- CORRECTING DEFECT 43 (vertices=75, convex hull=28, v0=107800)
- After retessellation of defect 43 (v0=107800), euler #=-6 (119823,359297,239468) : difference with theory (-6) = 0
- CORRECTING DEFECT 44 (vertices=22, convex hull=43, v0=110408)
- After retessellation of defect 44 (v0=110408), euler #=-5 (119832,359337,239500) : difference with theory (-5) = 0
- CORRECTING DEFECT 45 (vertices=6, convex hull=23, v0=110985)
- After retessellation of defect 45 (v0=110985), euler #=-4 (119834,359348,239510) : difference with theory (-4) = 0
- CORRECTING DEFECT 46 (vertices=41, convex hull=67, v0=112905)
- After retessellation of defect 46 (v0=112905), euler #=-3 (119849,359421,239569) : difference with theory (-3) = 0
- CORRECTING DEFECT 47 (vertices=53, convex hull=25, v0=115711)
- After retessellation of defect 47 (v0=115711), euler #=-2 (119852,359438,239584) : difference with theory (-2) = 0
- CORRECTING DEFECT 48 (vertices=47, convex hull=80, v0=119603)
- After retessellation of defect 48 (v0=119603), euler #=-1 (119874,359537,239662) : difference with theory (-1) = 0
- CORRECTING DEFECT 49 (vertices=55, convex hull=75, v0=122019)
- After retessellation of defect 49 (v0=122019), euler #=0 (119891,359621,239730) : difference with theory (0) = 0
- CORRECTING DEFECT 50 (vertices=88, convex hull=39, v0=122736)
- After retessellation of defect 50 (v0=122736), euler #=1 (119898,359657,239760) : difference with theory (1) = 0
- CORRECTING DEFECT 51 (vertices=38, convex hull=78, v0=122896)
- After retessellation of defect 51 (v0=122896), euler #=2 (119917,359745,239830) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.89 +- 0.26 (0.14-->15.24) (max @ vno 83046 --> 86613)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.89 +- 0.26 (0.14-->15.24) (max @ vno 83046 --> 86613)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 176 mutations (33.0%), 357 crossovers (67.0%), 469 vertices were eliminated
- building final representation...
- 3545 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=119917, nf=239830, ne=359745, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 31.2 minutes
- 0 defective edges
- removing intersecting faces
- 000: 374 intersecting
- mris_fix_topology utimesec 1875.103940
- mris_fix_topology stimesec 0.196970
- mris_fix_topology ru_maxrss 409812
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 57561
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 16376
- mris_fix_topology ru_oublock 11600
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 565
- mris_fix_topology ru_nivcsw 7201
- FSRUNTIME@ mris_fix_topology rh 0.5207 hours 1 threads
- PIDs (24728 24731) completed and logs appended.
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 121622 - 364860 + 243240 = 2 --> 0 holes
- F =2V-4: 243240 = 243244-4 (0)
- 2E=3F: 729720 = 729720 (0)
- total defect index = 0
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 119917 - 359745 + 239830 = 2 --> 0 holes
- F =2V-4: 239830 = 239834-4 (0)
- 2E=3F: 719490 = 719490 (0)
- total defect index = 0
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 125 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 52 intersecting
- 001: 5 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Sun Oct 8 04:09:35 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050340 lh
- #--------------------------------------------
- #@# Make White Surf rh Sun Oct 8 04:09:35 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050340 rh
- Waiting for PID 26761 of (26761 26764) to complete...
- Waiting for PID 26764 of (26761 26764) to complete...
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050340 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-6.0.0/0050340/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- 13065 bright wm thresholded.
- 2133 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.orig...
- computing class statistics...
- border white: 229073 voxels (1.37%)
- border gray 266822 voxels (1.59%)
- WM (97.0): 97.6 +- 7.9 [70.0 --> 110.0]
- GM (75.0) : 73.5 +- 10.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70)
- setting MAX_BORDER_WHITE to 109.9 (was 105)
- setting MIN_BORDER_WHITE to 69.0 (was 85)
- setting MAX_CSF to 48.3 (was 40)
- setting MAX_GRAY to 94.1 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 58.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 38.0 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.23 (0.03-->4.63) (max @ vno 120951 --> 121071)
- face area 0.28 +- 0.13 (0.00-->4.36)
- mean absolute distance = 0.73 +- 0.85
- 3853 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=102+-5.2, GM=69+-9.6
- mean inside = 93.9, mean outside = 77.5
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=80.8, 102 (102) missing vertices, mean dist 0.4 [0.6 (%32.7)->0.8 (%67.3))]
- %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.93 +- 0.25 (0.09-->4.63) (max @ vno 120951 --> 121071)
- face area 0.28 +- 0.13 (0.00-->3.34)
- mean absolute distance = 0.39 +- 0.60
- 4015 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2746584.2, rms=9.776
- 001: dt: 0.5000, sse=1626610.5, rms=6.996 (28.438%)
- 002: dt: 0.5000, sse=1104060.8, rms=5.161 (26.232%)
- 003: dt: 0.5000, sse=862365.1, rms=4.024 (22.022%)
- 004: dt: 0.5000, sse=754096.2, rms=3.382 (15.959%)
- 005: dt: 0.5000, sse=704332.4, rms=3.082 (8.857%)
- 006: dt: 0.5000, sse=683768.4, rms=2.925 (5.115%)
- rms = 2.89, time step reduction 1 of 3 to 0.250...
- 007: dt: 0.5000, sse=678478.6, rms=2.888 (1.249%)
- 008: dt: 0.2500, sse=571379.4, rms=1.808 (37.387%)
- 009: dt: 0.2500, sse=553200.4, rms=1.561 (13.704%)
- 010: dt: 0.2500, sse=549665.9, rms=1.504 (3.629%)
- rms = 1.49, time step reduction 2 of 3 to 0.125...
- 011: dt: 0.2500, sse=560378.8, rms=1.486 (1.176%)
- rms = 1.46, time step reduction 3 of 3 to 0.062...
- 012: dt: 0.1250, sse=546839.4, rms=1.463 (1.578%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- mean border=83.8, 83 (26) missing vertices, mean dist -0.2 [0.4 (%71.7)->0.3 (%28.3))]
- %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 0.91 +- 0.25 (0.10-->4.45) (max @ vno 120627 --> 120657)
- face area 0.36 +- 0.17 (0.00-->4.82)
- mean absolute distance = 0.28 +- 0.43
- 3692 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1099073.4, rms=4.521
- 013: dt: 0.5000, sse=806503.6, rms=2.806 (37.934%)
- 014: dt: 0.5000, sse=767579.4, rms=2.483 (11.513%)
- 015: dt: 0.5000, sse=758735.9, rms=2.429 (2.182%)
- rms = 2.56, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.2500, sse=697135.8, rms=1.770 (27.130%)
- 017: dt: 0.2500, sse=676110.3, rms=1.432 (19.063%)
- 018: dt: 0.2500, sse=670977.6, rms=1.331 (7.065%)
- rms = 1.29, time step reduction 2 of 3 to 0.125...
- 019: dt: 0.2500, sse=662942.6, rms=1.294 (2.827%)
- rms = 1.26, time step reduction 3 of 3 to 0.062...
- 020: dt: 0.1250, sse=660612.9, rms=1.256 (2.942%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=85.4, 78 (9) missing vertices, mean dist -0.1 [0.3 (%64.1)->0.2 (%35.9))]
- %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.08-->4.62) (max @ vno 120627 --> 120657)
- face area 0.34 +- 0.16 (0.00-->4.66)
- mean absolute distance = 0.26 +- 0.37
- 3091 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=771860.5, rms=2.696
- 021: dt: 0.5000, sse=699218.4, rms=1.979 (26.588%)
- rms = 2.04, time step reduction 1 of 3 to 0.250...
- 022: dt: 0.2500, sse=656842.6, rms=1.500 (24.239%)
- 023: dt: 0.2500, sse=644564.8, rms=1.227 (18.153%)
- 024: dt: 0.2500, sse=636800.9, rms=1.162 (5.311%)
- rms = 1.15, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.2500, sse=640807.5, rms=1.152 (0.831%)
- rms = 1.12, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=632838.9, rms=1.120 (2.806%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=86.2, 109 (6) missing vertices, mean dist -0.0 [0.3 (%55.2)->0.2 (%44.8))]
- %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white.preaparc...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=652593.0, rms=1.570
- 027: dt: 0.5000, sse=645520.1, rms=1.372 (12.608%)
- rms = 1.73, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=619799.9, rms=1.015 (26.038%)
- 029: dt: 0.2500, sse=617971.4, rms=0.952 (6.240%)
- 030: dt: 0.2500, sse=612071.6, rms=0.896 (5.849%)
- rms = 0.93, time step reduction 2 of 3 to 0.125...
- rms = 0.88, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=610472.5, rms=0.882 (1.613%)
- positioning took 0.6 minutes
- generating cortex label...
- 9 non-cortical segments detected
- only using segment with 6934 vertices
- erasing segment 1 (vno[0] = 56818)
- erasing segment 2 (vno[0] = 75289)
- erasing segment 3 (vno[0] = 84321)
- erasing segment 4 (vno[0] = 86043)
- erasing segment 5 (vno[0] = 87596)
- erasing segment 6 (vno[0] = 88421)
- erasing segment 7 (vno[0] = 90040)
- erasing segment 8 (vno[0] = 121233)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.area
- vertex spacing 0.90 +- 0.25 (0.04-->4.62) (max @ vno 120627 --> 120657)
- face area 0.34 +- 0.16 (0.00-->4.88)
- refinement took 4.6 minutes
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050340 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-6.0.0/0050340/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- 13065 bright wm thresholded.
- 2133 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.orig...
- computing class statistics...
- border white: 229073 voxels (1.37%)
- border gray 266822 voxels (1.59%)
- WM (97.0): 97.6 +- 7.9 [70.0 --> 110.0]
- GM (75.0) : 73.5 +- 10.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 59.7 (was 70)
- setting MAX_BORDER_WHITE to 108.9 (was 105)
- setting MIN_BORDER_WHITE to 70.0 (was 85)
- setting MAX_CSF to 49.3 (was 40)
- setting MAX_GRAY to 93.1 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 59.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 39.0 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.03-->5.47) (max @ vno 42316 --> 46682)
- face area 0.28 +- 0.13 (0.00-->4.77)
- mean absolute distance = 0.72 +- 0.86
- 3702 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=101+-5.2, GM=70+-8.7
- mean inside = 93.6, mean outside = 77.6
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- mean border=81.1, 116 (116) missing vertices, mean dist 0.3 [0.6 (%34.0)->0.8 (%66.0))]
- %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.08-->7.09) (max @ vno 46682 --> 47728)
- face area 0.28 +- 0.13 (0.00-->6.30)
- mean absolute distance = 0.39 +- 0.62
- 4170 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2599617.2, rms=9.523
- 001: dt: 0.5000, sse=1566268.5, rms=6.868 (27.875%)
- 002: dt: 0.5000, sse=1106555.0, rms=5.155 (24.945%)
- 003: dt: 0.5000, sse=870905.3, rms=4.062 (21.204%)
- 004: dt: 0.5000, sse=746163.3, rms=3.420 (15.810%)
- 005: dt: 0.5000, sse=703175.2, rms=3.127 (8.547%)
- 006: dt: 0.5000, sse=684637.7, rms=2.967 (5.138%)
- 007: dt: 0.5000, sse=677518.5, rms=2.912 (1.857%)
- rms = 2.87, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=669398.0, rms=2.872 (1.373%)
- 009: dt: 0.2500, sse=566995.4, rms=1.832 (36.217%)
- 010: dt: 0.2500, sse=551777.8, rms=1.613 (11.960%)
- 011: dt: 0.2500, sse=546699.8, rms=1.549 (3.962%)
- rms = 1.51, time step reduction 2 of 3 to 0.125...
- 012: dt: 0.2500, sse=548308.3, rms=1.513 (2.319%)
- 013: dt: 0.1250, sse=539852.9, rms=1.454 (3.869%)
- rms = 1.45, time step reduction 3 of 3 to 0.062...
- 014: dt: 0.1250, sse=539366.5, rms=1.450 (0.312%)
- positioning took 1.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=83.9, 94 (30) missing vertices, mean dist -0.2 [0.4 (%70.8)->0.3 (%29.2))]
- %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.25 (0.10-->7.72) (max @ vno 46682 --> 47728)
- face area 0.35 +- 0.17 (0.00-->9.41)
- mean absolute distance = 0.29 +- 0.42
- 3484 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1061727.9, rms=4.416
- 015: dt: 0.5000, sse=798493.4, rms=2.820 (36.140%)
- 016: dt: 0.5000, sse=758405.8, rms=2.454 (12.987%)
- 017: dt: 0.5000, sse=740733.5, rms=2.393 (2.495%)
- rms = 2.51, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=685772.3, rms=1.796 (24.955%)
- 019: dt: 0.2500, sse=666773.1, rms=1.497 (16.618%)
- 020: dt: 0.2500, sse=667121.5, rms=1.414 (5.537%)
- rms = 1.37, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=662307.4, rms=1.370 (3.105%)
- 022: dt: 0.1250, sse=655670.6, rms=1.318 (3.856%)
- rms = 1.29, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=652869.2, rms=1.288 (2.259%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=85.6, 113 (14) missing vertices, mean dist -0.1 [0.3 (%64.5)->0.2 (%35.5))]
- %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.04-->7.97) (max @ vno 46682 --> 47728)
- face area 0.34 +- 0.17 (0.00-->9.66)
- mean absolute distance = 0.26 +- 0.37
- 2954 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=766610.9, rms=2.717
- 024: dt: 0.5000, sse=694328.2, rms=1.990 (26.756%)
- rms = 1.99, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=652750.6, rms=1.528 (23.221%)
- 026: dt: 0.2500, sse=648584.2, rms=1.290 (15.590%)
- 027: dt: 0.2500, sse=642024.5, rms=1.235 (4.228%)
- rms = 1.21, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.2500, sse=638528.4, rms=1.209 (2.130%)
- rms = 1.16, time step reduction 3 of 3 to 0.062...
- 029: dt: 0.1250, sse=629913.1, rms=1.161 (3.911%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=86.3, 142 (7) missing vertices, mean dist -0.0 [0.3 (%55.3)->0.2 (%44.7))]
- %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white.preaparc...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=649883.4, rms=1.598
- 030: dt: 0.5000, sse=642397.1, rms=1.449 (9.338%)
- rms = 1.72, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.2500, sse=618278.2, rms=1.094 (24.465%)
- rms = 1.05, time step reduction 2 of 3 to 0.125...
- 032: dt: 0.2500, sse=621372.2, rms=1.048 (4.263%)
- 033: dt: 0.1250, sse=609836.7, rms=0.958 (8.598%)
- rms = 0.93, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=607845.2, rms=0.933 (2.586%)
- positioning took 0.5 minutes
- generating cortex label...
- 7 non-cortical segments detected
- only using segment with 6462 vertices
- erasing segment 1 (vno[0] = 87194)
- erasing segment 2 (vno[0] = 87252)
- erasing segment 3 (vno[0] = 88984)
- erasing segment 4 (vno[0] = 89863)
- erasing segment 5 (vno[0] = 91509)
- erasing segment 6 (vno[0] = 95241)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.area
- vertex spacing 0.90 +- 0.26 (0.03-->7.83) (max @ vno 46682 --> 47728)
- face area 0.34 +- 0.16 (0.00-->9.86)
- refinement took 4.7 minutes
- PIDs (26761 26764) completed and logs appended.
- #--------------------------------------------
- #@# Smooth2 lh Sun Oct 8 04:14:20 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
- #--------------------------------------------
- #@# Smooth2 rh Sun Oct 8 04:14:20 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
- Waiting for PID 27050 of (27050 27053) to complete...
- Waiting for PID 27053 of (27050 27053) 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 (27050 27053) completed and logs appended.
- #--------------------------------------------
- #@# Inflation2 lh Sun Oct 8 04:14:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- #--------------------------------------------
- #@# Inflation2 rh Sun Oct 8 04:14:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Waiting for PID 27099 of (27099 27102) to complete...
- Waiting for PID 27102 of (27099 27102) to complete...
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- Reading ../surf/lh.smoothwm
- avg radius = 45.7 mm, total surface area = 74672 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.178 (target=0.015)
step 005: RMS=0.126 (target=0.015)
step 010: RMS=0.094 (target=0.015)
step 015: RMS=0.078 (target=0.015)
step 020: RMS=0.065 (target=0.015)
step 025: RMS=0.056 (target=0.015)
step 030: RMS=0.048 (target=0.015)
step 035: RMS=0.041 (target=0.015)
step 040: RMS=0.035 (target=0.015)
step 045: RMS=0.031 (target=0.015)
step 050: RMS=0.028 (target=0.015)
step 055: RMS=0.026 (target=0.015)
step 060: RMS=0.025 (target=0.015)
- inflation complete.
- inflation took 0.6 minutes
- mris_inflate utimesec 38.788103
- mris_inflate stimesec 0.092985
- mris_inflate ru_maxrss 178600
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 26319
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 8560
- mris_inflate ru_oublock 9528
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2211
- mris_inflate ru_nivcsw 4472
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Reading ../surf/rh.smoothwm
- avg radius = 45.0 mm, total surface area = 73818 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.177 (target=0.015)
step 005: RMS=0.126 (target=0.015)
step 010: RMS=0.095 (target=0.015)
step 015: RMS=0.078 (target=0.015)
step 020: RMS=0.066 (target=0.015)
step 025: RMS=0.056 (target=0.015)
step 030: RMS=0.048 (target=0.015)
step 035: RMS=0.040 (target=0.015)
step 040: RMS=0.035 (target=0.015)
step 045: RMS=0.032 (target=0.015)
step 050: RMS=0.029 (target=0.015)
step 055: RMS=0.027 (target=0.015)
step 060: RMS=0.025 (target=0.015)
- inflation complete.
- inflation took 0.6 minutes
- mris_inflate utimesec 38.224189
- mris_inflate stimesec 0.118981
- mris_inflate ru_maxrss 176072
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 25685
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 8440
- mris_inflate ru_oublock 9400
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 3989
- mris_inflate ru_nivcsw 2933
- PIDs (27099 27102) completed and logs appended.
