ABIDE_fs-6.0.0/0050008/scripts/recon-all.log

Sat Oct  7 18:13:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050008 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050008/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050008
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-584 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   57579056    8414792    1764328          0   53983376
-/+ buffers/cache:    3595680   62398168
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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:21-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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: 2017/10/07-16:13:22-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-584  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-6.0.0/0050008

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050008/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050008/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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/Pitt/0050008/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-6.0.0/0050008/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 18:13:26 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/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-6.0.0/0050008/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 18:13:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/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-584 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 18:13:36 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.16272
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16272/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.16272/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.16272/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:13:38 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.16272/nu0.mnc ./tmp.mri_nu_correct.mni.16272/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.16272/0/ -iterations 1000 -distance 50
[ntraut@tars-584:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/] [2017-10-07 18:13:38] 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.16272/0/ ./tmp.mri_nu_correct.mni.16272/nu0.mnc ./tmp.mri_nu_correct.mni.16272/nu1.imp

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Number of iterations: 76 
CV of field change: 0.000994033
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.16272/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.16272/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.16272/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 18:15:08 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 18:15:08 CEST 2017
Ended   at Sat Oct  7 18:15:37 CEST 2017
talairach_avi done

 cp transforms/talairach.auto.xfm transforms/talairach.xfm 

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 18:15:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5489, pval=0.2115 >= 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-6.0.0/0050008/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/transforms/talairach_avi.log 

TalAviQA: 0.97537
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 18:15:39 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-6.0.0/0050008/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-584 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 18:15:39 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.17479
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17479/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.17479/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.17479/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 18:15:42 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.17479/nu0.mnc ./tmp.mri_nu_correct.mni.17479/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17479/0/
[ntraut@tars-584:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/] [2017-10-07 18:15:42] 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.17479/0/ ./tmp.mri_nu_correct.mni.17479/nu0.mnc ./tmp.mri_nu_correct.mni.17479/nu1.imp

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Number of iterations: 50 
CV of field change: 0.00118586
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 18:16:34 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.17479/nu1.mnc ./tmp.mri_nu_correct.mni.17479/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.17479/1/
[ntraut@tars-584:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/] [2017-10-07 18:16:34] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.17479/1/ ./tmp.mri_nu_correct.mni.17479/nu1.mnc ./tmp.mri_nu_correct.mni.17479/nu2.imp

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Number of iterations: 29 
CV of field change: 0.000986017
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.17479/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17479/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-6.0.0/0050008/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.17479/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17479/ones.mgz 
sysname  Linux
hostname tars-584
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.17479/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.17479/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.17479/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17479/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17479/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.17479/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17479/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17479/input.mean.dat 
sysname  Linux
hostname tars-584
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.17479/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.17479/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17479/ones.mgz --i ./tmp.mri_nu_correct.mni.17479/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17479/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17479/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.17479/ones.mgz --i ./tmp.mri_nu_correct.mni.17479/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17479/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17479/output.mean.dat 
sysname  Linux
hostname tars-584
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.17479/ones.mgz
Loading ./tmp.mri_nu_correct.mni.17479/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.17479/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.17479/nu2.mnc ./tmp.mri_nu_correct.mni.17479/nu2.mnc mul .87403201796845441053
Saving result to './tmp.mri_nu_correct.mni.17479/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.17479/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.17479/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.17479/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 ( 7, 161) to ( 3, 110)
 
 
Sat Oct  7 18:17:48 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 18:17:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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
 1.10420   0.04158  -0.00549   1.01956;
-0.04965   0.95364   0.43749  -0.12233;
-0.00475  -0.39778   1.00312   9.44867;
 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 = 21
Starting OpenSpline(): npoints = 21
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 72 (72), valley at 49 (49)
csf peak at 27, setting threshold to 57
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 73 (73), valley at 53 (53)
csf peak at 24, 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 58 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 18:19:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 

aligning to atlas containing skull, setting unknown_nbr_spacing = 5

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9   using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1 
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=7.0
skull bounding box = (39, 50, 14) --> (210, 255, 197)
using (96, 118, 106) as brain centroid...
mean wm in atlas = 108, using box (75,93,83) --> (117, 143,128) to find MRI wm
before smoothing, mri peak at 109
robust fit to distribution - 108 +- 4.6
after smoothing, mri peak at 108, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.420
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.335026 @ (9.091, -27.273, -9.091)
max log p =    -4.211854 @ (-13.636, 4.545, -4.545)
max log p =    -4.162974 @ (2.273, 2.273, -2.273)
max log p =    -4.135601 @ (1.136, 1.136, 3.409)
max log p =    -4.128590 @ (-0.568, 0.568, -0.568)
max log p =    -4.128590 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, -18.8, -13.1): log p = -4.129
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.844, old_max_log_p =-4.129 (thresh=-4.1)
 1.06375   0.00000   0.00000  -9.77401;
 0.00000   1.05267   0.45704  -69.02377;
 0.00000  -0.36573   0.93367   55.96858;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.844, old_max_log_p =-3.844 (thresh=-3.8)
 1.06375   0.00000   0.00000  -9.77401;
 0.00000   1.05267   0.45704  -69.02377;
 0.00000  -0.36573   0.93367   55.96858;
 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=-3.779, old_max_log_p =-3.844 (thresh=-3.8)
 1.08303   0.03550   0.01788  -17.55781;
-0.03280   1.00607   0.50684  -65.56749;
 0.00000  -0.43379   0.90178   69.89925;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.774, old_max_log_p =-3.779 (thresh=-3.8)
 1.08352   0.00170   0.00325  -10.78676;
 0.00267   1.01353   0.43874  -64.94348;
-0.00211  -0.36018   0.91550   55.54744;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.773, old_max_log_p =-3.774 (thresh=-3.8)
 1.08352   0.00170   0.00325  -10.78676;
 0.00269   1.00556   0.40089  -59.17333;
-0.00202  -0.32683   0.92937   50.67539;
 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=-3.752, old_max_log_p =-3.773 (thresh=-3.8)
 1.07883   0.00626  -0.03813  -6.91957;
 0.01209   1.00447   0.40011  -59.62560;
 0.04232  -0.32688   0.92981   45.56776;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.752, old_max_log_p =-3.752 (thresh=-3.7)
 1.07883   0.00626  -0.03813  -6.91957;
 0.01209   1.00447   0.40011  -59.62560;
 0.04237  -0.32726   0.93090   45.49118;
 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
 1.07883   0.00626  -0.03813  -6.91957;
 0.01209   1.00447   0.40011  -59.62560;
 0.04237  -0.32726   0.93090   45.49118;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.07883   0.00626  -0.03813  -6.91957;
 0.01209   1.00447   0.40011  -59.62560;
 0.04237  -0.32726   0.93090   45.49118;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.07883   0.00626  -0.03813  -6.91957;
 0.01209   1.00447   0.40011  -59.62560;
 0.04237  -0.32726   0.93090   45.49118;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.752 (old=-4.420)
transform before final EM align:
 1.07883   0.00626  -0.03813  -6.91957;
 0.01209   1.00447   0.40011  -59.62560;
 0.04237  -0.32726   0.93090   45.49118;
 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
 1.07883   0.00626  -0.03813  -6.91957;
 0.01209   1.00447   0.40011  -59.62560;
 0.04237  -0.32726   0.93090   45.49118;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.07883   0.00626  -0.03813  -6.91957;
 0.01209   1.00447   0.40011  -59.62560;
 0.04237  -0.32726   0.93090   45.49118;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.1  tol 0.000000
final transform:
 1.07883   0.00626  -0.03813  -6.91957;
 0.01209   1.00447   0.40011  -59.62560;
 0.04237  -0.32726   0.93090   45.49118;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1191.384881
mri_em_register stimesec    1.242811
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   157609
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    171
mri_em_register ru_nivcsw   5087
registration took 10 minutes and 21 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