- #--------------------------------------------
- #@# Curv .H and .K lh Sun Oct 8 04:15:04 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf
- mris_curvature -w lh.white.preaparc
- rm -f lh.white.H
- ln -s lh.white.preaparc.H lh.white.H
- rm -f lh.white.K
- ln -s lh.white.preaparc.K lh.white.K
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
- #--------------------------------------------
- #@# Curv .H and .K rh Sun Oct 8 04:15:05 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf
- reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 27200 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- Waiting for PID 27203 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- Waiting for PID 27206 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- Waiting for PID 27209 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- Waiting for PID 27212 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- Waiting for PID 27215 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- Waiting for PID 27218 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- Waiting for PID 27221 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- Waiting for PID 27224 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- Waiting for PID 27227 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- Waiting for PID 27232 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- Waiting for PID 27235 of (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) to complete...
- mris_curvature -w lh.white.preaparc
- total integrated curvature = 11.904*4pi (149.589) --> -11 handles
- ICI = 171.9, FI = 1511.8, variation=24637.630
- 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
- 134 vertices thresholded to be in k1 ~ [-0.58 0.37], k2 ~ [-0.09 0.83]
- total integrated curvature = 0.523*4pi (6.577) --> 0 handles
- ICI = 1.3, FI = 7.6, variation=133.905
- 125 vertices thresholded to be in [-0.06 0.01]
- writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 96 vertices thresholded to be in [-0.17 0.17]
- done.
- writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.021
- done.
- mris_curvature -w rh.white.preaparc
- total integrated curvature = 18.379*4pi (230.956) --> -17 handles
- ICI = 173.7, FI = 1503.7, variation=24493.355
- 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
- 127 vertices thresholded to be in k1 ~ [-0.34 0.31], k2 ~ [-0.11 0.08]
- total integrated curvature = 0.595*4pi (7.480) --> 0 handles
- ICI = 1.3, FI = 6.9, variation=122.386
- 89 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
- 113 vertices thresholded to be in [-0.14 0.15]
- done.
- writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.020
- done.
- PIDs (27200 27203 27206 27209 27212 27215 27218 27221 27224 27227 27232 27235) completed and logs appended.
- #-----------------------------------------
- #@# Curvature Stats lh Sun Oct 8 04:16:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050340 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 [ 0050340/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 [ 210 ]
- Gb_filter = 0
- WARN: S lookup min: -0.397253
- WARN: S explicit min: 0.000000 vertex = 336
- WARN: C lookup max: 176.346786
- WARN: C explicit max: 89.507462 vertex = 120614
- #-----------------------------------------
- #@# Curvature Stats rh Sun Oct 8 04:16:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050340 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 [ 0050340/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 [ 210 ]
- Gb_filter = 0
- WARN: S lookup min: -1.274895
- WARN: S explicit min: 0.000000 vertex = 2
- #--------------------------------------------
- #@# Sphere lh Sun Oct 8 04:16:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- #--------------------------------------------
- #@# Sphere rh Sun Oct 8 04:16:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- Waiting for PID 27458 of (27458 27462) to complete...
- Waiting for PID 27462 of (27458 27462) to complete...
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0.293...
- 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 %41.86
- pass 1: epoch 2 of 3 starting distance error %19.72
- unfolding complete - removing small folds...
- starting distance error %19.58
- removing remaining folds...
- final distance error %19.61
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 193 negative triangles
- 160: dt=0.9900, 193 negative triangles
- 161: dt=0.9900, 121 negative triangles
- 162: dt=0.9900, 84 negative triangles
- 163: dt=0.9900, 63 negative triangles
- 164: dt=0.9900, 55 negative triangles
- 165: dt=0.9900, 37 negative triangles
- 166: dt=0.9900, 38 negative triangles
- 167: dt=0.9900, 35 negative triangles
- 168: dt=0.9900, 23 negative triangles
- 169: dt=0.9900, 29 negative triangles
- 170: dt=0.9900, 25 negative triangles
- 171: dt=0.9900, 22 negative triangles
- 172: dt=0.9900, 13 negative triangles
- 173: dt=0.9900, 22 negative triangles
- 174: dt=0.9900, 12 negative triangles
- 175: dt=0.9900, 11 negative triangles
- 176: dt=0.9900, 9 negative triangles
- 177: dt=0.9900, 14 negative triangles
- 178: dt=0.9900, 7 negative triangles
- 179: dt=0.9900, 3 negative triangles
- 180: dt=0.9900, 8 negative triangles
- 181: dt=0.9900, 4 negative triangles
- 182: dt=0.9900, 8 negative triangles
- 183: dt=0.9900, 4 negative triangles
- 184: dt=0.9900, 4 negative triangles
- 185: dt=0.9900, 4 negative triangles
- 186: dt=0.9900, 1 negative triangles
- 187: dt=0.9900, 1 negative triangles
- 188: dt=0.9900, 3 negative triangles
- 189: dt=0.9900, 1 negative triangles
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.53 hours
- mris_sphere utimesec 1919.457198
- mris_sphere stimesec 0.946856
- mris_sphere ru_maxrss 250772
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 44474
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 8600
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 85386
- mris_sphere ru_nivcsw 158905
- FSRUNTIME@ mris_sphere 0.5340 hours 1 threads
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0.296...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %40.31
- pass 1: epoch 2 of 3 starting distance error %19.26
- unfolding complete - removing small folds...
- starting distance error %19.15
- removing remaining folds...
- final distance error %19.17
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 183 negative triangles
- 137: dt=0.9900, 183 negative triangles
- 138: dt=0.9900, 101 negative triangles
- 139: dt=0.9900, 73 negative triangles
- 140: dt=0.9900, 54 negative triangles
- 141: dt=0.9900, 65 negative triangles
- 142: dt=0.9900, 55 negative triangles
- 143: dt=0.9900, 52 negative triangles
- 144: dt=0.9900, 54 negative triangles
- 145: dt=0.9900, 41 negative triangles
- 146: dt=0.9900, 44 negative triangles
- 147: dt=0.9900, 36 negative triangles
- 148: dt=0.9900, 36 negative triangles
- 149: dt=0.9900, 25 negative triangles
- 150: dt=0.9900, 23 negative triangles
- 151: dt=0.9900, 27 negative triangles
- 152: dt=0.9900, 21 negative triangles
- 153: dt=0.9900, 30 negative triangles
- 154: dt=0.9900, 27 negative triangles
- 155: dt=0.9900, 29 negative triangles
- 156: dt=0.9900, 33 negative triangles
- 157: dt=0.9900, 28 negative triangles
- 158: dt=0.9900, 32 negative triangles
- 159: dt=0.9900, 34 negative triangles
- 160: dt=0.9900, 33 negative triangles
- 161: dt=0.9900, 32 negative triangles
- 162: dt=0.9405, 31 negative triangles
- 163: dt=0.9405, 32 negative triangles
- 164: dt=0.9405, 35 negative triangles
- 165: dt=0.9405, 36 negative triangles
- 166: dt=0.9405, 33 negative triangles
- 167: dt=0.9405, 32 negative triangles
- 168: dt=0.9405, 34 negative triangles
- 169: dt=0.9405, 34 negative triangles
- 170: dt=0.9405, 41 negative triangles
- 171: dt=0.9405, 36 negative triangles
- 172: dt=0.8935, 33 negative triangles
- 173: dt=0.8935, 36 negative triangles
- 174: dt=0.8935, 34 negative triangles
- 175: dt=0.8935, 30 negative triangles
- 176: dt=0.8935, 31 negative triangles
- 177: dt=0.8935, 34 negative triangles
- 178: dt=0.8935, 35 negative triangles
- 179: dt=0.8935, 31 negative triangles
- 180: dt=0.8935, 31 negative triangles
- 181: dt=0.8935, 32 negative triangles
- 182: dt=0.8488, 34 negative triangles
- 183: dt=0.8488, 34 negative triangles
- 184: dt=0.8488, 34 negative triangles
- 185: dt=0.8488, 32 negative triangles
- 186: dt=0.8488, 30 negative triangles
- 187: dt=0.8488, 30 negative triangles
- 188: dt=0.8488, 33 negative triangles
- 189: dt=0.8488, 34 negative triangles
- 190: dt=0.8488, 30 negative triangles
- 191: dt=0.8488, 32 negative triangles
- 192: dt=0.8064, 30 negative triangles
- 193: dt=0.8064, 29 negative triangles
- 194: dt=0.8064, 34 negative triangles
- 195: dt=0.8064, 30 negative triangles
- 196: dt=0.8064, 34 negative triangles
- 197: dt=0.8064, 31 negative triangles
- 198: dt=0.8064, 29 negative triangles
- 199: dt=0.8064, 31 negative triangles
- 200: dt=0.8064, 31 negative triangles
- 201: dt=0.8064, 35 negative triangles
- 202: dt=0.7660, 27 negative triangles
- expanding nbhd size to 1
- 203: dt=0.9900, 25 negative triangles
- 204: dt=0.9900, 25 negative triangles
- 205: dt=0.9900, 27 negative triangles
- 206: dt=0.9900, 24 negative triangles
- 207: dt=0.9900, 24 negative triangles
- 208: dt=0.9900, 23 negative triangles
- 209: dt=0.9900, 21 negative triangles
- 210: dt=0.9900, 19 negative triangles
- 211: dt=0.9900, 17 negative triangles
- 212: dt=0.9900, 17 negative triangles
- 213: dt=0.9900, 19 negative triangles
- 214: dt=0.9900, 15 negative triangles
- 215: dt=0.9900, 17 negative triangles
- 216: dt=0.9900, 15 negative triangles
- 217: dt=0.9900, 15 negative triangles
- 218: dt=0.9900, 15 negative triangles
- 219: dt=0.9900, 21 negative triangles
- 220: dt=0.9900, 18 negative triangles
- 221: dt=0.9900, 16 negative triangles
- 222: dt=0.9900, 14 negative triangles
- 223: dt=0.9900, 12 negative triangles
- 224: dt=0.9900, 12 negative triangles
- 225: dt=0.9900, 12 negative triangles
- 226: dt=0.9900, 17 negative triangles
- 227: dt=0.9900, 16 negative triangles
- 228: dt=0.9900, 12 negative triangles
- 229: dt=0.9900, 13 negative triangles
- 230: dt=0.9900, 11 negative triangles
- 231: dt=0.9900, 10 negative triangles
- 232: dt=0.9900, 10 negative triangles
- 233: dt=0.9900, 11 negative triangles
- 234: dt=0.9900, 11 negative triangles
- 235: dt=0.9900, 8 negative triangles
- 236: dt=0.9900, 6 negative triangles
- 237: dt=0.9900, 4 negative triangles
- 238: dt=0.9900, 4 negative triangles
- 239: dt=0.9900, 9 negative triangles
- 240: dt=0.9900, 5 negative triangles
- 241: dt=0.9900, 5 negative triangles
- 242: dt=0.9900, 2 negative triangles
- 243: dt=0.9900, 6 negative triangles
- 244: dt=0.9900, 7 negative triangles
- 245: dt=0.9900, 4 negative triangles
- 246: dt=0.9900, 3 negative triangles
- 247: dt=0.9900, 4 negative triangles
- 248: dt=0.9900, 3 negative triangles
- 249: dt=0.9900, 6 negative triangles
- 250: dt=0.9900, 4 negative triangles
- 251: dt=0.9900, 1 negative triangles
- 252: dt=0.9900, 4 negative triangles
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.54 hours
- mris_sphere utimesec 1938.191350
- mris_sphere stimesec 0.959854
- mris_sphere ru_maxrss 247496
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 43693
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 8536
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 80589
- mris_sphere ru_nivcsw 160401
- FSRUNTIME@ mris_sphere 0.5359 hours 1 threads
- PIDs (27458 27462) completed and logs appended.
- #--------------------------------------------
- #@# Surf Reg lh Sun Oct 8 04:48:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg
- #--------------------------------------------
- #@# Surf Reg rh Sun Oct 8 04:48:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 29979 of (29979 29982) to complete...
- Waiting for PID 29982 of (29979 29982) to complete...
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 5.558
- curvature mean = 0.041, std = 0.819
- curvature mean = 0.015, std = 0.876
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 16.00) sse = 297716.6, tmin=0.9265
- d=32.00 min @ (0.00, 8.00, -8.00) sse = 196049.1, tmin=1.8791
- d=16.00 min @ (4.00, 0.00, 0.00) sse = 178781.0, tmin=2.8414
- d=8.00 min @ (-2.00, -2.00, 0.00) sse = 171298.6, tmin=3.8091
- d=4.00 min @ (0.00, 0.00, 1.00) sse = 169980.9, tmin=4.7873
- d=2.00 min @ (0.50, 0.00, -0.50) sse = 169696.5, tmin=5.7678
- d=1.00 min @ (-0.25, -0.25, 0.25) sse = 169489.6, tmin=6.7435
- d=0.50 min @ (0.12, 0.00, 0.00) sse = 169476.8, tmin=7.7337
- tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 7.73 min
- curvature mean = 0.007, std = 0.837
- curvature mean = 0.005, std = 0.955
- curvature mean = 0.003, std = 0.848
- curvature mean = 0.001, std = 0.983
- curvature mean = 0.001, std = 0.850
- curvature mean = 0.000, std = 0.993
- 2 Reading smoothwm
- curvature mean = -0.035, std = 0.320
- curvature mean = 0.040, std = 0.249
- curvature mean = 0.058, std = 0.337
- curvature mean = 0.033, std = 0.310
- curvature mean = 0.039, std = 0.499
- curvature mean = 0.032, std = 0.337
- curvature mean = 0.024, std = 0.615
- curvature mean = 0.031, std = 0.349
- curvature mean = 0.010, std = 0.708
- MRISregister() return, current seed 0
- -01: dt=0.0000, 93 negative triangles
- 112: dt=0.9900, 93 negative triangles
- expanding nbhd size to 1
- 113: dt=0.9900, 120 negative triangles
- 114: dt=0.9900, 97 negative triangles
- 115: dt=0.9900, 84 negative triangles
- 116: dt=0.9900, 85 negative triangles
- 117: dt=0.9900, 82 negative triangles
- 118: dt=0.9900, 79 negative triangles
- 119: dt=0.9900, 72 negative triangles
- 120: dt=0.9900, 69 negative triangles
- 121: dt=0.9900, 70 negative triangles
- 122: dt=0.9900, 68 negative triangles
- 123: dt=0.9900, 55 negative triangles
- 124: dt=0.9900, 51 negative triangles
- 125: dt=0.9900, 50 negative triangles
- 126: dt=0.9900, 46 negative triangles
- 127: dt=0.9900, 48 negative triangles
- 128: dt=0.9900, 49 negative triangles
- 129: dt=0.9900, 45 negative triangles
- 130: dt=0.9900, 43 negative triangles
- 131: dt=0.9900, 38 negative triangles
- 132: dt=0.9900, 32 negative triangles
- 133: dt=0.9900, 32 negative triangles
- 134: dt=0.9900, 29 negative triangles
- 135: dt=0.9900, 30 negative triangles
- 136: dt=0.9900, 22 negative triangles
- 137: dt=0.9900, 24 negative triangles
- 138: dt=0.9900, 20 negative triangles
- 139: dt=0.9900, 15 negative triangles
- 140: dt=0.9900, 13 negative triangles
- 141: dt=0.9900, 9 negative triangles
- 142: dt=0.9900, 10 negative triangles
- 143: dt=0.9900, 7 negative triangles
- 144: dt=0.9900, 8 negative triangles
- 145: dt=0.9900, 6 negative triangles
- 146: dt=0.9900, 7 negative triangles
- 147: dt=0.9900, 8 negative triangles
- 148: dt=0.9900, 6 negative triangles
- 149: dt=0.9900, 4 negative triangles
- 150: dt=0.9900, 2 negative triangles
- 151: dt=0.9900, 1 negative triangles
- 152: dt=0.9900, 1 negative triangles
- 153: dt=0.9900, 1 negative triangles
- 154: dt=0.9900, 1 negative triangles
- 155: dt=0.9900, 1 negative triangles
- 156: dt=0.9900, 1 negative triangles
- writing registered surface to ../surf/lh.sphere.reg...
- registration took 1.00 hours
- mris_register utimesec 3609.329298
- mris_register stimesec 1.776729
- mris_register ru_maxrss 233648
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 33881
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 8560
- mris_register ru_oublock 8656
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 277355
- mris_register ru_nivcsw 194898
- FSRUNTIME@ mris_register 1.0026 hours 1 threads
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 5.661
- curvature mean = 0.038, std = 0.815
- curvature mean = 0.016, std = 0.875
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 16.00) sse = 312917.3, tmin=0.9132
- d=32.00 min @ (-8.00, -8.00, 0.00) sse = 207337.7, tmin=1.8509
- d=16.00 min @ (0.00, -4.00, -4.00) sse = 197683.1, tmin=2.7981
- d=8.00 min @ (2.00, 2.00, 2.00) sse = 184871.0, tmin=3.7635
- d=4.00 min @ (0.00, 0.00, -1.00) sse = 184833.0, tmin=4.7407
- d=2.00 min @ (-0.50, 0.00, 0.50) sse = 183780.2, tmin=5.7201
- d=0.50 min @ (0.12, 0.00, 0.00) sse = 183765.7, tmin=7.6560
- tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 7.66 min
- curvature mean = 0.009, std = 0.833
- curvature mean = 0.005, std = 0.955
- curvature mean = 0.006, std = 0.844
- curvature mean = 0.002, std = 0.983
- curvature mean = 0.005, std = 0.847
- curvature mean = 0.000, std = 0.994
- 2 Reading smoothwm
- curvature mean = -0.033, std = 0.309
- curvature mean = 0.036, std = 0.245
- curvature mean = 0.060, std = 0.350
- curvature mean = 0.030, std = 0.304
- curvature mean = 0.041, std = 0.516
- curvature mean = 0.029, std = 0.331
- curvature mean = 0.025, std = 0.638
- curvature mean = 0.029, std = 0.343
- curvature mean = 0.011, std = 0.739
- MRISregister() return, current seed 0
- -01: dt=0.0000, 57 negative triangles
- 104: dt=0.9900, 57 negative triangles
- expanding nbhd size to 1
- 105: dt=0.9900, 80 negative triangles
- 106: dt=0.9900, 58 negative triangles
- 107: dt=0.9900, 67 negative triangles
- 108: dt=0.9900, 61 negative triangles
- 109: dt=0.9900, 61 negative triangles
- 110: dt=0.9405, 63 negative triangles
- 111: dt=0.9405, 56 negative triangles
- 112: dt=0.9405, 51 negative triangles
- 113: dt=0.9405, 54 negative triangles
- 114: dt=0.9405, 53 negative triangles
- 115: dt=0.9405, 46 negative triangles
- 116: dt=0.9405, 41 negative triangles
- 117: dt=0.9405, 38 negative triangles
- 118: dt=0.9405, 31 negative triangles
- 119: dt=0.9405, 33 negative triangles
- 120: dt=0.9405, 28 negative triangles
- 121: dt=0.9405, 31 negative triangles
- 122: dt=0.9405, 28 negative triangles
- 123: dt=0.9405, 25 negative triangles
- 124: dt=0.9405, 22 negative triangles
- 125: dt=0.9405, 22 negative triangles
- 126: dt=0.9405, 22 negative triangles
- 127: dt=0.9405, 20 negative triangles
- 128: dt=0.9405, 15 negative triangles
- 129: dt=0.9405, 17 negative triangles
- 130: dt=0.9405, 17 negative triangles
- 131: dt=0.9405, 17 negative triangles
- 132: dt=0.9405, 14 negative triangles
- 133: dt=0.9405, 12 negative triangles
- 134: dt=0.9405, 14 negative triangles
- 135: dt=0.9405, 10 negative triangles
- 136: dt=0.9405, 9 negative triangles
- 137: dt=0.9405, 8 negative triangles
- 138: dt=0.9405, 7 negative triangles
- 139: dt=0.9405, 11 negative triangles
- 140: dt=0.9405, 8 negative triangles
- 141: dt=0.9405, 7 negative triangles
- 142: dt=0.9405, 5 negative triangles
- 143: dt=0.9405, 9 negative triangles
- 144: dt=0.9405, 7 negative triangles
- 145: dt=0.9405, 6 negative triangles
- 146: dt=0.9405, 4 negative triangles
- 147: dt=0.9405, 5 negative triangles
- 148: dt=0.9405, 4 negative triangles
- 149: dt=0.9405, 6 negative triangles
- 150: dt=0.9405, 4 negative triangles
- 151: dt=0.9405, 6 negative triangles
- 152: dt=0.9405, 4 negative triangles
- 153: dt=0.9405, 2 negative triangles
- 154: dt=0.9405, 2 negative triangles
- 155: dt=0.9405, 4 negative triangles
- 156: dt=0.9405, 1 negative triangles
- 157: dt=0.9405, 2 negative triangles
- 158: dt=0.9405, 1 negative triangles
- 159: dt=0.9405, 3 negative triangles
- 160: dt=0.9405, 1 negative triangles
- writing registered surface to ../surf/rh.sphere.reg...
- registration took 1.07 hours
- mris_register utimesec 4019.939876
- mris_register stimesec 2.327646
- mris_register ru_maxrss 230776
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 32363
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 8528
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 315355
- mris_register ru_nivcsw 195696
- FSRUNTIME@ mris_register 1.0735 hours 1 threads
- PIDs (29979 29982) completed and logs appended.
- #--------------------------------------------
- #@# Jacobian white lh Sun Oct 8 05:53:01 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# Jacobian white rh Sun Oct 8 05:53:01 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- Waiting for PID 1232 of (1232 1235) to complete...
- Waiting for PID 1235 of (1232 1235) 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 (1232 1235) completed and logs appended.
- #--------------------------------------------
- #@# AvgCurv lh Sun Oct 8 05:53:03 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
- #--------------------------------------------
- #@# AvgCurv rh Sun Oct 8 05:53:03 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 1282 of (1282 1285) to complete...
- Waiting for PID 1285 of (1282 1285) 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 (1282 1285) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc lh Sun Oct 8 05:53:04 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot
- #-----------------------------------------
- #@# Cortical Parc rh Sun Oct 8 05:53:04 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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 1328 of (1328 1331) to complete...
- Waiting for PID 1331 of (1328 1331) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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...
- 1354 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2712 changed, 121622 examined...
- 001: 691 changed, 11595 examined...
- 002: 179 changed, 3844 examined...
- 003: 53 changed, 1032 examined...
- 004: 16 changed, 341 examined...
- 005: 9 changed, 93 examined...
- 006: 9 changed, 58 examined...
- 007: 3 changed, 52 examined...
- 008: 1 changed, 23 examined...
- 009: 1 changed, 7 examined...
- 010: 0 changed, 6 examined...
- 198 labels changed using aseg
- 000: 117 total segments, 75 labels (307 vertices) changed
- 001: 44 total segments, 3 labels (5 vertices) changed
- 002: 41 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 1 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1931 vertices marked for relabeling...
- 1931 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 13 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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...
- 1241 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2457 changed, 119917 examined...
- 001: 569 changed, 10741 examined...
- 002: 138 changed, 3215 examined...
- 003: 60 changed, 843 examined...
- 004: 21 changed, 370 examined...
- 005: 5 changed, 124 examined...
- 006: 2 changed, 38 examined...
- 007: 0 changed, 16 examined...
- 164 labels changed using aseg
- 000: 97 total segments, 60 labels (224 vertices) changed
- 001: 39 total segments, 2 labels (6 vertices) changed
- 002: 37 total segments, 0 labels (0 vertices) changed
- 9 filter iterations complete (10 requested, 0 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1611 vertices marked for relabeling...
- 1611 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 12 seconds.
- PIDs (1328 1331) completed and logs appended.
- #--------------------------------------------
- #@# Make Pial Surf lh Sun Oct 8 05:53:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050340 lh
- #--------------------------------------------
- #@# Make Pial Surf rh Sun Oct 8 05:53:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050340 rh
- Waiting for PID 1380 of (1380 1383) to complete...
- Waiting for PID 1383 of (1380 1383) to complete...
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050340 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-6.0.0/0050340/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- 13065 bright wm thresholded.
- 2133 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.orig...
- computing class statistics...
- border white: 229073 voxels (1.37%)
- border gray 266822 voxels (1.59%)
- WM (97.0): 97.6 +- 7.9 [70.0 --> 110.0]
- GM (75.0) : 73.5 +- 10.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70)
- setting MAX_BORDER_WHITE to 109.9 (was 105)
- setting MIN_BORDER_WHITE to 69.0 (was 85)
- setting MAX_CSF to 48.3 (was 40)
- setting MAX_GRAY to 94.1 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 58.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 38.0 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=102+-5.2, GM=69+-9.6
- mean inside = 93.9, mean outside = 77.5
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.25 (0.04-->4.62) (max @ vno 120627 --> 120657)
- face area 0.34 +- 0.16 (0.00-->4.84)
- mean absolute distance = 0.62 +- 0.85
- 3268 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 3 with 150 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- deleting segment 5 with 18 points - only 0.00% unknown
- mean border=80.5, 132 (132) missing vertices, mean dist 0.4 [0.7 (%17.0)->0.6 (%83.0))]
- %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 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.93 +- 0.26 (0.06-->4.51) (max @ vno 120627 --> 120657)
- face area 0.34 +- 0.16 (0.00-->4.46)
- mean absolute distance = 0.39 +- 0.60
- 3656 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1899366.5, rms=7.518
- 001: dt: 0.5000, sse=1105996.0, rms=4.697 (37.518%)
- 002: dt: 0.5000, sse=837870.1, rms=3.306 (29.611%)
- 003: dt: 0.5000, sse=772723.8, rms=2.863 (13.416%)
- 004: dt: 0.5000, sse=749067.6, rms=2.661 (7.045%)
- rms = 2.69, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.2500, sse=681018.9, rms=2.003 (24.736%)
- 006: dt: 0.2500, sse=656116.5, rms=1.654 (17.402%)
- 007: dt: 0.2500, sse=646690.6, rms=1.552 (6.157%)
- rms = 1.50, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=643855.6, rms=1.503 (3.195%)
- rms = 1.46, time step reduction 3 of 3 to 0.062...
- 009: dt: 0.1250, sse=640965.1, rms=1.463 (2.623%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 2 with 44 points - only 0.00% unknown
- deleting segment 3 with 19 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- mean border=83.7, 81 (35) missing vertices, mean dist -0.3 [0.4 (%72.8)->0.2 (%27.2))]
- %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.08-->4.68) (max @ vno 46767 --> 46768)
- face area 0.36 +- 0.18 (0.00-->4.98)
- mean absolute distance = 0.28 +- 0.42
- 3523 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1106662.9, rms=4.515
- 010: dt: 0.5000, sse=816369.9, rms=2.788 (38.251%)
- 011: dt: 0.5000, sse=769132.4, rms=2.406 (13.680%)
- 012: dt: 0.5000, sse=762395.7, rms=2.342 (2.686%)
- rms = 2.47, time step reduction 1 of 3 to 0.250...
- 013: dt: 0.2500, sse=698470.7, rms=1.678 (28.351%)
- 014: dt: 0.2500, sse=675869.6, rms=1.324 (21.104%)
- 015: dt: 0.2500, sse=674159.1, rms=1.235 (6.739%)
- rms = 1.21, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=669123.4, rms=1.211 (1.937%)
- rms = 1.18, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=666462.9, rms=1.181 (2.444%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 1 with 54 points - only 0.00% unknown
- deleting segment 2 with 22 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- mean border=85.4, 109 (21) missing vertices, mean dist -0.1 [0.3 (%64.6)->0.2 (%35.4))]
- %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.26 (0.06-->4.71) (max @ vno 46767 --> 46768)
- face area 0.35 +- 0.17 (0.00-->4.85)
- mean absolute distance = 0.26 +- 0.37
- 3047 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=775504.8, rms=2.691
- 018: dt: 0.5000, sse=702740.1, rms=1.955 (27.353%)
- rms = 2.02, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=659749.4, rms=1.465 (25.043%)
- 020: dt: 0.2500, sse=649105.2, rms=1.197 (18.325%)
- 021: dt: 0.2500, sse=639712.9, rms=1.129 (5.666%)
- rms = 1.12, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=639633.2, rms=1.124 (0.451%)
- rms = 1.09, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=637053.0, rms=1.088 (3.170%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 50 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 2 with 24 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- deleting segment 4 with 13 points - only 0.00% unknown
- mean border=86.1, 113 (15) missing vertices, mean dist -0.0 [0.3 (%55.1)->0.2 (%44.9))]
- %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=654481.8, rms=1.525
- 024: dt: 0.5000, sse=646804.1, rms=1.355 (11.189%)
- rms = 1.72, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=622425.6, rms=0.998 (26.306%)
- 026: dt: 0.2500, sse=619401.9, rms=0.936 (6.293%)
- 027: dt: 0.2500, sse=616626.1, rms=0.885 (5.399%)
- rms = 0.91, time step reduction 2 of 3 to 0.125...
- rms = 0.87, time step reduction 3 of 3 to 0.062...
- 028: dt: 0.1250, sse=614792.2, rms=0.869 (1.796%)
- positioning took 0.6 minutes
- generating cortex label...
- 10 non-cortical segments detected
- only using segment with 6925 vertices
- erasing segment 1 (vno[0] = 74227)
- erasing segment 2 (vno[0] = 78908)
- erasing segment 3 (vno[0] = 81531)
- erasing segment 4 (vno[0] = 84321)
- erasing segment 5 (vno[0] = 86043)
- erasing segment 6 (vno[0] = 87596)
- erasing segment 7 (vno[0] = 88421)
- erasing segment 8 (vno[0] = 90040)
- erasing segment 9 (vno[0] = 121233)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.area
- vertex spacing 0.90 +- 0.26 (0.04-->4.77) (max @ vno 46767 --> 46768)
- face area 0.34 +- 0.17 (0.00-->4.90)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=56.8, 129 (129) missing vertices, mean dist 1.8 [0.8 (%0.1)->3.0 (%99.9))]
- %14 local maxima, %43 large gradients and %38 min vals, 566 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=21580402.0, rms=30.076
- 001: dt: 0.0500, sse=19365454.0, rms=28.445 (5.423%)
- 002: dt: 0.0500, sse=17761332.0, rms=27.203 (4.368%)
- 003: dt: 0.0500, sse=16516768.0, rms=26.198 (3.693%)
- 004: dt: 0.0500, sse=15496659.0, rms=25.345 (3.257%)
- 005: dt: 0.0500, sse=14626565.0, rms=24.594 (2.964%)
- 006: dt: 0.0500, sse=13863962.0, rms=23.916 (2.756%)
- 007: dt: 0.0500, sse=13181819.0, rms=23.293 (2.606%)
- 008: dt: 0.0500, sse=12562952.0, rms=22.713 (2.491%)
- 009: dt: 0.0500, sse=11994850.0, rms=22.167 (2.404%)
- 010: dt: 0.0500, sse=11470442.0, rms=21.650 (2.329%)
- positioning took 0.8 minutes
- mean border=56.6, 102 (61) missing vertices, mean dist 1.5 [0.4 (%0.1)->2.5 (%99.9))]
- %15 local maxima, %43 large gradients and %37 min vals, 538 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=12146528.0, rms=22.311
- 011: dt: 0.0500, sse=11654303.0, rms=21.830 (2.155%)
- 012: dt: 0.0500, sse=11195148.0, rms=21.372 (2.100%)
- 013: dt: 0.0500, sse=10764958.0, rms=20.933 (2.052%)
- 014: dt: 0.0500, sse=10361075.0, rms=20.513 (2.008%)
- 015: dt: 0.0500, sse=9981607.0, rms=20.109 (1.965%)
- 016: dt: 0.0500, sse=9625494.0, rms=19.724 (1.919%)
- 017: dt: 0.0500, sse=9290741.0, rms=19.354 (1.875%)
- 018: dt: 0.0500, sse=8976233.0, rms=19.000 (1.829%)
- 019: dt: 0.0500, sse=8679966.0, rms=18.660 (1.788%)
- 020: dt: 0.0500, sse=8401549.0, rms=18.335 (1.742%)
- positioning took 0.8 minutes
- mean border=56.5, 130 (51) missing vertices, mean dist 1.3 [0.1 (%1.0)->2.2 (%99.0))]
- %16 local maxima, %43 large gradients and %37 min vals, 524 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=8499231.0, rms=18.454
- 021: dt: 0.0500, sse=8231438.0, rms=18.138 (1.714%)
- 022: dt: 0.0500, sse=7980170.0, rms=17.836 (1.664%)
- 023: dt: 0.0500, sse=7742240.0, rms=17.545 (1.630%)
- 024: dt: 0.0500, sse=7518705.0, rms=17.268 (1.583%)
- 025: dt: 0.0500, sse=7309095.0, rms=17.003 (1.532%)
- 026: dt: 0.0500, sse=7111351.0, rms=16.749 (1.491%)
- 027: dt: 0.0500, sse=6924478.0, rms=16.506 (1.453%)
- 028: dt: 0.0500, sse=6746713.0, rms=16.271 (1.423%)
- 029: dt: 0.0500, sse=6577139.5, rms=16.044 (1.397%)
- 030: dt: 0.0500, sse=6415323.0, rms=15.824 (1.372%)
- positioning took 0.8 minutes
- mean border=56.4, 172 (46) missing vertices, mean dist 1.1 [0.1 (%7.8)->2.0 (%92.2))]
- %16 local maxima, %43 large gradients and %36 min vals, 474 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=6491114.0, rms=15.926
- 031: dt: 0.5000, sse=5368080.0, rms=14.317 (10.103%)
- 032: dt: 0.5000, sse=4558397.5, rms=13.027 (9.010%)
- 033: dt: 0.5000, sse=3914014.2, rms=11.902 (8.642%)
- 034: dt: 0.5000, sse=3387371.8, rms=10.890 (8.499%)
- 035: dt: 0.5000, sse=2939488.8, rms=9.951 (8.623%)
- 036: dt: 0.5000, sse=2561440.2, rms=9.080 (8.748%)
- 037: dt: 0.5000, sse=2233541.8, rms=8.255 (9.089%)
- 038: dt: 0.5000, sse=1966830.9, rms=7.515 (8.963%)
- 039: dt: 0.5000, sse=1752777.1, rms=6.868 (8.616%)
- 040: dt: 0.5000, sse=1602711.6, rms=6.372 (7.222%)
- 041: dt: 0.5000, sse=1493620.2, rms=5.989 (6.003%)
- 042: dt: 0.5000, sse=1425187.8, rms=5.733 (4.270%)
- 043: dt: 0.5000, sse=1377356.4, rms=5.549 (3.219%)
- 044: dt: 0.5000, sse=1344583.4, rms=5.418 (2.365%)
- 045: dt: 0.5000, sse=1318798.0, rms=5.314 (1.917%)
- 046: dt: 0.5000, sse=1306892.4, rms=5.262 (0.970%)
- 047: dt: 0.5000, sse=1291795.0, rms=5.202 (1.147%)
- rms = 5.16, time step reduction 1 of 3 to 0.250...
- 048: dt: 0.5000, sse=1282866.6, rms=5.162 (0.769%)
- 049: dt: 0.2500, sse=1198317.6, rms=4.749 (7.992%)
- 050: dt: 0.2500, sse=1173798.0, rms=4.634 (2.421%)
- rms = 4.63, time step reduction 2 of 3 to 0.125...
- 051: dt: 0.2500, sse=1174079.8, rms=4.633 (0.022%)
- 052: dt: 0.1250, sse=1155451.9, rms=4.540 (2.026%)
- rms = 4.52, time step reduction 3 of 3 to 0.062...
- 053: dt: 0.1250, sse=1151561.5, rms=4.521 (0.408%)
- positioning took 2.6 minutes
- mean border=55.1, 1889 (23) missing vertices, mean dist 0.2 [0.2 (%43.5)->0.6 (%56.5))]
- %28 local maxima, %34 large gradients and %32 min vals, 233 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=1460955.1, rms=5.073
- 054: dt: 0.5000, sse=1355623.0, rms=4.610 (9.119%)
- 055: dt: 0.5000, sse=1291179.2, rms=4.327 (6.137%)
- rms = 4.45, time step reduction 1 of 3 to 0.250...
- 056: dt: 0.2500, sse=1201828.1, rms=3.809 (11.981%)
- 057: dt: 0.2500, sse=1178547.9, rms=3.656 (4.025%)
- rms = 3.64, time step reduction 2 of 3 to 0.125...
- 058: dt: 0.2500, sse=1174891.4, rms=3.635 (0.555%)
- 059: dt: 0.1250, sse=1150706.1, rms=3.477 (4.354%)
- rms = 3.45, time step reduction 3 of 3 to 0.062...
- 060: dt: 0.1250, sse=1146255.9, rms=3.450 (0.776%)
- positioning took 1.0 minutes
- mean border=54.4, 2176 (17) missing vertices, mean dist 0.1 [0.2 (%46.2)->0.4 (%53.8))]
- %35 local maxima, %27 large gradients and %31 min vals, 274 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=1189576.4, rms=3.700
- rms = 4.07, time step reduction 1 of 3 to 0.250...