Mode:          T1 normalized volume
Mode:          Use the information of atlas (default parms, --help for details)

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=126 y=128 z=111 r=82
      first estimation of the main basin volume: 2361571 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=105, y=118, z=72, Imax=255
      CSF=13, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 10 percent
done.
Analyze...

      main basin size=9243544355 voxels, voxel volume =1.000 
                     = 9243544355 mmm3 = 9243544.576 cm3
done.
PostAnalyze...Basin Prior
 28 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template 

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=125,y=134, z=105, r=10657 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=6, CSF_MAX=32 , nb = 44003
  RIGHT_CER    CSF_MIN=0, CSF_intensity=4, CSF_MAX=23 , nb = -1028314581
  LEFT_CER     CSF_MIN=0, CSF_intensity=5, CSF_MAX=25 , nb = -1046446835
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=5, CSF_MAX=32 , nb = 1057146944
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=9, CSF_MAX=33 , nb = -1084767022
    OTHER      CSF_MIN=0, CSF_intensity=8, CSF_MAX=46 , nb = 1082312790
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    32,      38,        45,   70
  after  analyzing :    32,      42,        45,   49
   RIGHT_CER   
  before analyzing :    23,      29,        42,   75
  after  analyzing :    23,      37,        42,   46
   LEFT_CER    
  before analyzing :    25,      28,        34,   74
  after  analyzing :    25,      32,        34,   42
  RIGHT_BRAIN  
  before analyzing :    32,      37,        43,   69
  after  analyzing :    32,      41,        43,   48
  LEFT_BRAIN   
  before analyzing :    33,      40,        47,   70
  after  analyzing :    33,      44,        47,   50
     OTHER     
  before analyzing :    46,      32,        0,   92
  after  analyzing :    26,      32,        32,   47
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...67 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.011
curvature mean = 70.250, std = 7.714

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 5.36, sigma = 8.84
      after  rotation: sse = 5.36, sigma = 8.84
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  7.30, its var is 12.02   
      before Erosion-Dilatation  5.65% of inacurate vertices
      after  Erosion-Dilatation  4.24% 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...50 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1792564 voxels, voxel volume = 1.000 mm3
           = 1792564 mmm3 = 1792.564 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    26.838919
mri_watershed stimesec    0.447931
mri_watershed ru_maxrss   854032
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   220847
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2840
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1353
mri_watershed ru_nivcsw   140
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 18:30:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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=22.0
skull bounding box = (60, 69, 32) --> (188, 211, 190)
using (103, 116, 111) as brain centroid...
mean wm in atlas = 107, using box (87,99,92) --> (118, 133,130) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 107 +- 4.1
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.101
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.100893 @ (0.000, 0.000, 0.000)
max log p =    -3.956166 @ (4.545, -13.636, -4.545)
max log p =    -3.911853 @ (-6.818, -2.273, 2.273)
max log p =    -3.889229 @ (3.409, 5.682, -1.136)
max log p =    -3.881335 @ (-1.705, -0.568, -0.568)
max log p =    -3.881335 @ (0.000, 0.000, 0.000)
Found translation: (-0.6, -10.8, -4.0): log p = -3.881
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.488, old_max_log_p =-3.881 (thresh=-3.9)
 1.06375   0.00000   0.00000  -8.68389;
 0.00000   0.99317   0.41138  -54.92143;
 0.00000  -0.35398   0.85459   65.48183;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.488, old_max_log_p =-3.488 (thresh=-3.5)
 1.06375   0.00000   0.00000  -8.68389;
 0.00000   0.99317   0.41138  -54.92143;
 0.00000  -0.35398   0.85459   65.48183;
 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=-3.353, old_max_log_p =-3.488 (thresh=-3.5)
 1.08320   0.01024  -0.02790  -7.92584;
 0.00232   0.99879   0.44699  -61.51686;
 0.03737  -0.40053   0.87166   61.56016;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.348, old_max_log_p =-3.353 (thresh=-3.3)
 1.06240   0.04211  -0.01301  -11.13508;
-0.03250   0.97921   0.43927  -53.70830;
 0.03807  -0.40804   0.88801   60.73734;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.334, old_max_log_p =-3.348 (thresh=-3.3)
 1.08105   0.02231  -0.05695  -6.17799;
 0.00097   0.97466   0.40071  -53.21948;
 0.07039  -0.36719   0.88410   51.64485;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.334, old_max_log_p =-3.334 (thresh=-3.3)
 1.08105   0.02231  -0.05695  -6.17799;
 0.00097   0.97466   0.40071  -53.21948;
 0.07039  -0.36719   0.88410   51.64485;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.303, old_max_log_p =-3.334 (thresh=-3.3)
 1.08277   0.00976  -0.02822  -8.71202;
 0.00155   0.97809   0.40210  -53.89827;
 0.03506  -0.36858   0.88757   55.43582;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.303, old_max_log_p =-3.303 (thresh=-3.3)
 1.08277   0.00976  -0.02822  -8.71202;
 0.00155   0.97809   0.40210  -53.89827;
 0.03506  -0.36858   0.88757   55.43582;
 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
 1.08277   0.00976  -0.02822  -8.71202;
 0.00155   0.97809   0.40210  -53.89827;
 0.03506  -0.36858   0.88757   55.43582;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.08277   0.00976  -0.02822  -8.71202;
 0.00155   0.97809   0.40210  -53.89827;
 0.03506  -0.36858   0.88757   55.43582;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.08277   0.00976  -0.02822  -8.71202;
 0.00155   0.97809   0.40210  -53.89827;
 0.03506  -0.36858   0.88757   55.43582;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.303 (old=-4.101)
transform before final EM align:
 1.08277   0.00976  -0.02822  -8.71202;
 0.00155   0.97809   0.40210  -53.89827;
 0.03506  -0.36858   0.88757   55.43582;
 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
 1.08277   0.00976  -0.02822  -8.71202;
 0.00155   0.97809   0.40210  -53.89827;
 0.03506  -0.36858   0.88757   55.43582;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.08277   0.00976  -0.02822  -8.71202;
 0.00155   0.97809   0.40210  -53.89827;
 0.03506  -0.36858   0.88757   55.43582;
 0.00000   0.00000   0.00000   1.00000;
dfp_em_step_func: 011: -log(p) = 3.8
after pass:transform: ( 1.08, 0.01, -0.03, -8.71)
                      ( 0.00, 0.98, 0.40, -53.90)
                      ( 0.04, -0.37, 0.89, 55.44)
pass 2 through quasi-newton minimization...
outof QuasiNewtonEMA: 013: -log(p) =    3.8  tol 0.000000
final transform:
 1.08277   0.00976  -0.02822  -8.71202;
 0.00155   0.97809   0.40210  -53.89827;
 0.03506  -0.36858   0.88757   55.43582;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1187.820423
mri_em_register stimesec    1.357793
mri_em_register ru_maxrss   599052
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   158954
mri_em_register ru_majflt   1
mri_em_register ru_nswap    0
mri_em_register ru_inblock  2888
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    161
mri_em_register ru_nivcsw   4358
registration took 10 minutes and 25 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 18:41:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri

 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz 

writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=22.0
skull bounding box = (60, 69, 32) --> (188, 211, 190)
using (103, 116, 111) as brain centroid...
mean wm in atlas = 107, using box (87,99,92) --> (118, 133,130) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 107 +- 4.1
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
using 246344 sample points...
INFO: compute sample coordinates transform
 1.08277   0.00976  -0.02822  -8.71202;
 0.00155   0.97809   0.40210  -53.89827;
 0.03506  -0.36858   0.88757   55.43582;
 0.00000   0.00000   0.00000   1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (124, 69, 30) --> (187, 190, 198)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
1 of 4741 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 68, 31) --> (129, 182, 198)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
7 of 4888 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 162, 65) --> (171, 203, 121)
Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0
0 of 46 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 162, 63) --> (125, 202, 122)
Right_Cerebellum_White_Matter: limiting intensities to 99.0 --> 132.0
3 of 32 (9.4%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 144, 98) --> (143, 210, 131)
Brain_Stem: limiting intensities to 92.0 --> 132.0
0 of 291 (0.0%) samples deleted
using 9998 total control points for intensity normalization...
bias field = 0.961 +- 0.052
100 of 9987 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (124, 69, 30) --> (187, 190, 198)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
6 of 5360 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 68, 31) --> (129, 182, 198)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
6 of 5725 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 162, 65) --> (171, 203, 121)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
26 of 134 (19.4%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 162, 63) --> (125, 202, 122)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
34 of 86 (39.5%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 144, 98) --> (143, 210, 131)
Brain_Stem: limiting intensities to 88.0 --> 132.0
10 of 381 (2.6%) samples deleted
using 11686 total control points for intensity normalization...
bias field = 1.030 +- 0.047
112 of 11524 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (124, 69, 30) --> (187, 190, 198)
Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
5 of 5349 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 68, 31) --> (129, 182, 198)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
9 of 5762 (0.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (127, 162, 65) --> (171, 203, 121)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
89 of 181 (49.2%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 162, 63) --> (125, 202, 122)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
79 of 125 (63.2%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 144, 98) --> (143, 210, 131)
Brain_Stem: limiting intensities to 88.0 --> 102.0
101 of 470 (21.5%) samples deleted
using 11887 total control points for intensity normalization...
bias field = 1.026 +- 0.040
87 of 11445 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 38 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 18:42:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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) = 1.10 (predicted orig area = 7.3)
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=0.788, neg=0, invalid=762
0001: dt=189.062665, rms=0.716 (9.164%), neg=0, invalid=762
0002: dt=177.798271, rms=0.696 (2.779%), neg=0, invalid=762
0003: dt=162.630137, rms=0.688 (1.170%), neg=0, invalid=762
0004: dt=129.472000, rms=0.684 (0.603%), neg=0, invalid=762
0005: dt=517.888000, rms=0.677 (1.072%), neg=0, invalid=762
0006: dt=129.939394, rms=0.674 (0.368%), neg=0, invalid=762
0007: dt=443.904000, rms=0.672 (0.344%), neg=0, invalid=762
0008: dt=129.472000, rms=0.669 (0.357%), neg=0, invalid=762
0009: dt=295.936000, rms=0.668 (0.173%), neg=0, invalid=762
0010: dt=295.936000, rms=0.668 (0.093%), neg=0, invalid=762
0011: dt=295.936000, rms=0.664 (0.521%), neg=0, invalid=762
0012: dt=295.936000, rms=0.661 (0.465%), neg=0, invalid=762
0013: dt=295.936000, rms=0.659 (0.288%), neg=0, invalid=762
0014: dt=295.936000, rms=0.657 (0.300%), neg=0, invalid=762
0015: dt=295.936000, rms=0.655 (0.330%), neg=0, invalid=762
0016: dt=295.936000, rms=0.654 (0.223%), neg=0, invalid=762
0017: dt=295.936000, rms=0.654 (-0.008%), neg=0, invalid=762
0018: dt=73.984000, rms=0.653 (0.056%), neg=0, invalid=762