- 061: dt: 0.2500, sse=1163811.5, rms=3.540 (4.316%)
- rms = 3.49, time step reduction 2 of 3 to 0.125...
- 062: dt: 0.2500, sse=1155400.2, rms=3.494 (1.306%)
- 063: dt: 0.1250, sse=1146441.6, rms=3.434 (1.726%)
- rms = 3.41, time step reduction 3 of 3 to 0.062...
- 064: dt: 0.1250, sse=1142229.1, rms=3.410 (0.697%)
- positioning took 0.7 minutes
- mean border=53.8, 4561 (16) missing vertices, mean dist 0.1 [0.2 (%46.8)->0.3 (%53.2))]
- %39 local maxima, %23 large gradients and %30 min vals, 265 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing pial surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1153928.2, rms=3.474
- rms = 3.71, time step reduction 1 of 3 to 0.250...
- 065: dt: 0.2500, sse=1138889.1, rms=3.378 (2.761%)
- 066: dt: 0.2500, sse=1128137.5, rms=3.326 (1.533%)
- rms = 3.32, time step reduction 2 of 3 to 0.125...
- 067: dt: 0.2500, sse=1125477.4, rms=3.320 (0.194%)
- 068: dt: 0.1250, sse=1109833.0, rms=3.212 (3.245%)
- rms = 3.18, time step reduction 3 of 3 to 0.062...
- 069: dt: 0.1250, sse=1105193.0, rms=3.185 (0.842%)
- positioning took 0.8 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.area.pial
- vertex spacing 1.04 +- 0.47 (0.05-->7.86) (max @ vno 45749 --> 46752)
- face area 0.43 +- 0.35 (0.00-->6.92)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 121622 vertices processed
- 25000 of 121622 vertices processed
- 50000 of 121622 vertices processed
- 75000 of 121622 vertices processed
- 100000 of 121622 vertices processed
- 0 of 121622 vertices processed
- 25000 of 121622 vertices processed
- 50000 of 121622 vertices processed
- 75000 of 121622 vertices processed
- 100000 of 121622 vertices processed
- thickness calculation complete, 452:1401 truncations.
- 24624 vertices at 0 distance
- 78087 vertices at 1 distance
- 74655 vertices at 2 distance
- 35625 vertices at 3 distance
- 12538 vertices at 4 distance
- 4179 vertices at 5 distance
- 1433 vertices at 6 distance
- 521 vertices at 7 distance
- 239 vertices at 8 distance
- 148 vertices at 9 distance
- 67 vertices at 10 distance
- 50 vertices at 11 distance
- 24 vertices at 12 distance
- 21 vertices at 13 distance
- 12 vertices at 14 distance
- 9 vertices at 15 distance
- 15 vertices at 16 distance
- 14 vertices at 17 distance
- 10 vertices at 18 distance
- 14 vertices at 19 distance
- 19 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.thickness
- positioning took 13.9 minutes
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050340 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-6.0.0/0050340/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- 13065 bright wm thresholded.
- 2133 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.orig...
- computing class statistics...
- border white: 229073 voxels (1.37%)
- border gray 266822 voxels (1.59%)
- WM (97.0): 97.6 +- 7.9 [70.0 --> 110.0]
- GM (75.0) : 73.5 +- 10.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 59.7 (was 70)
- setting MAX_BORDER_WHITE to 108.9 (was 105)
- setting MIN_BORDER_WHITE to 70.0 (was 85)
- setting MAX_CSF to 49.3 (was 40)
- setting MAX_GRAY to 93.1 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 59.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 39.0 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=101+-5.2, GM=70+-8.7
- mean inside = 93.6, mean outside = 77.6
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.26 (0.03-->7.83) (max @ vno 46682 --> 47728)
- face area 0.34 +- 0.16 (0.00-->9.78)
- mean absolute distance = 0.63 +- 0.85
- 3160 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 2 with 165 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 5 with 1 points - only 0.00% unknown
- mean border=80.8, 152 (152) missing vertices, mean dist 0.4 [0.7 (%16.5)->0.6 (%83.5))]
- %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 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.93 +- 0.26 (0.09-->7.93) (max @ vno 46682 --> 47728)
- face area 0.34 +- 0.17 (0.00-->9.20)
- mean absolute distance = 0.39 +- 0.62
- 3880 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1807746.6, rms=7.301
- 001: dt: 0.5000, sse=1066233.8, rms=4.580 (37.265%)
- 002: dt: 0.5000, sse=818003.1, rms=3.218 (29.745%)
- 003: dt: 0.5000, sse=761274.4, rms=2.819 (12.383%)
- 004: dt: 0.5000, sse=735714.6, rms=2.605 (7.598%)
- rms = 2.67, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.2500, sse=673792.6, rms=1.992 (23.554%)
- 006: dt: 0.2500, sse=650773.1, rms=1.689 (15.186%)
- 007: dt: 0.2500, sse=645030.1, rms=1.610 (4.707%)
- 008: dt: 0.2500, sse=643867.4, rms=1.556 (3.300%)
- rms = 1.53, time step reduction 2 of 3 to 0.125...
- 009: dt: 0.2500, sse=642473.4, rms=1.529 (1.766%)
- 010: dt: 0.1250, sse=635012.4, rms=1.466 (4.102%)
- rms = 1.44, time step reduction 3 of 3 to 0.062...
- 011: dt: 0.1250, sse=634952.6, rms=1.443 (1.558%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- deleting segment 2 with 75 points - only 0.00% unknown
- mean border=83.8, 117 (40) missing vertices, mean dist -0.3 [0.5 (%71.4)->0.2 (%28.6))]
- %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.06-->8.12) (max @ vno 46682 --> 47728)
- face area 0.36 +- 0.18 (0.00-->10.93)
- mean absolute distance = 0.29 +- 0.43
- 2943 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1067343.9, rms=4.387
- 012: dt: 0.5000, sse=803273.6, rms=2.773 (36.776%)
- 013: dt: 0.5000, sse=756263.0, rms=2.365 (14.739%)
- 014: dt: 0.5000, sse=742896.2, rms=2.308 (2.383%)
- rms = 2.41, time step reduction 1 of 3 to 0.250...
- 015: dt: 0.2500, sse=701202.3, rms=1.710 (25.936%)
- 016: dt: 0.2500, sse=671960.1, rms=1.388 (18.806%)
- 017: dt: 0.2500, sse=665020.5, rms=1.313 (5.383%)
- rms = 1.28, time step reduction 2 of 3 to 0.125...
- 018: dt: 0.2500, sse=667913.8, rms=1.280 (2.577%)
- 019: dt: 0.1250, sse=660522.6, rms=1.223 (4.440%)
- rms = 1.21, time step reduction 3 of 3 to 0.062...
- 020: dt: 0.1250, sse=659820.6, rms=1.213 (0.817%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- deleting segment 2 with 96 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- mean border=85.6, 134 (18) missing vertices, mean dist -0.1 [0.3 (%64.9)->0.2 (%35.1))]
- %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.26 (0.06-->8.19) (max @ vno 46682 --> 47728)
- face area 0.35 +- 0.17 (0.00-->10.84)
- mean absolute distance = 0.27 +- 0.38
- 2969 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=769914.9, rms=2.701
- 021: dt: 0.5000, sse=699001.4, rms=1.965 (27.259%)
- rms = 1.95, time step reduction 1 of 3 to 0.250...
- 022: dt: 0.5000, sse=694048.2, rms=1.952 (0.642%)
- 023: dt: 0.2500, sse=644179.5, rms=1.275 (34.709%)
- 024: dt: 0.2500, sse=636775.1, rms=1.173 (7.944%)
- rms = 1.18, time step reduction 2 of 3 to 0.125...
- rms = 1.15, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=633585.6, rms=1.145 (2.395%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 16 points - only 0.00% unknown
- deleting segment 2 with 100 points - only 0.00% unknown
- deleting segment 3 with 8 points - only 0.00% unknown
- mean border=86.3, 159 (10) missing vertices, mean dist -0.0 [0.3 (%55.5)->0.2 (%44.5))]
- %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=653294.9, rms=1.592
- 026: dt: 0.5000, sse=656641.4, rms=1.500 (5.760%)
- rms = 1.85, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=622819.6, rms=1.077 (28.198%)
- rms = 1.04, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.2500, sse=620004.1, rms=1.037 (3.763%)
- 029: dt: 0.1250, sse=618372.4, rms=0.917 (11.494%)
- rms = 0.89, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=612092.9, rms=0.888 (3.216%)
- positioning took 0.5 minutes
- generating cortex label...
- 9 non-cortical segments detected
- only using segment with 6487 vertices
- erasing segment 0 (vno[0] = 26406)
- erasing segment 2 (vno[0] = 71077)
- erasing segment 3 (vno[0] = 87194)
- erasing segment 4 (vno[0] = 87252)
- erasing segment 5 (vno[0] = 88984)
- erasing segment 6 (vno[0] = 89863)
- erasing segment 7 (vno[0] = 91509)
- erasing segment 8 (vno[0] = 95241)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.area
- vertex spacing 0.90 +- 0.27 (0.03-->8.13) (max @ vno 46682 --> 47728)
- face area 0.34 +- 0.17 (0.00-->10.56)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- deleting segment 0 with 1 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=57.6, 131 (131) missing vertices, mean dist 1.8 [2.2 (%0.0)->2.9 (%100.0))]
- %15 local maxima, %44 large gradients and %36 min vals, 591 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=20408548.0, rms=29.413
- 001: dt: 0.0500, sse=18309564.0, rms=27.813 (5.441%)
- 002: dt: 0.0500, sse=16789010.0, rms=26.593 (4.385%)
- 003: dt: 0.0500, sse=15610624.0, rms=25.608 (3.705%)
- 004: dt: 0.0500, sse=14646511.0, rms=24.772 (3.262%)
- 005: dt: 0.0500, sse=13824793.0, rms=24.037 (2.967%)
- 006: dt: 0.0500, sse=13104972.0, rms=23.375 (2.758%)
- 007: dt: 0.0500, sse=12461850.0, rms=22.766 (2.604%)
- 008: dt: 0.0500, sse=11878083.0, rms=22.199 (2.490%)
- 009: dt: 0.0500, sse=11342533.0, rms=21.666 (2.402%)
- 010: dt: 0.0500, sse=10847932.0, rms=21.161 (2.328%)
- positioning took 0.8 minutes
- mean border=57.4, 128 (78) missing vertices, mean dist 1.5 [0.1 (%0.1)->2.4 (%99.9))]
- %16 local maxima, %44 large gradients and %36 min vals, 541 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=11513734.0, rms=21.837
- 011: dt: 0.0500, sse=11049723.0, rms=21.368 (2.148%)
- 012: dt: 0.0500, sse=10617016.0, rms=20.921 (2.091%)
- 013: dt: 0.0500, sse=10211636.0, rms=20.493 (2.044%)
- 014: dt: 0.0500, sse=9831656.0, rms=20.084 (1.996%)
- 015: dt: 0.0500, sse=9475515.0, rms=19.693 (1.948%)
- 016: dt: 0.0500, sse=9140648.0, rms=19.318 (1.905%)
- 017: dt: 0.0500, sse=8826024.0, rms=18.958 (1.860%)
- 018: dt: 0.0500, sse=8530604.0, rms=18.614 (1.813%)
- 019: dt: 0.0500, sse=8252879.5, rms=18.285 (1.768%)
- 020: dt: 0.0500, sse=7991695.5, rms=17.970 (1.724%)
- positioning took 0.8 minutes
- mean border=57.3, 151 (63) missing vertices, mean dist 1.3 [0.1 (%1.1)->2.1 (%98.9))]
- %16 local maxima, %44 large gradients and %35 min vals, 547 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=8077674.5, rms=18.079
- 021: dt: 0.0500, sse=7826690.0, rms=17.773 (1.694%)
- 022: dt: 0.0500, sse=7591056.5, rms=17.480 (1.646%)
- 023: dt: 0.0500, sse=7368005.0, rms=17.199 (1.611%)
- 024: dt: 0.0500, sse=7158465.5, rms=16.930 (1.563%)
- 025: dt: 0.0500, sse=6961092.0, rms=16.672 (1.520%)
- 026: dt: 0.0500, sse=6775065.0, rms=16.426 (1.477%)
- 027: dt: 0.0500, sse=6598864.5, rms=16.189 (1.442%)
- 028: dt: 0.0500, sse=6430541.0, rms=15.960 (1.419%)
- 029: dt: 0.0500, sse=6269295.0, rms=15.736 (1.399%)
- 030: dt: 0.0500, sse=6115394.0, rms=15.520 (1.373%)
- positioning took 0.8 minutes
- mean border=57.2, 168 (46) missing vertices, mean dist 1.1 [0.1 (%8.5)->1.9 (%91.5))]
- %16 local maxima, %45 large gradients and %35 min vals, 495 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=6182341.5, rms=15.613
- 031: dt: 0.5000, sse=5104997.5, rms=14.018 (10.217%)
- 032: dt: 0.5000, sse=4330064.5, rms=12.740 (9.115%)
- 033: dt: 0.5000, sse=3712054.8, rms=11.622 (8.776%)
- 034: dt: 0.5000, sse=3205165.0, rms=10.611 (8.701%)
- 035: dt: 0.5000, sse=2788919.0, rms=9.704 (8.548%)
- 036: dt: 0.5000, sse=2442450.0, rms=8.875 (8.541%)
- 037: dt: 0.5000, sse=2149780.0, rms=8.113 (8.588%)
- 038: dt: 0.5000, sse=1908280.9, rms=7.422 (8.513%)
- 039: dt: 0.5000, sse=1705555.5, rms=6.795 (8.457%)
- 040: dt: 0.5000, sse=1550840.9, rms=6.270 (7.726%)
- 041: dt: 0.5000, sse=1434894.1, rms=5.849 (6.702%)
- 042: dt: 0.5000, sse=1362893.0, rms=5.568 (4.805%)
- 043: dt: 0.5000, sse=1311564.2, rms=5.363 (3.683%)
- 044: dt: 0.5000, sse=1280024.9, rms=5.229 (2.505%)
- 045: dt: 0.5000, sse=1256800.1, rms=5.131 (1.868%)
- 046: dt: 0.5000, sse=1241845.2, rms=5.064 (1.311%)
- 047: dt: 0.5000, sse=1227281.8, rms=5.003 (1.197%)
- rms = 4.98, time step reduction 1 of 3 to 0.250...
- 048: dt: 0.5000, sse=1222123.1, rms=4.978 (0.515%)
- 049: dt: 0.2500, sse=1137956.1, rms=4.546 (8.661%)
- 050: dt: 0.2500, sse=1114729.9, rms=4.430 (2.551%)
- rms = 4.42, time step reduction 2 of 3 to 0.125...
- 051: dt: 0.2500, sse=1112668.5, rms=4.418 (0.285%)
- 052: dt: 0.1250, sse=1096986.9, rms=4.333 (1.911%)
- rms = 4.31, time step reduction 3 of 3 to 0.062...
- 053: dt: 0.1250, sse=1093048.5, rms=4.313 (0.462%)
- positioning took 2.5 minutes
- mean border=55.9, 1844 (19) missing vertices, mean dist 0.2 [0.2 (%44.3)->0.6 (%55.7))]
- %29 local maxima, %35 large gradients and %30 min vals, 197 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=1417579.2, rms=4.968
- 054: dt: 0.5000, sse=1314785.0, rms=4.500 (9.422%)
- 055: dt: 0.5000, sse=1253552.2, rms=4.217 (6.283%)
- rms = 4.34, time step reduction 1 of 3 to 0.250...
- 056: dt: 0.2500, sse=1169453.6, rms=3.710 (12.026%)
- 057: dt: 0.2500, sse=1146950.6, rms=3.558 (4.109%)
- rms = 3.54, time step reduction 2 of 3 to 0.125...
- 058: dt: 0.2500, sse=1144232.9, rms=3.542 (0.439%)
- 059: dt: 0.1250, sse=1121915.8, rms=3.391 (4.271%)
- rms = 3.36, time step reduction 3 of 3 to 0.062...
- 060: dt: 0.1250, sse=1117015.8, rms=3.360 (0.918%)
- positioning took 1.0 minutes
- mean border=55.2, 2057 (12) missing vertices, mean dist 0.1 [0.2 (%46.4)->0.4 (%53.6))]
- %36 local maxima, %28 large gradients and %30 min vals, 218 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=1161311.2, rms=3.624
- rms = 3.95, time step reduction 1 of 3 to 0.250...
- 061: dt: 0.2500, sse=1134411.9, rms=3.450 (4.783%)
- 062: dt: 0.2500, sse=1123789.9, rms=3.386 (1.863%)
- rms = 3.39, time step reduction 2 of 3 to 0.125...
- rms = 3.36, time step reduction 3 of 3 to 0.062...
- 063: dt: 0.1250, sse=1119671.1, rms=3.357 (0.856%)
- positioning took 0.6 minutes
- mean border=54.7, 4182 (11) missing vertices, mean dist 0.1 [0.2 (%47.3)->0.3 (%52.7))]
- %41 local maxima, %23 large gradients and %28 min vals, 231 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-6.0.0/0050340/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=1135882.9, rms=3.456
- rms = 3.72, time step reduction 1 of 3 to 0.250...
- 064: dt: 0.2500, sse=1117968.0, rms=3.338 (3.429%)
- 065: dt: 0.2500, sse=1104542.8, rms=3.267 (2.135%)
- rms = 3.26, time step reduction 2 of 3 to 0.125...
- 066: dt: 0.2500, sse=1102385.4, rms=3.263 (0.113%)
- 067: dt: 0.1250, sse=1086868.2, rms=3.153 (3.369%)
- rms = 3.12, time step reduction 3 of 3 to 0.062...
- 068: dt: 0.1250, sse=1081908.5, rms=3.124 (0.919%)
- positioning took 0.8 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.area.pial
- vertex spacing 1.04 +- 0.47 (0.08-->7.38) (max @ vno 80091 --> 79091)
- face area 0.43 +- 0.35 (0.00-->9.74)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 119917 vertices processed
- 25000 of 119917 vertices processed
- 50000 of 119917 vertices processed
- 75000 of 119917 vertices processed
- 100000 of 119917 vertices processed
- 0 of 119917 vertices processed
- 25000 of 119917 vertices processed
- 50000 of 119917 vertices processed
- 75000 of 119917 vertices processed
- 100000 of 119917 vertices processed
- thickness calculation complete, 426:1456 truncations.
- 25286 vertices at 0 distance
- 79460 vertices at 1 distance
- 73130 vertices at 2 distance
- 34050 vertices at 3 distance
- 11585 vertices at 4 distance
- 3689 vertices at 5 distance
- 1270 vertices at 6 distance
- 478 vertices at 7 distance
- 212 vertices at 8 distance
- 77 vertices at 9 distance
- 55 vertices at 10 distance
- 22 vertices at 11 distance
- 19 vertices at 12 distance
- 14 vertices at 13 distance
- 14 vertices at 14 distance
- 16 vertices at 15 distance
- 13 vertices at 16 distance
- 10 vertices at 17 distance
- 5 vertices at 18 distance
- 8 vertices at 19 distance
- 13 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.thickness
- positioning took 13.6 minutes
- PIDs (1380 1383) completed and logs appended.
- #--------------------------------------------
- #@# Surf Volume lh Sun Oct 8 06:07:09 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label
- Total face volume 245242
- Total vertex volume 242494 (mask=0)
- #@# 0050340 lh 242494
-
- vertexvol Done
- #--------------------------------------------
- #@# Surf Volume rh Sun Oct 8 06:07:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label
- Total face volume 240534
- Total vertex volume 237315 (mask=0)
- #@# 0050340 rh 237315
-
- vertexvol Done
- #--------------------------------------------
- #@# Cortical ribbon mask Sun Oct 8 06:07:14 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340
- 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 = 431
- writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/ribbon.mgz
- mris_volmask took 8.55 minutes
- writing ribbon files
- #-----------------------------------------
- #@# Parcellation Stats lh Sun Oct 8 06:15:47 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 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 0050340 lh pial
- #-----------------------------------------
- #@# Parcellation Stats rh Sun Oct 8 06:15:47 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 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 0050340 rh pial
- Waiting for PID 2870 of (2870 2873 2876 2879) to complete...
- Waiting for PID 2873 of (2870 2873 2876 2879) to complete...
- Waiting for PID 2876 of (2870 2873 2876 2879) to complete...
- Waiting for PID 2879 of (2870 2873 2876 2879) 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 0050340 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 245242
- Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 1314 917 2464 2.810 0.518 0.100 0.018 9 1.0 bankssts
- 793 503 1459 2.816 0.638 0.131 0.026 10 0.7 caudalanteriorcingulate
- 2728 1842 6109 2.946 0.565 0.108 0.020 22 2.1 caudalmiddlefrontal
- 2049 1337 3139 2.098 0.583 0.153 0.042 32 3.5 cuneus
- 556 381 1327 2.923 0.979 0.141 0.050 9 1.2 entorhinal
- 3691 2576 8351 2.816 0.687 0.137 0.039 50 5.5 fusiform
- 5662 3898 11987 2.695 0.613 0.127 0.030 67 7.1 inferiorparietal
- 4630 3109 10021 2.735 0.866 0.135 0.043 72 8.6 inferiortemporal
- 1344 858 2584 2.675 0.915 0.126 0.034 18 1.5 isthmuscingulate
- 7386 5003 13650 2.328 0.668 0.144 0.040 99 12.0 lateraloccipital
- 4041 2700 7892 2.728 0.754 0.143 0.044 64 7.6 lateralorbitofrontal
- 4547 3200 7431 2.095 0.673 0.151 0.040 64 7.6 lingual
- 3018 2057 5467 2.397 0.787 0.128 0.042 40 5.2 medialorbitofrontal
- 4210 2970 12304 3.138 0.763 0.128 0.034 54 5.8 middletemporal
- 865 553 1908 2.737 0.915 0.081 0.017 4 0.5 parahippocampal
- 2026 1340 3945 2.753 0.672 0.108 0.024 15 2.2 paracentral
- 2223 1505 5498 3.047 0.524 0.113 0.024 22 2.1 parsopercularis
- 1023 674 2856 3.134 0.656 0.139 0.037 16 1.7 parsorbitalis
- 1881 1268 4323 2.776 0.722 0.137 0.037 28 2.7 parstriangularis
- 1908 1312 2105 1.704 0.461 0.130 0.037 20 3.0 pericalcarine
- 5423 3528 8965 2.255 0.721 0.112 0.025 53 5.3 postcentral
- 1545 1072 3243 2.760 0.774 0.150 0.037 24 2.2 posteriorcingulate
- 7139 4402 14254 2.926 0.643 0.110 0.028 68 8.5 precentral
- 4594 3155 9283 2.512 0.676 0.134 0.031 56 5.8 precuneus
- 1121 755 2759 2.960 0.719 0.131 0.034 15 1.5 rostralanteriorcingulate
- 7435 5281 17130 2.711 0.692 0.150 0.042 111 13.4 rostralmiddlefrontal
- 9620 6566 24949 3.201 0.738 0.129 0.031 116 12.3 superiorfrontal
- 6646 4481 12027 2.466 0.581 0.127 0.030 74 8.1 superiorparietal
- 5131 3519 12405 2.862 0.740 0.109 0.024 41 5.4 superiortemporal
- 4625 3236 10587 2.889 0.585 0.139 0.030 60 5.8 supramarginal
- 400 269 1300 2.960 0.648 0.183 0.074 12 0.9 frontalpole
- 566 460 3053 4.182 0.626 0.161 0.048 10 1.1 temporalpole
- 664 410 1100 2.418 0.448 0.108 0.029 6 0.7 transversetemporal
- 3441 2303 6603 2.947 0.764 0.126 0.035 39 4.7 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 0050340 lh pial
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 245242
- Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 1314 839 2464 2.810 0.518 0.132 0.035 20 2.1 bankssts
- 793 615 1459 2.816 0.638 0.214 0.061 77 1.8 caudalanteriorcingulate
- 2728 2211 6109 2.946 0.565 0.122 0.028 30 3.5 caudalmiddlefrontal
- 2049 1692 3139 2.098 0.583 0.149 0.037 31 3.3 cuneus
- 556 528 1327 2.923 0.979 0.232 0.074 20 2.0 entorhinal
- 3691 3345 8351 2.816 0.687 0.168 0.044 53 7.5 fusiform
- 5662 4922 11987 2.695 0.613 0.153 0.036 76 9.6 inferiorparietal
- 4630 4047 10021 2.735 0.866 0.162 0.042 73 9.6 inferiortemporal
- 1344 1053 2584 2.675 0.915 0.153 0.039 19 2.3 isthmuscingulate
- 7386 6432 13650 2.328 0.668 0.155 0.038 98 12.9 lateraloccipital
- 4041 2985 7892 2.728 0.754 0.140 0.037 69 6.8 lateralorbitofrontal
- 4547 4019 7431 2.095 0.673 0.163 0.041 82 8.2 lingual
- 3018 2578 5467 2.397 0.787 0.153 0.041 46 5.5 medialorbitofrontal
- 4210 4553 12304 3.138 0.763 0.167 0.035 48 7.1 middletemporal
- 865 877 1908 2.737 0.915 0.166 0.039 8 1.6 parahippocampal
- 2026 1607 3945 2.753 0.672 0.126 0.027 20 2.5 paracentral
- 2223 2054 5498 3.047 0.524 0.151 0.032 22 3.2 parsopercularis
- 1023 1085 2856 3.134 0.656 0.157 0.029 11 1.5 parsorbitalis
- 1881 1740 4323 2.776 0.722 0.162 0.037 39 3.5 parstriangularis
- 1908 1209 2105 1.704 0.461 0.134 0.036 27 2.9 pericalcarine
- 5423 4438 8965 2.255 0.721 0.127 0.028 51 7.1 postcentral
- 1545 1268 3243 2.760 0.774 0.165 0.042 30 2.8 posteriorcingulate
- 7139 5191 14254 2.926 0.643 0.106 0.023 76 6.9 precentral
- 4594 4002 9283 2.512 0.676 0.156 0.037 62 7.7 precuneus
- 1121 1081 2759 2.960 0.719 0.157 0.040 15 1.9 rostralanteriorcingulate
- 7435 7004 17130 2.711 0.692 0.179 0.040 120 14.6 rostralmiddlefrontal
- 9620 8749 24949 3.201 0.738 0.155 0.037 134 16.0 superiorfrontal
- 6646 5237 12027 2.466 0.581 0.132 0.029 74 8.7 superiorparietal
- 5131 4750 12405 2.862 0.740 0.148 0.030 55 7.3 superiortemporal
- 4625 4063 10587 2.889 0.585 0.152 0.034 75 6.9 supramarginal
- 400 552 1300 2.960 0.648 0.264 0.066 10 1.6 frontalpole
- 566 958 3053 4.182 0.626 0.232 0.041 6 1.1 temporalpole
- 664 529 1100 2.418 0.448 0.123 0.030 4 0.9 transversetemporal
- 3441 2123 6603 2.947 0.764 0.123 0.035 59 5.0 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 0050340 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 240534
- Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 1269 889 2356 2.931 0.569 0.121 0.023 10 1.2 bankssts
- 1019 673 2032 2.780 0.630 0.126 0.021 12 0.8 caudalanteriorcingulate
- 2671 1751 6021 3.060 0.540 0.108 0.023 22 2.4 caudalmiddlefrontal
- 1864 1270 2889 2.069 0.544 0.164 0.050 31 4.1 cuneus
- 606 388 1405 2.967 1.018 0.134 0.077 11 2.2 entorhinal
- 3824 2594 8522 2.773 0.733 0.138 0.040 55 6.5 fusiform
- 6912 4850 14443 2.484 0.661 0.128 0.031 86 9.1 inferiorparietal
- 4297 2825 8980 2.640 0.804 0.138 0.055 88 12.2 inferiortemporal
- 1427 927 3062 2.659 0.878 0.125 0.035 17 1.8 isthmuscingulate
- 6487 4435 12330 2.298 0.659 0.149 0.040 91 10.2 lateraloccipital
- 3947 2655 7608 2.578 0.748 0.146 0.053 65 9.1 lateralorbitofrontal
- 4350 2993 6866 2.056 0.619 0.142 0.038 54 6.8 lingual
- 2716 1857 5955 2.717 0.879 0.129 0.037 40 4.4 medialorbitofrontal
- 4604 3223 12027 3.050 0.764 0.130 0.035 64 6.9 middletemporal
- 1070 654 2008 2.534 0.860 0.108 0.037 13 1.6 parahippocampal
- 2173 1388 3996 2.681 0.679 0.098 0.021 12 1.9 paracentral
- 1895 1252 4828 3.122 0.681 0.114 0.023 16 1.9 parsopercularis
- 1116 784 3263 3.121 0.719 0.153 0.037 17 1.7 parsorbitalis
- 2166 1488 4811 2.778 0.684 0.120 0.025 22 2.3 parstriangularis
- 1612 1184 1940 1.766 0.521 0.123 0.033 13 2.1 pericalcarine
- 4970 3294 8059 2.169 0.710 0.109 0.026 46 5.0 postcentral
- 1700 1183 3295 2.413 0.906 0.150 0.033 28 2.2 posteriorcingulate
- 7050 4441 14631 2.935 0.597 0.109 0.029 62 8.8 precentral
- 5090 3492 9180 2.477 0.663 0.126 0.027 57 5.4 precuneus
- 753 503 1803 3.244 0.626 0.136 0.037 9 1.1 rostralanteriorcingulate
- 7675 5391 17447 2.637 0.690 0.146 0.039 108 12.5 rostralmiddlefrontal
- 9422 6257 23712 3.137 0.711 0.125 0.036 110 14.6 superiorfrontal
- 7185 4768 12707 2.327 0.572 0.123 0.029 80 8.4 superiorparietal
- 4860 3324 11522 2.856 0.730 0.111 0.028 52 6.0 superiortemporal
- 3877 2619 8795 2.871 0.602 0.129 0.031 44 4.6 supramarginal
- 418 292 1338 2.946 0.877 0.178 0.053 9 1.0 frontalpole
- 568 403 2480 3.737 0.774 0.144 0.039 10 0.9 temporalpole
- 519 316 928 2.569 0.574 0.110 0.029 6 0.5 transversetemporal
- 2915 2016 6038 3.038 0.670 0.129 0.036 30 4.0 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 0050340 rh pial
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 240534
- Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 1269 709 2356 2.931 0.569 0.121 0.030 17 1.5 bankssts
- 1019 829 2032 2.780 0.630 0.169 0.040 27 1.8 caudalanteriorcingulate
- 2671 2140 6021 3.060 0.540 0.118 0.026 29 3.0 caudalmiddlefrontal
- 1864 1592 2889 2.069 0.544 0.156 0.040 25 3.2 cuneus
- 606 486 1405 2.967 1.018 0.160 0.051 14 1.3 entorhinal
- 3824 3344 8522 2.773 0.733 0.153 0.041 48 6.7 fusiform
- 6912 6454 14443 2.484 0.661 0.157 0.034 85 10.6 inferiorparietal
- 4297 3656 8980 2.640 0.804 0.162 0.043 71 8.6 inferiortemporal
- 1427 1230 3062 2.659 0.878 0.160 0.042 25 2.7 isthmuscingulate
- 6487 5930 12330 2.298 0.659 0.164 0.039 98 11.9 lateraloccipital
- 3947 3160 7608 2.578 0.748 0.160 0.050 78 10.6 lateralorbitofrontal
- 4350 3782 6866 2.056 0.619 0.154 0.038 57 7.4 lingual
- 2716 2492 5955 2.717 0.879 0.161 0.041 43 5.1 medialorbitofrontal
- 4604 4538 12027 3.050 0.764 0.165 0.039 53 8.7 middletemporal
- 1070 876 2008 2.534 0.860 0.154 0.042 14 2.2 parahippocampal
- 2173 1570 3996 2.681 0.679 0.114 0.024 17 2.3 paracentral
- 1895 1675 4828 3.122 0.681 0.140 0.033 17 2.7 parsopercularis
- 1116 1270 3263 3.121 0.719 0.167 0.030 11 1.5 parsorbitalis
- 2166 1918 4811 2.778 0.684 0.162 0.033 30 3.3 parstriangularis
- 1612 1103 1940 1.766 0.521 0.132 0.034 21 2.3 pericalcarine
- 4970 4090 8059 2.169 0.710 0.123 0.024 47 5.3 postcentral
- 1700 1459 3295 2.413 0.906 0.160 0.038 31 2.9 posteriorcingulate
- 7050 5244 14631 2.935 0.597 0.109 0.024 73 7.6 precentral
- 5090 3942 9180 2.477 0.663 0.141 0.038 78 8.5 precuneus
- 753 646 1803 3.244 0.626 0.151 0.044 14 1.4 rostralanteriorcingulate
- 7675 7386 17447 2.637 0.690 0.177 0.041 115 14.8 rostralmiddlefrontal
- 9422 8322 23712 3.137 0.711 0.150 0.037 126 15.8 superiorfrontal
- 7185 5858 12707 2.327 0.572 0.139 0.030 85 9.8 superiorparietal
- 4860 4584 11522 2.856 0.730 0.159 0.039 76 9.5 superiortemporal
- 3877 3283 8795 2.871 0.602 0.143 0.032 44 5.8 supramarginal
- 418 593 1338 2.946 0.877 0.248 0.046 7 1.0 frontalpole
- 568 810 2480 3.737 0.774 0.205 0.040 6 1.1 temporalpole
- 519 429 928 2.569 0.574 0.131 0.033 4 0.8 transversetemporal
- 2915 1831 6038 3.038 0.670 0.128 0.046 51 6.6 insula
- PIDs (2870 2873 2876 2879) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 2 lh Sun Oct 8 06:16:55 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot
- #-----------------------------------------
- #@# Cortical Parc 2 rh Sun Oct 8 06:16:55 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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 3003 of (3003 3006) to complete...
- Waiting for PID 3006 of (3003 3006) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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...
- 15 labels changed using aseg
- relabeling using gibbs priors...
- 000: 8033 changed, 121622 examined...
- 001: 1932 changed, 31209 examined...
- 002: 529 changed, 10129 examined...
- 003: 237 changed, 3043 examined...
- 004: 104 changed, 1359 examined...
- 005: 53 changed, 602 examined...
- 006: 23 changed, 294 examined...
- 007: 16 changed, 138 examined...
- 008: 11 changed, 90 examined...
- 009: 6 changed, 59 examined...
- 010: 2 changed, 34 examined...
- 011: 2 changed, 10 examined...
- 012: 3 changed, 16 examined...
- 013: 4 changed, 18 examined...
- 014: 2 changed, 19 examined...
- 015: 1 changed, 15 examined...
- 016: 0 changed, 7 examined...
- 3 labels changed using aseg
- 000: 253 total segments, 166 labels (2019 vertices) changed
- 001: 94 total segments, 7 labels (9 vertices) changed
- 002: 87 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 41 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1361 vertices marked for relabeling...
- 1361 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 0 minutes and 16 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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...
- 13 labels changed using aseg
- relabeling using gibbs priors...
- 000: 7923 changed, 119917 examined...
- 001: 1863 changed, 31124 examined...
- 002: 521 changed, 9925 examined...
- 003: 259 changed, 2964 examined...
- 004: 109 changed, 1439 examined...
- 005: 40 changed, 615 examined...
- 006: 22 changed, 216 examined...
- 007: 16 changed, 118 examined...
- 008: 12 changed, 86 examined...
- 009: 5 changed, 68 examined...
- 010: 4 changed, 26 examined...
- 011: 2 changed, 21 examined...
- 012: 3 changed, 16 examined...
- 013: 0 changed, 17 examined...
- 15 labels changed using aseg
- 000: 219 total segments, 135 labels (1684 vertices) changed
- 001: 87 total segments, 4 labels (9 vertices) changed
- 002: 83 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 34 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1217 vertices marked for relabeling...
- 1217 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 0 minutes and 16 seconds.
- PIDs (3003 3006) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Sun Oct 8 06:17:12 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 lh white
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Sun Oct 8 06:17:12 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 rh white
- Waiting for PID 3053 of (3053 3056) to complete...