0019: dt=129.472000, rms=0.653 (0.010%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.654, neg=0, invalid=762
0020: dt=295.936000, rms=0.651 (0.413%), neg=0, invalid=762
0021: dt=295.936000, rms=0.650 (0.136%), neg=0, invalid=762
0022: dt=295.936000, rms=0.650 (0.089%), neg=0, invalid=762
0023: dt=295.936000, rms=0.649 (0.113%), neg=0, invalid=762
0024: dt=295.936000, rms=0.648 (0.134%), neg=0, invalid=762
0025: dt=295.936000, rms=0.647 (0.143%), neg=0, invalid=762
0026: dt=295.936000, rms=0.647 (0.077%), neg=0, invalid=762
0027: dt=295.936000, rms=0.646 (0.071%), neg=0, invalid=762
0028: dt=369.920000, rms=0.646 (0.088%), neg=0, invalid=762
0029: dt=73.984000, rms=0.645 (0.014%), neg=0, invalid=762
0030: dt=73.984000, rms=0.645 (0.003%), neg=0, invalid=762
0031: dt=73.984000, rms=0.645 (-0.003%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.650, neg=0, invalid=762
0032: dt=94.485804, rms=0.646 (0.552%), neg=0, invalid=762
0033: dt=331.776000, rms=0.637 (1.448%), neg=0, invalid=762
0034: dt=78.139535, rms=0.634 (0.467%), neg=0, invalid=762
0035: dt=162.273224, rms=0.629 (0.714%), neg=0, invalid=762
0036: dt=36.288000, rms=0.628 (0.243%), neg=0, invalid=762
0037: dt=36.288000, rms=0.627 (0.083%), neg=0, invalid=762
0038: dt=36.288000, rms=0.626 (0.113%), neg=0, invalid=762
0039: dt=36.288000, rms=0.625 (0.197%), neg=0, invalid=762
0040: dt=36.288000, rms=0.623 (0.322%), neg=0, invalid=762
0041: dt=36.288000, rms=0.621 (0.383%), neg=0, invalid=762
0042: dt=36.288000, rms=0.618 (0.377%), neg=0, invalid=762
0043: dt=36.288000, rms=0.616 (0.354%), neg=0, invalid=762
0044: dt=36.288000, rms=0.614 (0.331%), neg=0, invalid=762
0045: dt=36.288000, rms=0.612 (0.285%), neg=0, invalid=762
0046: dt=36.288000, rms=0.611 (0.273%), neg=0, invalid=762
0047: dt=36.288000, rms=0.609 (0.294%), neg=0, invalid=762
0048: dt=36.288000, rms=0.607 (0.273%), neg=0, invalid=762
0049: dt=36.288000, rms=0.606 (0.243%), neg=0, invalid=762
0050: dt=36.288000, rms=0.605 (0.210%), neg=0, invalid=762
0051: dt=36.288000, rms=0.603 (0.176%), neg=0, invalid=762
0052: dt=36.288000, rms=0.602 (0.162%), neg=0, invalid=762
0053: dt=36.288000, rms=0.602 (0.158%), neg=0, invalid=762
0054: dt=36.288000, rms=0.601 (0.158%), neg=0, invalid=762
0055: dt=36.288000, rms=0.600 (0.157%), neg=0, invalid=762
0056: dt=36.288000, rms=0.599 (0.138%), neg=0, invalid=762
0057: dt=36.288000, rms=0.598 (0.117%), neg=0, invalid=762
0058: dt=36.288000, rms=0.597 (0.103%), neg=0, invalid=762
0059: dt=103.680000, rms=0.597 (0.024%), neg=0, invalid=762
0060: dt=103.680000, rms=0.597 (-0.005%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.598, neg=0, invalid=762
0061: dt=145.152000, rms=0.595 (0.518%), neg=0, invalid=762
0062: dt=67.918367, rms=0.594 (0.114%), neg=0, invalid=762
0063: dt=67.918367, rms=0.594 (0.053%), neg=0, invalid=762
0064: dt=67.918367, rms=0.594 (0.066%), neg=0, invalid=762
0065: dt=67.918367, rms=0.593 (0.066%), neg=0, invalid=762
0066: dt=67.918367, rms=0.593 (0.037%), neg=0, invalid=762
0067: dt=67.918367, rms=0.593 (0.036%), neg=0, invalid=762
0068: dt=103.680000, rms=0.593 (0.033%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.612, neg=0, invalid=762
0069: dt=2.800000, rms=0.611 (0.122%), neg=0, invalid=762
0070: dt=2.800000, rms=0.611 (0.012%), neg=0, invalid=762
0071: dt=2.800000, rms=0.611 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.612, neg=0, invalid=762
0072: dt=2.000000, rms=0.611 (0.107%), neg=0, invalid=762
0073: dt=0.700000, rms=0.611 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.664, neg=0, invalid=762
0074: dt=6.157676, rms=0.646 (2.703%), neg=0, invalid=762
0075: dt=2.304000, rms=0.646 (0.057%), neg=0, invalid=762
0076: dt=2.304000, rms=0.646 (-0.021%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.646, neg=0, invalid=762
0077: dt=0.000000, rms=0.646 (0.096%), neg=0, invalid=762
0078: dt=0.000000, rms=0.646 (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=0.696, neg=0, invalid=762
0079: dt=1.024000, rms=0.693 (0.374%), neg=0, invalid=762
0080: dt=1.927928, rms=0.689 (0.577%), neg=0, invalid=762
0081: dt=1.024000, rms=0.689 (0.059%), neg=0, invalid=762
0082: dt=1.024000, rms=0.688 (0.157%), neg=0, invalid=762
0083: dt=1.024000, rms=0.687 (0.078%), neg=0, invalid=762
0084: dt=1.024000, rms=0.687 (-0.140%), neg=0, invalid=762
0085: dt=0.000000, rms=0.687 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.688, neg=0, invalid=762
0086: dt=1.024000, rms=0.687 (0.181%), neg=0, invalid=762
0087: dt=1.280000, rms=0.686 (0.037%), neg=0, invalid=762
0088: dt=1.280000, rms=0.686 (0.002%), neg=0, invalid=762
0089: dt=1.280000, rms=0.686 (-0.042%), 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=0.656, neg=0, invalid=762
0090: dt=0.731436, rms=0.641 (2.314%), neg=0, invalid=762
0091: dt=0.064000, rms=0.641 (0.079%), neg=0, invalid=762
0092: dt=0.064000, rms=0.641 (-0.069%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.641, neg=0, invalid=762
0093: dt=0.024000, rms=0.641 (0.118%), neg=0, invalid=762
0094: dt=0.000438, rms=0.641 (-0.001%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.25160 (23)
Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (1596 voxels, overlap=0.501)
Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (1596 voxels, peak = 26), gca=26.1
gca peak = 0.15565 (16)
mri peak = 0.17519 (23)
Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (1660 voxels, overlap=0.368)
Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (1660 voxels, peak = 22), gca=22.3
gca peak = 0.26829 (96)
mri peak = 0.11402 (96)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (954 voxels, overlap=0.983)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (954 voxels, peak = 98), gca=98.4
gca peak = 0.20183 (93)
mri peak = 0.09707 (98)
Left_Pallidum (13): linear fit = 1.04 x + 0.0 (936 voxels, overlap=0.596)
Left_Pallidum (13): linear fit = 1.04 x + 0.0 (936 voxels, peak = 97), gca=97.2
gca peak = 0.21683 (55)
mri peak = 0.09490 (68)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1118 voxels, overlap=0.046)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1118 voxels, peak = 64), gca=63.5
gca peak = 0.30730 (58)
mri peak = 0.10735 (68)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (1131 voxels, overlap=0.045)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (1131 voxels, peak = 68), gca=67.6
gca peak = 0.11430 (101)
mri peak = 0.11180 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (73075 voxels, overlap=0.619)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (73075 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.11300 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (72902 voxels, overlap=0.587)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (72902 voxels, peak = 106), gca=105.6
gca peak = 0.14995 (59)
mri peak = 0.03532 (70)
Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (29173 voxels, overlap=0.285)
Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (29173 voxels, peak = 69), gca=69.3
gca peak = 0.15082 (58)
mri peak = 0.03880 (69)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (31541 voxels, overlap=0.536)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (31541 voxels, peak = 68), gca=67.6
gca peak = 0.14161 (67)
mri peak = 0.20152 (75)
Right_Caudate (50): linear fit = 1.11 x + 0.0 (489 voxels, overlap=0.202)
Right_Caudate (50): linear fit = 1.11 x + 0.0 (489 voxels, peak = 74), gca=74.0
gca peak = 0.15243 (71)
mri peak = 0.11144 (77)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (914 voxels, overlap=0.650)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (914 voxels, peak = 73), gca=73.5
gca peak = 0.13336 (57)
mri peak = 0.03461 (56)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (31347 voxels, overlap=0.977)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (31347 voxels, peak = 60), gca=59.6
gca peak = 0.13252 (56)
mri peak = 0.03502 (56)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (34260 voxels, overlap=0.979)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (34260 voxels, peak = 59), gca=58.5
gca peak = 0.18181 (84)
mri peak = 0.07435 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (10135 voxels, overlap=0.893)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (10135 voxels, peak = 87), gca=86.9
gca peak = 0.20573 (83)
mri peak = 0.07682 (83)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (8636 voxels, overlap=0.872)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (8636 voxels, peak = 86), gca=85.9
gca peak = 0.21969 (57)
mri peak = 0.11111 (72)
Left_Amygdala (18): linear fit = 1.27 x + 0.0 (533 voxels, overlap=0.045)
Left_Amygdala (18): linear fit = 1.27 x + 0.0 (533 voxels, peak = 73), gca=72.7
gca peak = 0.39313 (56)
mri peak = 0.09662 (70)
Right_Amygdala (54): linear fit = 1.23 x + 0.0 (617 voxels, overlap=0.014)
Right_Amygdala (54): linear fit = 1.23 x + 0.0 (617 voxels, peak = 69), gca=68.6
gca peak = 0.14181 (85)
mri peak = 0.07969 (91)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6026 voxels, overlap=0.696)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6026 voxels, peak = 91), gca=90.5
gca peak = 0.11978 (83)
mri peak = 0.09735 (90)
Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (5043 voxels, overlap=0.693)
Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (5043 voxels, peak = 88), gca=87.6
gca peak = 0.13399 (79)
mri peak = 0.06003 (84)
Left_Putamen (12): linear fit = 1.11 x + 0.0 (2633 voxels, overlap=0.607)
Left_Putamen (12): linear fit = 1.11 x + 0.0 (2633 voxels, peak = 87), gca=87.3