- Waiting for PID 3056 of (3053 3056) 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 0050340 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 245242
- Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 1195 845 2528 2.523 0.659 0.144 0.037 16 1.9 G&S_frontomargin
- 1436 976 3687 2.815 0.652 0.145 0.037 19 2.0 G&S_occipital_inf
- 1680 1031 3138 2.573 0.709 0.111 0.028 15 2.0 G&S_paracentral
- 1209 797 2828 2.959 0.532 0.133 0.027 15 1.3 G&S_subcentral
- 744 545 2456 2.944 0.775 0.198 0.066 23 2.1 G&S_transv_frontopol
- 2135 1469 4555 2.942 0.683 0.123 0.030 20 2.5 G&S_cingul-Ant
- 1023 738 2232 2.998 0.686 0.117 0.021 7 0.8 G&S_cingul-Mid-Ant
- 1201 840 2571 2.827 0.667 0.123 0.026 12 1.2 G&S_cingul-Mid-Post
- 548 379 1622 3.112 0.787 0.183 0.054 13 1.3 G_cingul-Post-dorsal
- 362 202 798 3.066 0.871 0.138 0.053 7 0.5 G_cingul-Post-ventral
- 1902 1229 3102 2.066 0.633 0.154 0.050 34 4.1 G_cuneus
- 1388 904 3938 3.178 0.518 0.133 0.031 20 1.7 G_front_inf-Opercular
- 491 304 1345 3.236 0.710 0.141 0.052 8 1.0 G_front_inf-Orbital
- 1120 741 3367 3.213 0.583 0.140 0.040 20 1.5 G_front_inf-Triangul
- 3824 2653 11427 3.074 0.663 0.153 0.043 66 7.0 G_front_middle
- 6843 4515 19956 3.336 0.726 0.137 0.036 99 10.1 G_front_sup
- 698 448 1376 3.021 0.788 0.147 0.043 11 1.2 G_Ins_lg&S_cent_ins
- 753 499 2246 3.224 0.720 0.145 0.048 15 1.3 G_insular_short
- 2099 1410 5112 2.655 0.618 0.141 0.045 31 3.6 G_occipital_middle
- 1236 843 1977 2.074 0.518 0.152 0.039 18 1.8 G_occipital_sup
- 1590 1077 4037 2.935 0.646 0.162 0.049 30 3.0 G_oc-temp_lat-fusifor
- 3302 2314 5565 1.996 0.696 0.164 0.047 55 6.6 G_oc-temp_med-Lingual
- 1078 690 2606 2.819 0.932 0.121 0.044 15 1.7 G_oc-temp_med-Parahip
- 2530 1654 6175 2.768 0.871 0.165 0.065 58 7.1 G_orbital
- 2154 1482 5737 2.826 0.635 0.150 0.042 38 3.8 G_pariet_inf-Angular
- 2308 1618 6248 3.032 0.583 0.146 0.031 36 3.1 G_pariet_inf-Supramar
- 2865 1919 6070 2.540 0.619 0.132 0.033 37 4.2 G_parietal_sup
- 2113 1272 3888 2.341 0.721 0.126 0.034 30 2.8 G_postcentral
- 2680 1486 6563 3.238 0.621 0.114 0.038 33 4.2 G_precentral
- 2265 1544 6127 2.839 0.606 0.158 0.042 40 3.8 G_precuneus
- 956 657 2277 2.507 0.742 0.153 0.065 18 2.4 G_rectus
- 900 589 941 1.865 0.813 0.104 0.045 10 1.6 G_subcallosal
- 529 317 982 2.394 0.542 0.113 0.037 6 0.8 G_temp_sup-G_T_transv
- 1743 1222 6279 3.408 0.717 0.150 0.041 26 3.0 G_temp_sup-Lateral
- 600 421 1670 3.235 0.998 0.100 0.024 3 0.5 G_temp_sup-Plan_polar
- 744 513 1449 2.555 0.571 0.080 0.012 2 0.4 G_temp_sup-Plan_tempo
- 2374 1558 6267 2.766 0.981 0.151 0.062 54 6.4 G_temporal_inf
- 2269 1612 8418 3.408 0.704 0.152 0.048 43 4.4 G_temporal_middle
- 204 143 349 2.513 0.395 0.097 0.012 1 0.1 Lat_Fis-ant-Horizont
- 166 118 281 2.628 0.497 0.103 0.017 1 0.1 Lat_Fis-ant-Vertical
- 939 641 1255 2.659 0.597 0.116 0.023 7 0.8 Lat_Fis-post
- 2177 1454 3839 2.189 0.711 0.151 0.047 33 4.4 Pole_occipital
- 1379 1039 5267 3.517 0.767 0.150 0.041 22 2.4 Pole_temporal
- 2296 1599 2636 1.853 0.534 0.122 0.028 17 2.6 S_calcarine
- 2993 2021 3885 2.192 0.750 0.104 0.023 21 2.8 S_central
- 1141 789 1724 2.515 0.608 0.104 0.018 7 0.8 S_cingul-Marginalis
- 538 355 932 3.179 0.552 0.106 0.019 3 0.4 S_circular_insula_ant
- 1500 1015 2301 2.699 0.625 0.083 0.015 5 1.0 S_circular_insula_inf
- 1576 1065 2260 2.611 0.525 0.098 0.020 7 1.3 S_circular_insula_sup
- 645 448 1300 3.243 0.837 0.109 0.021 4 0.6 S_collat_transv_ant
- 582 406 717 2.164 0.603 0.117 0.021 4 0.5 S_collat_transv_post
- 2112 1504 3822 2.648 0.455 0.125 0.028 19 2.4 S_front_inf
- 1167 843 2000 2.464 0.624 0.131 0.031 11 1.6 S_front_middle
- 2235 1575 3996 2.700 0.521 0.107 0.022 17 2.0 S_front_sup
- 165 122 392 2.965 0.847 0.133 0.034 2 0.2 S_interm_prim-Jensen
- 2669 1850 3829 2.452 0.497 0.119 0.022 23 2.2 S_intrapariet&P_trans
- 1080 756 1419 2.066 0.436 0.135 0.030 9 1.5 S_oc_middle&Lunatus
- 976 675 1306 2.117 0.386 0.117 0.032 10 1.0 S_oc_sup&transversal
- 749 516 1211 2.443 0.516 0.130 0.031 9 0.8 S_occipital_ant
- 928 643 1452 2.495 0.483 0.105 0.021 5 0.8 S_oc-temp_lat
- 1837 1301 3005 2.517 0.553 0.106 0.018 12 1.3 S_oc-temp_med&Lingual
- 425 286 555 2.110 0.422 0.107 0.019 2 0.3 S_orbital_lateral
- 646 468 926 2.202 0.613 0.129 0.028 6 0.6 S_orbital_med-olfact
- 1660 1127 3189 2.816 0.621 0.132 0.032 21 2.2 S_orbital-H_Shaped
- 1439 1001 2035 2.116 0.625 0.128 0.025 15 1.4 S_parieto_occipital
- 1268 757 1277 2.293 0.834 0.124 0.022 17 0.9 S_pericallosal
- 2440 1656 3952 2.611 0.507 0.112 0.021 18 2.2 S_postcentral
- 1456 1015 2616 2.838 0.489 0.091 0.013 6 0.8 S_precentral-inf-part
- 1290 903 2140 2.745 0.463 0.100 0.018 6 1.0 S_precentral-sup-part
- 667 477 1167 2.789 0.711 0.123 0.019 5 0.6 S_suborbital
- 793 551 1294 2.499 0.612 0.118 0.022 5 0.7 S_subparietal
- 1537 1077 2346 2.455 0.602 0.114 0.020 11 1.3 S_temporal_inf
- 5405 3729 9877 2.752 0.581 0.102 0.018 33 4.2 S_temporal_sup
- 282 201 384 2.231 0.404 0.129 0.017 2 0.2 S_temporal_transverse
- mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050340 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 240534
- Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 850 596 1703 2.309 0.759 0.148 0.040 12 1.6 G&S_frontomargin
- 1171 818 2897 2.699 0.685 0.151 0.044 17 1.9 G&S_occipital_inf
- 1371 791 2366 2.500 0.675 0.110 0.037 12 2.3 G&S_paracentral
- 1109 718 2680 3.067 0.565 0.133 0.035 14 1.4 G&S_subcentral
- 1026 767 3515 3.181 0.793 0.170 0.050 18 2.1 G&S_transv_frontopol
- 2566 1791 5526 2.924 0.668 0.120 0.028 23 3.0 G&S_cingul-Ant
- 1265 894 2717 3.096 0.532 0.118 0.023 11 1.1 G&S_cingul-Mid-Ant
- 1343 953 2655 2.715 0.683 0.139 0.030 16 1.5 G&S_cingul-Mid-Post
- 568 392 1708 3.105 0.845 0.180 0.047 12 1.2 G_cingul-Post-dorsal
- 344 209 932 2.919 0.804 0.126 0.042 5 0.5 G_cingul-Post-ventral
- 1841 1247 2944 2.022 0.593 0.164 0.051 33 4.1 G_cuneus
- 1256 808 3984 3.371 0.636 0.132 0.030 16 1.5 G_front_inf-Opercular
- 360 241 1282 3.387 0.526 0.162 0.045 7 0.7 G_front_inf-Orbital
- 981 665 2854 3.161 0.609 0.140 0.032 16 1.2 G_front_inf-Triangul
- 3009 1991 9164 3.083 0.690 0.148 0.044 54 5.3 G_front_middle
- 6492 4108 18458 3.287 0.684 0.137 0.045 102 12.8 G_front_sup
- 498 358 1332 3.383 0.685 0.130 0.036 7 0.5 G_Ins_lg&S_cent_ins
- 612 388 1650 3.197 0.671 0.140 0.049 10 1.1 G_insular_short
- 1785 1200 3795 2.351 0.660 0.152 0.043 30 3.1 G_occipital_middle
- 1432 932 2556 2.244 0.580 0.145 0.039 20 2.3 G_occipital_sup
- 1699 1076 4105 2.806 0.766 0.156 0.059 37 4.3 G_oc-temp_lat-fusifor
- 2758 1873 4656 2.040 0.651 0.154 0.043 41 4.8 G_oc-temp_med-Lingual
- 1157 679 2568 2.797 0.979 0.134 0.073 23 3.7 G_oc-temp_med-Parahip
- 2528 1736 6949 2.932 0.780 0.161 0.058 48 6.8 G_orbital
- 2530 1802 7455 2.849 0.674 0.164 0.046 54 4.8 G_pariet_inf-Angular
- 1900 1277 5009 3.057 0.638 0.147 0.040 30 2.7 G_pariet_inf-Supramar
- 2099 1408 5013 2.614 0.566 0.135 0.036 33 3.0 G_parietal_sup
- 1706 1119 3097 2.137 0.572 0.121 0.032 22 2.3 G_postcentral
- 2693 1554 7249 3.238 0.552 0.114 0.038 33 4.4 G_precentral
- 2615 1758 5239 2.402 0.638 0.135 0.033 38 3.2 G_precuneus
- 779 535 2363 2.868 0.924 0.152 0.057 18 2.0 G_rectus
- 652 392 804 2.219 1.077 0.102 0.047 10 0.9 G_subcallosal
- 402 245 800 2.582 0.647 0.122 0.038 5 0.5 G_temp_sup-G_T_transv
- 1663 1124 5477 3.248 0.688 0.144 0.039 29 2.8 G_temp_sup-Lateral
- 878 585 1757 2.621 0.763 0.109 0.048 10 2.0 G_temp_sup-Plan_polar
- 721 507 1431 2.641 0.503 0.090 0.018 6 0.5 G_temp_sup-Plan_tempo
- 2185 1348 5335 2.701 0.921 0.156 0.089 68 10.2 G_temporal_inf
- 2739 1925 8728 3.291 0.717 0.157 0.049 55 5.7 G_temporal_middle
- 373 256 458 2.095 0.433 0.094 0.013 2 0.2 Lat_Fis-ant-Horizont
- 271 178 467 2.908 0.454 0.097 0.017 1 0.2 Lat_Fis-ant-Vertical
- 1164 804 1648 2.453 0.519 0.111 0.023 7 1.1 Lat_Fis-post
- 2844 1939 5024 2.117 0.628 0.149 0.045 42 5.1 Pole_occipital
- 1420 1046 5706 3.619 0.786 0.147 0.039 22 2.3 Pole_temporal
- 1807 1307 2386 2.102 0.635 0.122 0.028 16 2.1 S_calcarine
- 2867 1959 3689 2.195 0.744 0.098 0.020 14 2.3 S_central
- 1111 785 1606 2.167 0.511 0.098 0.017 6 0.7 S_cingul-Marginalis
- 483 335 902 3.315 0.467 0.115 0.024 3 0.5 S_circular_insula_ant
- 1117 776 1729 2.768 0.642 0.100 0.019 6 0.9 S_circular_insula_inf
- 1302 897 2075 2.834 0.474 0.113 0.022 7 1.4 S_circular_insula_sup
- 733 535 1500 2.834 0.557 0.108 0.020 5 0.6 S_collat_transv_ant
- 630 433 872 2.034 0.542 0.142 0.040 7 1.0 S_collat_transv_post
- 2293 1610 3963 2.441 0.502 0.109 0.020 16 1.9 S_front_inf
- 1757 1248 3140 2.419 0.556 0.143 0.038 21 2.6 S_front_middle
- 2388 1651 4557 2.771 0.584 0.113 0.024 16 2.4 S_front_sup
- 175 131 403 2.798 0.313 0.122 0.021 1 0.2 S_interm_prim-Jensen
- 3220 2122 4238 2.142 0.496 0.102 0.017 20 2.2 S_intrapariet&P_trans
- 705 479 962 2.138 0.504 0.132 0.027 6 0.8 S_oc_middle&Lunatus
- 1104 767 1292 1.842 0.398 0.124 0.029 8 1.3 S_oc_sup&transversal
- 664 468 1308 2.377 0.553 0.126 0.025 8 0.7 S_occipital_ant
- 1085 746 1587 2.375 0.538 0.111 0.021 6 1.0 S_oc-temp_lat
- 2232 1549 3410 2.396 0.585 0.105 0.017 14 1.5 S_oc-temp_med&Lingual
- 421 287 661 2.707 0.547 0.119 0.031 3 0.5 S_orbital_lateral
- 713 509 1023 2.116 0.479 0.144 0.039 7 1.3 S_orbital_med-olfact
- 1328 914 2374 2.549 0.573 0.138 0.044 19 2.2 S_orbital-H_Shaped
- 1665 1182 2523 2.404 0.677 0.106 0.020 11 1.4 S_parieto_occipital
- 1607 985 1605 2.115 0.792 0.116 0.021 20 1.1 S_pericallosal
- 2023 1359 2963 2.292 0.520 0.101 0.018 13 1.4 S_postcentral
- 1654 1145 2820 2.747 0.444 0.101 0.017 9 1.1 S_precentral-inf-part
- 1320 903 2149 2.791 0.484 0.085 0.013 4 0.8 S_precentral-sup-part
- 402 283 640 2.776 0.884 0.099 0.016 2 0.2 S_suborbital
- 1058 721 2029 2.795 0.576 0.131 0.029 10 1.2 S_subparietal
- 1243 894 1978 2.496 0.655 0.126 0.021 13 1.2 S_temporal_inf
- 6039 4197 10542 2.658 0.601 0.099 0.018 35 4.7 S_temporal_sup
- 228 159 333 2.528 0.454 0.118 0.020 1 0.2 S_temporal_transverse
- PIDs (3053 3056) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 3 lh Sun Oct 8 06:17:47 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot
- #-----------------------------------------
- #@# Cortical Parc 3 rh Sun Oct 8 06:17:47 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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 3126 of (3126 3129) to complete...
- Waiting for PID 3129 of (3126 3129) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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...
- 1369 labels changed using aseg
- relabeling using gibbs priors...
- 000: 1854 changed, 121622 examined...
- 001: 428 changed, 8446 examined...
- 002: 105 changed, 2472 examined...
- 003: 46 changed, 614 examined...
- 004: 23 changed, 279 examined...
- 005: 21 changed, 128 examined...
- 006: 20 changed, 103 examined...
- 007: 8 changed, 92 examined...
- 008: 8 changed, 45 examined...
- 009: 8 changed, 40 examined...
- 010: 4 changed, 39 examined...
- 011: 5 changed, 23 examined...
- 012: 3 changed, 31 examined...
- 013: 3 changed, 15 examined...
- 014: 2 changed, 18 examined...
- 015: 1 changed, 7 examined...
- 016: 1 changed, 7 examined...
- 017: 3 changed, 10 examined...
- 018: 2 changed, 11 examined...
- 019: 1 changed, 13 examined...
- 020: 1 changed, 7 examined...
- 021: 1 changed, 7 examined...
- 022: 1 changed, 7 examined...
- 023: 3 changed, 9 examined...
- 024: 2 changed, 13 examined...
- 025: 5 changed, 14 examined...
- 026: 4 changed, 26 examined...
- 027: 2 changed, 26 examined...
- 028: 3 changed, 13 examined...
- 029: 1 changed, 17 examined...
- 030: 0 changed, 7 examined...
- 265 labels changed using aseg
- 000: 54 total segments, 21 labels (205 vertices) changed
- 001: 34 total segments, 1 labels (7 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 1 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 851 vertices marked for relabeling...
- 851 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas.annot...
- classification took 0 minutes and 13 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050340 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...
- 1174 labels changed using aseg
- relabeling using gibbs priors...
- 000: 1715 changed, 119917 examined...
- 001: 381 changed, 8021 examined...
- 002: 128 changed, 2190 examined...
- 003: 34 changed, 735 examined...
- 004: 23 changed, 201 examined...
- 005: 21 changed, 151 examined...
- 006: 19 changed, 121 examined...
- 007: 8 changed, 76 examined...
- 008: 12 changed, 55 examined...
- 009: 14 changed, 61 examined...
- 010: 15 changed, 71 examined...
- 011: 15 changed, 65 examined...
- 012: 10 changed, 66 examined...
- 013: 7 changed, 45 examined...
- 014: 4 changed, 29 examined...
- 015: 2 changed, 19 examined...
- 016: 0 changed, 14 examined...
- 219 labels changed using aseg
- 000: 52 total segments, 19 labels (147 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 5 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 924 vertices marked for relabeling...
- 924 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas.annot...
- classification took 0 minutes and 13 seconds.
- PIDs (3126 3129) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Sun Oct 8 06:18:00 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 lh white
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Sun Oct 8 06:18:00 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 rh white
- Waiting for PID 3214 of (3214 3217) to complete...