gca peak = 0.14159 (79)
mri peak = 0.07937 (85)
Right_Putamen (51): linear fit = 1.10 x + 0.0 (2861 voxels, overlap=0.661)
Right_Putamen (51): linear fit = 1.10 x + 0.0 (2861 voxels, peak = 87), gca=86.5
gca peak = 0.10025 (80)
mri peak = 0.10649 (90)
Brain_Stem (16): linear fit = 1.14 x + 0.0 (13084 voxels, overlap=0.203)
Brain_Stem (16): linear fit = 1.14 x + 0.0 (13084 voxels, peak = 92), gca=91.6
gca peak = 0.13281 (86)
mri peak = 0.10007 (92)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1469 voxels, overlap=0.459)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1469 voxels, peak = 93), gca=93.3
gca peak = 0.12801 (89)
mri peak = 0.07450 (93)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1594 voxels, overlap=0.620)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1594 voxels, peak = 95), gca=94.8
gca peak = 0.20494 (23)
mri peak = 0.16000 (20)
gca peak = 0.15061 (21)
mri peak = 0.16146 (20)
Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (430 voxels, overlap=0.689)
Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (430 voxels, peak = 20), gca=20.5
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 1.19 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 1.22 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=0.640, neg=0, invalid=762
0095: dt=114.123894, rms=0.627 (1.886%), neg=0, invalid=762
0096: dt=221.952000, rms=0.624 (0.519%), neg=0, invalid=762
0097: dt=129.472000, rms=0.623 (0.274%), neg=0, invalid=762
0098: dt=443.904000, rms=0.621 (0.280%), neg=0, invalid=762
0099: dt=110.976000, rms=0.619 (0.212%), neg=0, invalid=762
0100: dt=295.936000, rms=0.619 (0.139%), neg=0, invalid=762
0101: dt=110.976000, rms=0.618 (0.126%), neg=0, invalid=762
0102: dt=369.920000, rms=0.617 (0.133%), neg=0, invalid=762
0103: dt=110.976000, rms=0.616 (0.093%), neg=0, invalid=762
0104: dt=369.920000, rms=0.616 (0.101%), neg=0, invalid=762
0105: dt=92.480000, rms=0.615 (0.076%), neg=0, invalid=762
0106: dt=1775.616000, rms=0.613 (0.324%), neg=0, invalid=762
0107: dt=73.984000, rms=0.612 (0.173%), neg=0, invalid=762
0108: dt=221.952000, rms=0.612 (0.028%), neg=0, invalid=762
0109: dt=221.952000, rms=0.612 (0.051%), neg=0, invalid=762
0110: dt=221.952000, rms=0.611 (0.087%), neg=0, invalid=762
0111: dt=221.952000, rms=0.611 (0.090%), neg=0, invalid=762
0112: dt=221.952000, rms=0.610 (0.123%), neg=0, invalid=762
0113: dt=221.952000, rms=0.609 (0.123%), neg=0, invalid=762
0114: dt=221.952000, rms=0.609 (0.101%), neg=0, invalid=762
0115: dt=221.952000, rms=0.608 (0.116%), neg=0, invalid=762
0116: dt=221.952000, rms=0.607 (0.103%), neg=0, invalid=762
0117: dt=221.952000, rms=0.607 (0.089%), neg=0, invalid=762
0118: dt=221.952000, rms=0.606 (0.086%), neg=0, invalid=762
0119: dt=221.952000, rms=0.606 (0.072%), neg=0, invalid=762
0120: dt=221.952000, rms=0.605 (0.086%), neg=0, invalid=762
0121: dt=221.952000, rms=0.605 (0.075%), neg=0, invalid=762
0122: dt=221.952000, rms=0.604 (0.051%), neg=0, invalid=762
0123: dt=221.952000, rms=0.604 (0.079%), neg=0, invalid=762
0124: dt=221.952000, rms=0.604 (0.074%), neg=0, invalid=762
0125: dt=221.952000, rms=0.603 (0.068%), neg=0, invalid=762
0126: dt=221.952000, rms=0.603 (0.074%), neg=0, invalid=762
0127: dt=221.952000, rms=0.602 (0.058%), neg=0, invalid=762
0128: dt=221.952000, rms=0.602 (0.060%), neg=0, invalid=762
0129: dt=221.952000, rms=0.602 (0.067%), neg=0, invalid=762
0130: dt=221.952000, rms=0.601 (0.062%), neg=0, invalid=762
0131: dt=221.952000, rms=0.601 (0.053%), neg=0, invalid=762
0132: dt=221.952000, rms=0.601 (0.051%), neg=0, invalid=762
0133: dt=221.952000, rms=0.600 (0.054%), neg=0, invalid=762
0134: dt=221.952000, rms=0.600 (0.056%), neg=0, invalid=762
0135: dt=221.952000, rms=0.600 (0.050%), neg=0, invalid=762
0136: dt=221.952000, rms=0.599 (0.047%), neg=0, invalid=762
0137: dt=221.952000, rms=0.599 (0.048%), neg=0, invalid=762
0138: dt=221.952000, rms=0.599 (0.051%), neg=0, invalid=762
0139: dt=221.952000, rms=0.598 (0.056%), neg=0, invalid=762
0140: dt=221.952000, rms=0.598 (0.035%), neg=0, invalid=762
0141: dt=221.952000, rms=0.598 (0.044%), neg=0, invalid=762
0142: dt=221.952000, rms=0.598 (0.061%), neg=0, invalid=762
0143: dt=221.952000, rms=0.597 (0.041%), neg=0, invalid=762
0144: dt=221.952000, rms=0.597 (0.032%), neg=0, invalid=762
0145: dt=221.952000, rms=0.597 (0.029%), neg=0, invalid=762
0146: dt=221.952000, rms=0.597 (0.048%), neg=0, invalid=762
0147: dt=221.952000, rms=0.596 (0.037%), neg=0, invalid=762
0148: dt=221.952000, rms=0.596 (0.027%), neg=0, invalid=762
0149: dt=221.952000, rms=0.596 (0.036%), neg=0, invalid=762
0150: dt=221.952000, rms=0.596 (0.030%), neg=0, invalid=762
0151: dt=221.952000, rms=0.596 (0.041%), neg=0, invalid=762
0152: dt=221.952000, rms=0.596 (0.016%), neg=0, invalid=762
0153: dt=221.952000, rms=0.595 (0.036%), neg=0, invalid=762
0154: dt=221.952000, rms=0.595 (0.020%), neg=0, invalid=762
0155: dt=221.952000, rms=0.595 (0.024%), neg=0, invalid=762
0156: dt=221.952000, rms=0.595 (0.033%), neg=0, invalid=762
0157: dt=221.952000, rms=0.595 (0.013%), neg=0, invalid=762
0158: dt=221.952000, rms=0.595 (0.048%), neg=0, invalid=762
0159: dt=221.952000, rms=0.594 (0.026%), neg=0, invalid=762
0160: dt=221.952000, rms=0.594 (0.003%), neg=0, invalid=762
0161: dt=221.952000, rms=0.594 (0.040%), neg=0, invalid=762
0162: dt=221.952000, rms=0.594 (0.011%), neg=0, invalid=762
0163: dt=221.952000, rms=0.594 (0.026%), neg=0, invalid=762
0164: dt=221.952000, rms=0.594 (0.007%), neg=0, invalid=762
0165: dt=221.952000, rms=0.594 (0.023%), neg=0, invalid=762
0166: dt=221.952000, rms=0.594 (0.034%), neg=0, invalid=762
0167: dt=221.952000, rms=0.593 (0.005%), neg=0, invalid=762
0168: dt=221.952000, rms=0.593 (0.039%), neg=0, invalid=762
0169: dt=221.952000, rms=0.593 (0.007%), neg=0, invalid=762
0170: dt=221.952000, rms=0.593 (0.021%), neg=0, invalid=762
0171: dt=221.952000, rms=0.593 (0.030%), neg=0, invalid=762
0172: dt=221.952000, rms=0.593 (0.015%), neg=0, invalid=762
0173: dt=221.952000, rms=0.593 (0.023%), neg=0, invalid=762
0174: dt=221.952000, rms=0.593 (0.013%), neg=0, invalid=762
0175: dt=110.976000, rms=0.593 (0.007%), neg=0, invalid=762
0176: dt=110.976000, rms=0.593 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.593, neg=0, invalid=762
0177: dt=295.936000, rms=0.591 (0.261%), neg=0, invalid=762
0178: dt=129.472000, rms=0.591 (0.060%), neg=0, invalid=762
0179: dt=517.888000, rms=0.591 (0.040%), neg=0, invalid=762
0180: dt=517.888000, rms=0.591 (-0.129%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.593, neg=0, invalid=762
0181: dt=114.666667, rms=0.591 (0.404%), neg=0, invalid=762
0182: dt=145.152000, rms=0.587 (0.662%), neg=0, invalid=762
0183: dt=73.087613, rms=0.585 (0.361%), neg=0, invalid=762
0184: dt=145.152000, rms=0.582 (0.477%), neg=0, invalid=762
0185: dt=79.932489, rms=0.580 (0.315%), neg=0, invalid=762
0186: dt=145.152000, rms=0.578 (0.366%), neg=0, invalid=762
0187: dt=68.888889, rms=0.576 (0.308%), neg=0, invalid=762
0188: dt=145.152000, rms=0.574 (0.281%), neg=0, invalid=762
0189: dt=72.752137, rms=0.573 (0.269%), neg=0, invalid=762
0190: dt=124.416000, rms=0.572 (0.186%), neg=0, invalid=762
0191: dt=71.963134, rms=0.570 (0.242%), neg=0, invalid=762
0192: dt=82.944000, rms=0.570 (0.126%), neg=0, invalid=762
0193: dt=103.680000, rms=0.569 (0.210%), neg=0, invalid=762
0194: dt=36.288000, rms=0.568 (0.105%), neg=0, invalid=762
0195: dt=995.328000, rms=0.563 (0.902%), neg=0, invalid=762
0196: dt=78.000000, rms=0.560 (0.573%), neg=0, invalid=762
0197: dt=36.288000, rms=0.559 (0.166%), neg=0, invalid=762
0198: dt=145.152000, rms=0.558 (0.101%), neg=0, invalid=762
0199: dt=62.208000, rms=0.557 (0.107%), neg=0, invalid=762
0200: dt=103.680000, rms=0.557 (0.058%), neg=0, invalid=762
0201: dt=82.944000, rms=0.557 (0.104%), neg=0, invalid=762
0202: dt=36.288000, rms=0.556 (0.033%), neg=0, invalid=762
0203: dt=36.288000, rms=0.556 (0.036%), neg=0, invalid=762
0204: dt=36.288000, rms=0.556 (0.056%), neg=0, invalid=762
0205: dt=36.288000, rms=0.555 (0.082%), neg=0, invalid=762
0206: dt=36.288000, rms=0.555 (0.101%), neg=0, invalid=762
0207: dt=36.288000, rms=0.554 (0.115%), neg=0, invalid=762
0208: dt=36.288000, rms=0.553 (0.131%), neg=0, invalid=762
0209: dt=36.288000, rms=0.553 (0.141%), neg=0, invalid=762
0210: dt=36.288000, rms=0.552 (0.153%), neg=0, invalid=762
0211: dt=36.288000, rms=0.551 (0.154%), neg=0, invalid=762
0212: dt=36.288000, rms=0.550 (0.154%), neg=0, invalid=762
0213: dt=36.288000, rms=0.549 (0.151%), neg=0, invalid=762
0214: dt=36.288000, rms=0.549 (0.143%), neg=0, invalid=762
0215: dt=36.288000, rms=0.548 (0.144%), neg=0, invalid=762
0216: dt=36.288000, rms=0.547 (0.141%), neg=0, invalid=762
0217: dt=36.288000, rms=0.546 (0.138%), neg=0, invalid=762
0218: dt=36.288000, rms=0.546 (0.128%), neg=0, invalid=762
0219: dt=36.288000, rms=0.545 (0.122%), neg=0, invalid=762
0220: dt=36.288000, rms=0.544 (0.120%), neg=0, invalid=762
0221: dt=36.288000, rms=0.544 (0.113%), neg=0, invalid=762
0222: dt=36.288000, rms=0.543 (0.109%), neg=0, invalid=762
0223: dt=36.288000, rms=0.542 (0.102%), neg=0, invalid=762
0224: dt=36.288000, rms=0.542 (0.096%), neg=0, invalid=762
0225: dt=36.288000, rms=0.541 (0.096%), neg=0, invalid=762
0226: dt=36.288000, rms=0.541 (0.093%), neg=0, invalid=762
0227: dt=36.288000, rms=0.540 (0.086%), neg=0, invalid=762
0228: dt=36.288000, rms=0.540 (0.085%), neg=0, invalid=762
0229: dt=36.288000, rms=0.540 (0.079%), neg=0, invalid=762