- Waiting for PID 3217 of (3214 3217) 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 0050340 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 245242
- Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 1685 1104 3577 2.994 0.654 0.130 0.028 19 1.9 caudalanteriorcingulate
- 2981 2006 6577 2.924 0.566 0.108 0.019 24 2.3 caudalmiddlefrontal
- 2602 1721 4078 2.099 0.620 0.142 0.038 36 4.0 cuneus
- 456 312 1107 2.815 0.963 0.154 0.057 9 1.1 entorhinal
- 3445 2414 7401 2.777 0.679 0.136 0.037 45 4.9 fusiform
- 5658 3909 11955 2.663 0.619 0.127 0.030 67 7.0 inferiorparietal
- 4542 3054 10479 2.765 0.870 0.137 0.044 72 8.8 inferiortemporal
- 1308 836 2562 2.737 0.879 0.127 0.034 18 1.4 isthmuscingulate
- 7430 5012 13800 2.331 0.668 0.145 0.040 101 12.1 lateraloccipital
- 4634 3133 9104 2.603 0.808 0.151 0.052 82 10.2 lateralorbitofrontal
- 4601 3241 7469 2.084 0.673 0.152 0.040 64 7.8 lingual
- 2489 1705 4813 2.403 0.770 0.132 0.046 36 4.5 medialorbitofrontal
- 5565 3910 14616 3.072 0.723 0.124 0.031 65 7.1 middletemporal
- 945 599 2097 2.770 0.918 0.083 0.019 5 0.5 parahippocampal
- 2292 1532 4642 2.814 0.687 0.106 0.023 16 2.3 paracentral
- 2010 1363 5086 3.074 0.521 0.117 0.025 21 2.0 parsopercularis
- 1017 662 2462 3.095 0.642 0.117 0.024 9 0.9 parsorbitalis
- 2370 1616 5208 2.722 0.692 0.140 0.038 36 3.6 parstriangularis
- 1918 1318 2131 1.707 0.463 0.134 0.040 23 3.4 pericalcarine
- 6209 4038 10678 2.326 0.735 0.116 0.026 63 6.5 postcentral
- 1742 1212 3515 2.747 0.799 0.147 0.035 26 2.5 posteriorcingulate
- 6985 4299 13933 2.930 0.642 0.109 0.029 66 8.3 precentral
- 4508 3110 9385 2.542 0.667 0.138 0.033 58 6.0 precuneus
- 1531 1025 3373 2.980 0.736 0.125 0.032 17 1.8 rostralanteriorcingulate
- 5392 3798 13083 2.816 0.672 0.150 0.040 78 9.1 rostralmiddlefrontal
- 10192 6997 26137 3.078 0.793 0.133 0.034 136 14.4 superiorfrontal
- 5390 3632 9450 2.461 0.538 0.123 0.028 55 6.1 superiorparietal
- 6550 4551 16929 2.955 0.814 0.112 0.025 58 7.0 superiortemporal
- 4286 3007 9814 2.914 0.576 0.140 0.030 56 5.4 supramarginal
- 691 425 1116 2.399 0.453 0.110 0.031 7 0.8 transversetemporal
- 2825 1902 5916 3.118 0.646 0.123 0.032 31 3.5 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 0050340 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 240534
- Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 1054 707 2119 2.761 0.679 0.129 0.022 13 0.9 caudalanteriorcingulate
- 2934 1916 6398 3.031 0.546 0.110 0.024 24 2.8 caudalmiddlefrontal
- 2263 1542 3620 2.122 0.550 0.154 0.047 35 4.6 cuneus
- 442 303 1152 3.199 0.784 0.112 0.034 5 0.4 entorhinal
- 3592 2427 7560 2.696 0.679 0.136 0.040 52 6.0 fusiform
- 6725 4709 14064 2.469 0.669 0.129 0.032 87 9.0 inferiorparietal
- 4517 2972 10034 2.724 0.852 0.137 0.054 87 12.3 inferiortemporal
- 1403 903 2976 2.675 0.859 0.125 0.034 17 1.7 isthmuscingulate
- 6659 4551 12578 2.291 0.658 0.150 0.041 95 10.8 lateraloccipital
- 4079 2797 8765 2.627 0.734 0.157 0.054 70 10.2 lateralorbitofrontal
- 4331 2968 6826 2.059 0.615 0.142 0.038 54 6.8 lingual
- 2094 1409 4436 2.627 0.974 0.125 0.043 34 3.5 medialorbitofrontal
- 5687 3990 14131 3.023 0.745 0.129 0.033 76 8.2 middletemporal
- 1245 739 2198 2.459 0.857 0.120 0.058 21 3.5 parahippocampal
- 2288 1450 4229 2.665 0.683 0.097 0.021 13 2.0 paracentral
- 2117 1415 5198 3.070 0.697 0.115 0.024 18 2.2 parsopercularis
- 1023 707 2668 2.903 0.672 0.135 0.032 13 1.4 parsorbitalis
- 2168 1479 4815 2.778 0.679 0.125 0.027 23 2.4 parstriangularis
- 1554 1142 1846 1.756 0.522 0.122 0.032 12 2.0 pericalcarine
- 5451 3609 8885 2.188 0.721 0.112 0.027 53 5.7 postcentral
- 1800 1260 3471 2.427 0.892 0.149 0.033 29 2.4 posteriorcingulate
- 6745 4274 14214 2.940 0.603 0.109 0.029 59 8.4 precentral
- 5257 3606 9566 2.473 0.659 0.129 0.028 61 5.8 precuneus
- 1043 698 2271 3.100 0.794 0.122 0.031 10 1.3 rostralanteriorcingulate
- 5479 3861 12521 2.652 0.697 0.147 0.039 80 8.6 rostralmiddlefrontal
- 12010 8029 29940 3.057 0.726 0.130 0.037 149 19.1 superiorfrontal
- 5852 3915 10448 2.331 0.567 0.121 0.028 63 6.5 superiorparietal
- 6266 4302 15343 2.922 0.764 0.115 0.029 70 7.7 superiortemporal
- 3759 2533 8442 2.852 0.601 0.125 0.031 40 4.4 supramarginal
- 516 315 916 2.564 0.570 0.112 0.029 6 0.6 transversetemporal
- 2676 1846 5685 3.112 0.614 0.123 0.032 26 3.2 insula
- PIDs (3214 3217) completed and logs appended.
- #-----------------------------------------
- #@# WM/GM Contrast lh Sun Oct 8 06:18:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- pctsurfcon --s 0050340 --lh-only
- #-----------------------------------------
- #@# WM/GM Contrast rh Sun Oct 8 06:18:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts
- pctsurfcon --s 0050340 --rh-only
- Waiting for PID 3295 of (3295 3306) to complete...
- Waiting for PID 3306 of (3295 3306) to complete...
- pctsurfcon --s 0050340 --lh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts/pctsurfcon.log
- Sun Oct 8 06:18:33 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-6.0.0/0050340/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-593 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-6.0.0/0050340/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.wm.mgh --regheader 0050340 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00002;
- 0.00000 0.00000 1.00000 -0.00001;
- 0.00000 -1.00000 0.00000 0.00003;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 58165
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.wm.mgh
- Dim: 121622 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.gm.mgh --projfrac 0.3 --regheader 0050340 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00002;
- 0.00000 0.00000 1.00000 -0.00001;
- 0.00000 -1.00000 0.00000 0.00003;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 68884
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.gm.mgh
- Dim: 121622 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3295/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/lh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.w-g.pct.mgh --annot 0050340 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/lh.w-g.pct.mgh --annot 0050340 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-593
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/lh.w-g.pct.mgh
- Vertex Area is 0.677322 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 0050340 --rh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/scripts/pctsurfcon.log
- Sun Oct 8 06:18:33 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-6.0.0/0050340/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-593 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-6.0.0/0050340/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.wm.mgh --regheader 0050340 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00002;
- 0.00000 0.00000 1.00000 -0.00001;
- 0.00000 -1.00000 0.00000 0.00003;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 57491
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.wm.mgh
- Dim: 119917 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.gm.mgh --projfrac 0.3 --regheader 0050340 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00002;
- 0.00000 0.00000 1.00000 -0.00001;
- 0.00000 -1.00000 0.00000 0.00003;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 68145
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.gm.mgh
- Dim: 119917 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/tmp.pctsurfcon.3306/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.w-g.pct.mgh --annot 0050340 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.w-g.pct.mgh --annot 0050340 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-593
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.w-g.pct.mgh
- Vertex Area is 0.678036 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 (3295 3306) completed and logs appended.
- #-----------------------------------------
- #@# Relabel Hypointensities Sun Oct 8 06:18:39 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
- reading input surface ../surf/lh.white...
- relabeling lh hypointensities...
- 1543 voxels changed to hypointensity...
- reading input surface ../surf/rh.white...
- relabeling rh hypointensities...
- 1405 voxels changed to hypointensity...
- 2921 hypointense voxels neighboring cortex changed
- #-----------------------------------------
- #@# AParc-to-ASeg aparc Sun Oct 8 06:18:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340
- mri_aparc2aseg --s 0050340 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
- #-----------------------------------------
- #@# AParc-to-ASeg a2009s Sun Oct 8 06:18:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340
- mri_aparc2aseg --s 0050340 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s
- #-----------------------------------------
- #@# AParc-to-ASeg DKTatlas Sun Oct 8 06:18:58 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340
- mri_aparc2aseg --s 0050340 --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 3472 of (3472 3475 3478) to complete...
- Waiting for PID 3475 of (3472 3475 3478) to complete...
- Waiting for PID 3478 of (3472 3475 3478) to complete...
- mri_aparc2aseg --s 0050340 --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 0050340
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/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-6.0.0/0050340/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 6.21
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 105
- rescaling Left_Cerebral_Cortex from 61 --> 64
- rescaling Left_Lateral_Ventricle from 13 --> 20
- rescaling Left_Inf_Lat_Vent from 34 --> 30
- rescaling Left_Cerebellum_White_Matter from 86 --> 90
- rescaling Left_Cerebellum_Cortex from 60 --> 62
- rescaling Left_Thalamus from 94 --> 103
- rescaling Left_Thalamus_Proper from 84 --> 86
- rescaling Left_Caudate from 75 --> 70
- rescaling Left_Putamen from 80 --> 81
- rescaling Left_Pallidum from 98 --> 93
- rescaling Third_Ventricle from 25 --> 34
- rescaling Fourth_Ventricle from 22 --> 14
- rescaling Brain_Stem from 81 --> 89
- rescaling Left_Hippocampus from 57 --> 66
- rescaling Left_Amygdala from 56 --> 74
- rescaling CSF from 32 --> 49
- rescaling Left_Accumbens_area from 62 --> 63
- rescaling Left_VentralDC from 87 --> 90
- rescaling Right_Cerebral_White_Matter from 105 --> 104
- rescaling Right_Cerebral_Cortex from 58 --> 63
- rescaling Right_Lateral_Ventricle from 13 --> 28
- rescaling Right_Inf_Lat_Vent from 25 --> 27
- rescaling Right_Cerebellum_White_Matter from 87 --> 86
- rescaling Right_Cerebellum_Cortex from 59 --> 61
- rescaling Right_Thalamus_Proper from 85 --> 82
- rescaling Right_Caudate from 62 --> 72
- rescaling Right_Putamen from 80 --> 77
- rescaling Right_Pallidum from 97 --> 90
- rescaling Right_Hippocampus from 53 --> 64
- rescaling Right_Amygdala from 55 --> 72
- rescaling Right_Accumbens_area from 65 --> 70
- rescaling Right_VentralDC from 86 --> 95
- rescaling Fifth_Ventricle from 40 --> 42
- rescaling WM_hypointensities from 78 --> 77
- rescaling non_WM_hypointensities from 40 --> 43
- 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 = 475832
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 96 changed.
- pass 2: 7 changed.
- pass 3: 1 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aparc+aseg.mgz
- mri_aparc2aseg --s 0050340 --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 0050340
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/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-6.0.0/0050340/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 6.21
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 105
- rescaling Left_Cerebral_Cortex from 61 --> 64
- rescaling Left_Lateral_Ventricle from 13 --> 20
- rescaling Left_Inf_Lat_Vent from 34 --> 30
- rescaling Left_Cerebellum_White_Matter from 86 --> 90
- rescaling Left_Cerebellum_Cortex from 60 --> 62
- rescaling Left_Thalamus from 94 --> 103
- rescaling Left_Thalamus_Proper from 84 --> 86
- rescaling Left_Caudate from 75 --> 70
- rescaling Left_Putamen from 80 --> 81
- rescaling Left_Pallidum from 98 --> 93
- rescaling Third_Ventricle from 25 --> 34
- rescaling Fourth_Ventricle from 22 --> 14
- rescaling Brain_Stem from 81 --> 89
- rescaling Left_Hippocampus from 57 --> 66
- rescaling Left_Amygdala from 56 --> 74
- rescaling CSF from 32 --> 49
- rescaling Left_Accumbens_area from 62 --> 63
- rescaling Left_VentralDC from 87 --> 90
- rescaling Right_Cerebral_White_Matter from 105 --> 104
- rescaling Right_Cerebral_Cortex from 58 --> 63
- rescaling Right_Lateral_Ventricle from 13 --> 28
- rescaling Right_Inf_Lat_Vent from 25 --> 27
- rescaling Right_Cerebellum_White_Matter from 87 --> 86
- rescaling Right_Cerebellum_Cortex from 59 --> 61
- rescaling Right_Thalamus_Proper from 85 --> 82
- rescaling Right_Caudate from 62 --> 72
- rescaling Right_Putamen from 80 --> 77
- rescaling Right_Pallidum from 97 --> 90
- rescaling Right_Hippocampus from 53 --> 64
- rescaling Right_Amygdala from 55 --> 72
- rescaling Right_Accumbens_area from 65 --> 70
- rescaling Right_VentralDC from 86 --> 95
- rescaling Fifth_Ventricle from 40 --> 42
- rescaling WM_hypointensities from 78 --> 77
- rescaling non_WM_hypointensities from 40 --> 43
- 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 = 475868
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 96 changed.
- pass 2: 7 changed.
- pass 3: 1 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/aparc.a2009s+aseg.mgz
- mri_aparc2aseg --s 0050340 --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 0050340
- outvol mri/aparc.DKTatlas+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/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-6.0.0/0050340/mri/aseg.presurf.hypos.mgz
- ASeg Vox2RAS: -----------
- -1.00000 0.00000 0.00000 128.00000;
- 0.00000 0.00000 1.00000 -128.00000;
- 0.00000 -1.00000 0.00000 128.00000;
- 0.00000 0.00000 0.00000 1.00000;
- -------------------------
- Labeling Slice
- relabeling unlikely voxels in interior of white matter
- setting orig areas to linear transform determinant scaled 6.21
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 105
- rescaling Left_Cerebral_Cortex from 61 --> 64
- rescaling Left_Lateral_Ventricle from 13 --> 20
- rescaling Left_Inf_Lat_Vent from 34 --> 30
- rescaling Left_Cerebellum_White_Matter from 86 --> 90
- rescaling Left_Cerebellum_Cortex from 60 --> 62
- rescaling Left_Thalamus from 94 --> 103
- rescaling Left_Thalamus_Proper from 84 --> 86
- rescaling Left_Caudate from 75 --> 70
- rescaling Left_Putamen from 80 --> 81
- rescaling Left_Pallidum from 98 --> 93
- rescaling Third_Ventricle from 25 --> 34
- rescaling Fourth_Ventricle from 22 --> 14
- rescaling Brain_Stem from 81 --> 89
- rescaling Left_Hippocampus from 57 --> 66
- rescaling Left_Amygdala from 56 --> 74
- rescaling CSF from 32 --> 49
- rescaling Left_Accumbens_area from 62 --> 63
- rescaling Left_VentralDC from 87 --> 90
- rescaling Right_Cerebral_White_Matter from 105 --> 104
- rescaling Right_Cerebral_Cortex from 58 --> 63
- rescaling Right_Lateral_Ventricle from 13 --> 28
- rescaling Right_Inf_Lat_Vent from 25 --> 27
- rescaling Right_Cerebellum_White_Matter from 87 --> 86
- rescaling Right_Cerebellum_Cortex from 59 --> 61
- rescaling Right_Thalamus_Proper from 85 --> 82
- rescaling Right_Caudate from 62 --> 72
- rescaling Right_Putamen from 80 --> 77
- rescaling Right_Pallidum from 97 --> 90
- rescaling Right_Hippocampus from 53 --> 64
- rescaling Right_Amygdala from 55 --> 72
- rescaling Right_Accumbens_area from 65 --> 70
- rescaling Right_VentralDC from 86 --> 95
- rescaling Fifth_Ventricle from 40 --> 42
- rescaling WM_hypointensities from 78 --> 77
- rescaling non_WM_hypointensities from 40 --> 43
- 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 = 475868
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 96 changed.
- pass 2: 7 changed.
- pass 3: 1 changed.
- pass 4: 0 changed.
- nchanged = 0
- Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
- PIDs (3472 3475 3478) completed and logs appended.
- #-----------------------------------------
- #@# APas-to-ASeg Sun Oct 8 06:25:43 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri
- apas2aseg --i aparc+aseg.mgz --o aseg.mgz
- Sun Oct 8 06:25:43 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-6.0.0/0050340/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-593 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-6.0.0/0050340/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-593
- machine x86_64
- user ntraut
- input aparc+aseg.mgz
- frame 0
- nErode3d 0
- nErode2d 0
- output aseg.mgz
- Binarizing based on threshold
- min -infinity
- max +infinity
- binval 1
- binvalnot 0
- fstart = 0, fend = 0, nframes = 1
- Replacing 72
- 1: 1000 3
- 2: 2000 42
- 3: 1001 3
- 4: 2001 42
- 5: 1002 3
- 6: 2002 42
- 7: 1003 3
- 8: 2003 42
- 9: 1004 3
- 10: 2004 42
- 11: 1005 3
- 12: 2005 42
- 13: 1006 3
- 14: 2006 42
- 15: 1007 3
- 16: 2007 42
- 17: 1008 3
- 18: 2008 42
- 19: 1009 3
- 20: 2009 42
- 21: 1010 3
- 22: 2010 42
- 23: 1011 3
- 24: 2011 42
- 25: 1012 3
- 26: 2012 42
- 27: 1013 3
- 28: 2013 42
- 29: 1014 3
- 30: 2014 42
- 31: 1015 3
- 32: 2015 42
- 33: 1016 3
- 34: 2016 42
- 35: 1017 3
- 36: 2017 42
- 37: 1018 3
- 38: 2018 42
- 39: 1019 3
- 40: 2019 42
- 41: 1020 3
- 42: 2020 42
- 43: 1021 3
- 44: 2021 42
- 45: 1022 3
- 46: 2022 42
- 47: 1023 3
- 48: 2023 42
- 49: 1024 3
- 50: 2024 42
- 51: 1025 3
- 52: 2025 42
- 53: 1026 3
- 54: 2026 42
- 55: 1027 3
- 56: 2027 42
- 57: 1028 3
- 58: 2028 42
- 59: 1029 3
- 60: 2029 42
- 61: 1030 3
- 62: 2030 42
- 63: 1031 3
- 64: 2031 42
- 65: 1032 3
- 66: 2032 42
- 67: 1033 3
- 68: 2033 42
- 69: 1034 3
- 70: 2034 42
- 71: 1035 3
- 72: 2035 42
- Found 0 values in range
- Counting number of voxels in first frame
- Found 0 voxels in final mask
- Count: 0 0.000000 16777216 0.000000
- mri_binarize done
-
- Started at Sun Oct 8 06:25:43 CEST 2017
- Ended at Sun Oct 8 06:25:49 CEST 2017
- Apas2aseg-Run-Time-Sec 6
-
- apas2aseg Done
- #--------------------------------------------
- #@# ASeg Stats Sun Oct 8 06:25:49 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340
- 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 0050340
- $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 0050340
- sysname Linux
- hostname tars-593
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1444308 mm^3 (det: 1.348816 )
- Computing euler number
- orig.nofix lheno = -92, rheno = -104
- orig.nofix lhholes = 47, rhholes = 53
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- Loading mri/norm.mgz
- Loading mri/norm.mgz
- Voxel Volume is 1 mm^3
- Generating list of segmentation ids
- Found 50 segmentations
- Computing statistics for each segmentation
- Reporting on 45 segmentations
- Using PrintSegStat
- mri_segstats done
- #-----------------------------------------
- #@# WMParc Sun Oct 8 06:27:20 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340
- mri_aparc2aseg --s 0050340 --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 0050340
- 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-6.0.0/0050340/mri/aparc+aseg.mgz
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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-6.0.0/0050340/mri/ribbon.mgz
- Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/ribbon.mgz
- Ripping vertices labeled as unkown
- Ripped 7377 vertices from left hemi
- Ripped 6890 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-6.0.0/0050340/mri/aseg.mgz
- Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 = 891413
- Used brute-force search on 19 voxels
- Fixing Parahip LH WM
- Found 13 clusters
- 0 k 2.000000
- 1 k 3.000000
- 2 k 1.000000
- 3 k 1085.000000
- 4 k 1.000000
- 5 k 2.000000
- 6 k 1.000000
- 7 k 1.000000
- 8 k 7.000000
- 9 k 11.000000
- 10 k 1.000000
- 11 k 3.000000
- 12 k 1.000000
- Fixing Parahip RH WM
- Found 11 clusters
- 0 k 1.000000
- 1 k 1.000000
- 2 k 3.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 1441.000000
- 8 k 1.000000
- 9 k 1.000000
- 10 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 0050340 --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 0050340 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname tars-593
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1444308 mm^3 (det: 1.348816 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 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-6.0.0/0050340/label
- #--------------------------------------------
- #@# BA_exvivo Labels lh Sun Oct 8 06:35:32 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 5436 of (5436 5442 5448 5454 5457) to complete...
- Waiting for PID 5442 of (5436 5442 5448 5454 5457) to complete...
- Waiting for PID 5448 of (5436 5442 5448 5454 5457) to complete...
- Waiting for PID 5454 of (5436 5442 5448 5454 5457) to complete...
- Waiting for PID 5457 of (5436 5442 5448 5454 5457) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 190
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.label 4319
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 256
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.label 8165
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 96
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.label 4173
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 220
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.label 6203
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 348
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.label 6132
- mri_label2label: Done
- PIDs (5436 5442 5448 5454 5457) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 5517 of (5517 5523 5529 5535) to complete...
- Waiting for PID 5523 of (5517 5523 5529 5535) to complete...
- Waiting for PID 5529 of (5517 5523 5529 5535) to complete...
- Waiting for PID 5535 of (5517 5523 5529 5535) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 224
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.label 4294
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 851
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.label 14440
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 265
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.label 4446
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 671
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.label 4093
- mri_label2label: Done
- PIDs (5517 5523 5529 5535) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 5580 of (5580 5586 5592 5597 5603) to complete...
- Waiting for PID 5586 of (5580 5586 5592 5597 5603) to complete...
- Waiting for PID 5592 of (5580 5586 5592 5597 5603) to complete...
- Waiting for PID 5597 of (5580 5586 5592 5597 5603) to complete...
- Waiting for PID 5603 of (5580 5586 5592 5597 5603) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 1247
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.label 5888
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 2608
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.label 10722
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 446
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.label 2464
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 63
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.label 1353
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 21
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.label 1220
- mri_label2label: Done
- PIDs (5580 5586 5592 5597 5603) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 5651 of (5651 5657 5663 5669 5674) to complete...
- Waiting for PID 5657 of (5651 5657 5663 5669 5674) to complete...
- Waiting for PID 5663 of (5651 5657 5663 5669 5674) to complete...
- Waiting for PID 5669 of (5651 5657 5663 5669 5674) to complete...
- Waiting for PID 5674 of (5651 5657 5663 5669 5674) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 76
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.thresh.label 1090
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 81
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.thresh.label 2173
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 42
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.thresh.label 1546
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 55
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.thresh.label 2051
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 143
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.thresh.label 2462
- mri_label2label: Done
- PIDs (5651 5657 5663 5669 5674) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 5729 of (5729 5735 5741 5746) to complete...
- Waiting for PID 5735 of (5729 5735 5741 5746) to complete...
- Waiting for PID 5741 of (5729 5735 5741 5746) to complete...
- Waiting for PID 5746 of (5729 5735 5741 5746) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 84
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.thresh.label 1633
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 456
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.thresh.label 7491
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 94
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.thresh.label 2006
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 299
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.thresh.label 1450
- mri_label2label: Done
- PIDs (5729 5735 5741 5746) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 5789 of (5789 5795 5801 5807 5811) to complete...
- Waiting for PID 5795 of (5789 5795 5801 5807 5811) to complete...
- Waiting for PID 5801 of (5789 5795 5801 5807 5811) to complete...
- Waiting for PID 5807 of (5789 5795 5801 5807 5811) to complete...
- Waiting for PID 5811 of (5789 5795 5801 5807 5811) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 818
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.thresh.label 4223
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 1240
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.thresh.label 4574
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 94
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.thresh.label 607
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 53
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.thresh.label 523
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 121622
- Number of reverse mapping hits = 15
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.thresh.label 465
- mri_label2label: Done
- PIDs (5789 5795 5801 5807 5811) completed and logs appended.
- mris_label2annot --s 0050340 --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-6.0.0/0050340/label
- cmdline mris_label2annot --s 0050340 --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-593
- machine x86_64
- user ntraut
- subject 0050340
- 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-6.0.0/0050340/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 83379 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/lh.BA_exvivo.annot
- mris_label2annot --s 0050340 --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-6.0.0/0050340/label
- cmdline mris_label2annot --s 0050340 --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-593
- machine x86_64
- user ntraut
- subject 0050340
- 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-6.0.0/0050340/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 98785 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 245242
- Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 1077 612 1991 2.405 0.607 0.127 0.038 15 1.4 BA1_exvivo
- 3283 2202 6266 2.671 0.586 0.119 0.026 33 3.4 BA2_exvivo
- 1009 672 1035 1.933 0.489 0.130 0.026 10 1.0 BA3a_exvivo
- 2002 1375 3099 1.979 0.801 0.119 0.025 20 2.0 BA3b_exvivo
- 1558 949 3189 2.959 0.622 0.105 0.030 11 2.1 BA4a_exvivo
- 1330 820 2250 2.811 0.600 0.102 0.031 12 1.8 BA4p_exvivo
- 8441 5435 21257 3.237 0.679 0.114 0.028 86 9.5 BA6_exvivo
- 2006 1343 4659 3.016 0.507 0.111 0.022 18 1.7 BA44_exvivo
- 3016 2058 7163 2.835 0.655 0.139 0.035 44 4.1 BA45_exvivo
- 3336 2333 4455 1.808 0.608 0.143 0.043 45 6.2 V1_exvivo
- 8133 5455 13180 2.088 0.646 0.151 0.041 116 13.9 V2_exvivo
- 2075 1417 4189 2.586 0.583 0.140 0.034 26 3.0 MT_exvivo
- 490 316 1377 3.025 0.950 0.124 0.050 8 1.0 perirhinal_exvivo
- 487 359 1209 3.128 0.960 0.135 0.032 6 0.6 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 0050340 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 245242
- Total vertex volume 242494 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 700 363 1210 2.396 0.594 0.139 0.041 12 1.1 BA1_exvivo
- 1338 883 2452 2.540 0.630 0.105 0.024 12 1.3 BA2_exvivo
- 855 572 839 1.896 0.479 0.137 0.030 9 0.9 BA3a_exvivo
- 1228 875 1434 1.576 0.426 0.098 0.018 7 1.0 BA3b_exvivo
- 1588 946 3115 3.021 0.592 0.102 0.031 12 2.1 BA4a_exvivo
- 1092 695 1744 2.611 0.578 0.108 0.030 10 1.6 BA4p_exvivo
- 4741 2929 10918 3.137 0.684 0.108 0.030 45 5.6 BA6_exvivo
- 1250 865 3151 3.110 0.480 0.117 0.026 12 1.1 BA44_exvivo
- 1278 859 4029 3.246 0.583 0.154 0.041 25 2.1 BA45_exvivo
- 3585 2486 4929 1.838 0.627 0.144 0.043 48 6.8 V1_exvivo
- 4133 2807 5934 1.915 0.588 0.159 0.047 64 8.1 V2_exvivo
- 511 348 978 2.524 0.503 0.130 0.030 6 0.5 MT_exvivo
- 261 168 718 2.887 1.085 0.134 0.066 5 0.8 perirhinal_exvivo
- 277 201 695 3.109 0.886 0.139 0.038 3 0.5 entorhinal_exvivo
- #--------------------------------------------
- #@# BA_exvivo Labels rh Sun Oct 8 06:38:12 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 5934 of (5934 5940 5946 5952 5958) to complete...
- Waiting for PID 5940 of (5934 5940 5946 5952 5958) to complete...
- Waiting for PID 5946 of (5934 5940 5946 5952 5958) to complete...
- Waiting for PID 5952 of (5934 5940 5946 5952 5958) to complete...
- Waiting for PID 5958 of (5934 5940 5946 5952 5958) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 164
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.label 4126
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 177
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.label 6864
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 99
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.label 4079
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 127
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.label 4649
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 341
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.label 6088
- mri_label2label: Done
- PIDs (5934 5940 5946 5952 5958) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 6003 of (6003 6009 6015 6021) to complete...
- Waiting for PID 6009 of (6003 6009 6015 6021) to complete...
- Waiting for PID 6015 of (6003 6009 6015 6021) to complete...
- Waiting for PID 6021 of (6003 6009 6015 6021) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 232
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.label 4705
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 877
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.label 13133
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 524
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.label 7436
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 761
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.label 6116
- mri_label2label: Done
- PIDs (6003 6009 6015 6021) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 6075 of (6075 6081 6087 6092 6097) to complete...
- Waiting for PID 6081 of (6075 6081 6087 6092 6097) to complete...
- Waiting for PID 6087 of (6075 6081 6087 6092 6097) to complete...
- Waiting for PID 6092 of (6075 6081 6087 6092 6097) to complete...
- Waiting for PID 6097 of (6075 6081 6087 6092 6097) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 907
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.label 5634
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 1973
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.label 9989
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 283
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.label 2215
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 173
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.label 1211
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 84
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.label 836
- mri_label2label: Done
- PIDs (6075 6081 6087 6092 6097) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 6160 of (6160 6166 6172 6177 6183) to complete...
- Waiting for PID 6166 of (6160 6166 6172 6177 6183) to complete...
- Waiting for PID 6172 of (6160 6166 6172 6177 6183) to complete...
- Waiting for PID 6177 of (6160 6166 6172 6177 6183) to complete...
- Waiting for PID 6183 of (6160 6166 6172 6177 6183) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 46
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.thresh.label 922
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 44
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.thresh.label 2732
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 38
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.thresh.label 1736
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 56
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.thresh.label 2239
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 59
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.thresh.label 1447
- mri_label2label: Done
- PIDs (6160 6166 6172 6177 6183) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 6229 of (6229 6235 6241 6246) to complete...
- Waiting for PID 6235 of (6229 6235 6241 6246) to complete...
- Waiting for PID 6241 of (6229 6235 6241 6246) to complete...
- Waiting for PID 6246 of (6229 6235 6241 6246) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 92
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.thresh.label 1581
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 339
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.thresh.label 7298
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 69
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.thresh.label 1081
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 124
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.thresh.label 1302
- mri_label2label: Done
- PIDs (6229 6235 6241 6246) 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 0050340 --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 0050340 --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 0050340 --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 0050340 --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 0050340 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 6298 of (6298 6304 6310 6316 6322) to complete...
- Waiting for PID 6304 of (6298 6304 6310 6316 6322) to complete...
- Waiting for PID 6310 of (6298 6304 6310 6316 6322) to complete...
- Waiting for PID 6316 of (6298 6304 6310 6316 6322) to complete...
- Waiting for PID 6322 of (6298 6304 6310 6316 6322) 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 514
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.thresh.label 3746
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 975
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.thresh.label 4412
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 36
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.thresh.label 304
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 143
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.thresh.label 837
- 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 0050340 --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 = 0050340
- 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-6.0.0/0050340/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 119917
- Number of reverse mapping hits = 12
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.thresh.label 303
- mri_label2label: Done
- PIDs (6298 6304 6310 6316 6322) completed and logs appended.
- mris_label2annot --s 0050340 --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-6.0.0/0050340/label
- cmdline mris_label2annot --s 0050340 --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-593
- machine x86_64
- user ntraut
- subject 0050340
- 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-6.0.0/0050340/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 83420 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/label/rh.BA_exvivo.annot
- mris_label2annot --s 0050340 --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-6.0.0/0050340/label
- cmdline mris_label2annot --s 0050340 --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-593
- machine x86_64
- user ntraut
- subject 0050340
- 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-6.0.0/0050340/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 99885 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/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 0050340 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 240534
- Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 844 496 1560 2.233 0.621 0.146 0.048 16 1.8 BA1_exvivo
- 2478 1685 4164 2.317 0.555 0.104 0.020 19 1.8 BA2_exvivo
- 1048 687 1002 1.956 0.518 0.119 0.027 8 1.0 BA3a_exvivo
- 1674 1108 2276 1.830 0.649 0.103 0.022 13 1.4 BA3b_exvivo
- 1548 896 3206 3.050 0.486 0.093 0.028 11 2.0 BA4a_exvivo
- 1294 834 2277 2.768 0.549 0.105 0.029 8 1.8 BA4p_exvivo
- 7369 4631 17464 3.089 0.627 0.111 0.034 78 10.7 BA6_exvivo
- 3194 2147 7565 3.024 0.599 0.117 0.024 28 3.2 BA44_exvivo
- 4118 2836 9849 2.817 0.681 0.131 0.029 48 5.1 BA45_exvivo
- 3022 2198 4627 1.882 0.625 0.144 0.044 39 5.4 V1_exvivo
- 7166 4799 11441 2.121 0.581 0.149 0.042 100 12.1 V2_exvivo
- 1781 1256 3213 2.284 0.566 0.130 0.031 19 2.4 MT_exvivo
- 614 364 1484 2.934 1.088 0.136 0.089 13 2.7 perirhinal_exvivo
- 347 244 899 3.061 1.075 0.128 0.051 6 0.7 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 0050340 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050340/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 240534
- Total vertex volume 237315 (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) = 1444308 mm^3 (det: 1.348816 )
- lhCtxGM: 241175.837 240937.000 diff= 238.8 pctdiff= 0.099
- rhCtxGM: 235961.353 235310.000 diff= 651.4 pctdiff= 0.276
- lhCtxWM: 211472.678 210868.000 diff= 604.7 pctdiff= 0.286
- rhCtxWM: 205827.585 207174.000 diff=-1346.4 pctdiff=-0.654
- SubCortGMVol 57332.000
- SupraTentVol 960599.453 (957991.000) diff=2608.453 pctdiff=0.272
- SupraTentVolNotVent 954261.453 (951653.000) diff=2608.453 pctdiff=0.273
- BrainSegVol 1099333.000 (1097030.000) diff=2303.000 pctdiff=0.209
- BrainSegVolNotVent 1089936.000 (1089879.453) diff=56.547 pctdiff=0.005
- BrainSegVolNotVent 1089936.000
- CerebellumVol 138078.000
- VentChorVol 6338.000
- 3rd4th5thCSF 3059.000
- CSFVol 756.000, OptChiasmVol 205.000
- MaskVol 1454196.000
- 515 320 898 2.012 0.577 0.147 0.052 11 1.1 BA1_exvivo
- 1352 959 2381 2.276 0.483 0.093 0.017 8 0.9 BA2_exvivo
- 941 615 821 1.928 0.482 0.124 0.027 7 1.0 BA3a_exvivo
- 1329 937 1527 1.589 0.386 0.092 0.016 7 0.8 BA3b_exvivo
- 907 519 1779 3.027 0.518 0.098 0.032 6 1.4 BA4a_exvivo
- 1084 716 1953 2.833 0.536 0.103 0.030 7 1.5 BA4p_exvivo
- 4602 2931 10884 3.001 0.612 0.111 0.029 45 5.6 BA6_exvivo
- 790 522 2464 3.362 0.701 0.116 0.026 7 0.9 BA44_exvivo
- 960 670 2806 3.170 0.624 0.143 0.035 14 1.4 BA45_exvivo
- 2873 2076 4282 1.878 0.618 0.138 0.042 34 4.9 V1_exvivo
- 3794 2574 5826 1.992 0.577 0.160 0.048 60 7.5 V2_exvivo
- 255 184 567 2.439 0.543 0.124 0.029 3 0.3 MT_exvivo
- 418 225 844 2.664 1.085 0.166 0.136 15 2.9 perirhinal_exvivo
- 212 165 459 2.890 0.957 0.124 0.026 1 0.2 entorhinal_exvivo
- Started at Sat Oct 7 23:40:21 CEST 2017
- Ended at Sun Oct 8 06:40:50 CEST 2017
- #@#%# recon-all-run-time-hours 7.008
- recon-all -s 0050340 finished without error at Sun Oct 8 06:40:50 CEST 2017
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