0230: dt=36.288000, rms=0.539 (0.077%), neg=0, invalid=762
0231: dt=36.288000, rms=0.539 (0.074%), neg=0, invalid=762
0232: dt=36.288000, rms=0.538 (0.068%), neg=0, invalid=762
0233: dt=36.288000, rms=0.538 (0.065%), neg=0, invalid=762
0234: dt=36.288000, rms=0.538 (0.066%), neg=0, invalid=762
0235: dt=36.288000, rms=0.537 (0.062%), neg=0, invalid=762
0236: dt=36.288000, rms=0.537 (0.060%), neg=0, invalid=762
0237: dt=36.288000, rms=0.537 (0.060%), neg=0, invalid=762
0238: dt=36.288000, rms=0.536 (0.056%), neg=0, invalid=762
0239: dt=36.288000, rms=0.536 (0.054%), neg=0, invalid=762
0240: dt=36.288000, rms=0.536 (0.009%), neg=0, invalid=762
0241: dt=36.288000, rms=0.536 (0.005%), neg=0, invalid=762
0242: dt=0.141750, rms=0.536 (0.001%), neg=0, invalid=762
0243: dt=0.070875, rms=0.536 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.536, neg=0, invalid=762
0244: dt=124.416000, rms=0.534 (0.426%), neg=0, invalid=762
0245: dt=103.680000, rms=0.533 (0.158%), neg=0, invalid=762
0246: dt=62.208000, rms=0.533 (0.051%), neg=0, invalid=762
0247: dt=145.152000, rms=0.533 (0.078%), neg=0, invalid=762
0248: dt=62.208000, rms=0.532 (0.059%), neg=0, invalid=762
0249: dt=82.944000, rms=0.532 (0.024%), neg=0, invalid=762
0250: dt=82.944000, rms=0.532 (0.060%), neg=0, invalid=762
0251: dt=82.944000, rms=0.532 (0.074%), neg=0, invalid=762
0252: dt=82.944000, rms=0.531 (0.073%), neg=0, invalid=762
0253: dt=82.944000, rms=0.531 (0.109%), neg=0, invalid=762
0254: dt=82.944000, rms=0.530 (0.097%), neg=0, invalid=762
0255: dt=82.944000, rms=0.530 (0.086%), neg=0, invalid=762
0256: dt=82.944000, rms=0.529 (0.079%), neg=0, invalid=762
0257: dt=82.944000, rms=0.529 (0.093%), neg=0, invalid=762
0258: dt=82.944000, rms=0.528 (0.067%), neg=0, invalid=762
0259: dt=82.944000, rms=0.528 (0.073%), neg=0, invalid=762
0260: dt=82.944000, rms=0.528 (0.077%), neg=0, invalid=762
0261: dt=82.944000, rms=0.527 (0.073%), neg=0, invalid=762
0262: dt=82.944000, rms=0.527 (0.059%), neg=0, invalid=762
0263: dt=82.944000, rms=0.526 (0.069%), neg=0, invalid=762
0264: dt=82.944000, rms=0.526 (0.084%), neg=0, invalid=762
0265: dt=82.944000, rms=0.526 (0.074%), neg=0, invalid=762
0266: dt=82.944000, rms=0.525 (0.059%), neg=0, invalid=762
0267: dt=82.944000, rms=0.525 (0.080%), neg=0, invalid=762
0268: dt=82.944000, rms=0.524 (0.094%), neg=0, invalid=762
0269: dt=82.944000, rms=0.524 (0.074%), neg=0, invalid=762
0270: dt=82.944000, rms=0.524 (0.051%), neg=0, invalid=762
0271: dt=82.944000, rms=0.523 (0.083%), neg=0, invalid=762
0272: dt=82.944000, rms=0.523 (0.071%), neg=0, invalid=762
0273: dt=82.944000, rms=0.523 (0.056%), neg=0, invalid=762
0274: dt=82.944000, rms=0.522 (0.055%), neg=0, invalid=762
0275: dt=82.944000, rms=0.522 (0.065%), neg=0, invalid=762
0276: dt=82.944000, rms=0.522 (0.055%), neg=0, invalid=762
0277: dt=82.944000, rms=0.521 (0.051%), neg=0, invalid=762
0278: dt=82.944000, rms=0.521 (0.053%), neg=0, invalid=762
0279: dt=82.944000, rms=0.521 (0.050%), neg=0, invalid=762
0280: dt=82.944000, rms=0.521 (0.062%), neg=0, invalid=762
0281: dt=82.944000, rms=0.520 (0.043%), neg=0, invalid=762
0282: dt=82.944000, rms=0.520 (0.038%), neg=0, invalid=762
0283: dt=82.944000, rms=0.520 (0.060%), neg=0, invalid=762
0284: dt=82.944000, rms=0.520 (0.055%), neg=0, invalid=762
0285: dt=82.944000, rms=0.519 (0.031%), neg=0, invalid=762
0286: dt=82.944000, rms=0.519 (0.041%), neg=0, invalid=762
0287: dt=82.944000, rms=0.519 (0.055%), neg=0, invalid=762
0288: dt=82.944000, rms=0.519 (0.024%), neg=0, invalid=762
0289: dt=82.944000, rms=0.519 (0.051%), neg=0, invalid=762
0290: dt=82.944000, rms=0.518 (0.009%), neg=0, invalid=762
0291: dt=82.944000, rms=0.518 (0.055%), neg=0, invalid=762
0292: dt=82.944000, rms=0.518 (0.042%), neg=0, invalid=762
0293: dt=82.944000, rms=0.518 (0.036%), neg=0, invalid=762
0294: dt=82.944000, rms=0.518 (0.028%), neg=0, invalid=762
0295: dt=82.944000, rms=0.517 (0.039%), neg=0, invalid=762
0296: dt=82.944000, rms=0.517 (0.038%), neg=0, invalid=762
0297: dt=82.944000, rms=0.517 (0.036%), neg=0, invalid=762
0298: dt=82.944000, rms=0.517 (0.023%), neg=0, invalid=762
0299: dt=82.944000, rms=0.517 (0.046%), neg=0, invalid=762
0300: dt=82.944000, rms=0.517 (0.026%), neg=0, invalid=762
0301: dt=82.944000, rms=0.516 (0.019%), neg=0, invalid=762
0302: dt=82.944000, rms=0.516 (0.034%), neg=0, invalid=762
0303: dt=82.944000, rms=0.516 (0.041%), neg=0, invalid=762
0304: dt=82.944000, rms=0.516 (0.029%), neg=0, invalid=762
0305: dt=82.944000, rms=0.516 (0.013%), neg=0, invalid=762
0306: dt=82.944000, rms=0.516 (0.023%), neg=0, invalid=762
0307: dt=82.944000, rms=0.516 (0.037%), neg=0, invalid=762
0308: dt=82.944000, rms=0.515 (0.026%), neg=0, invalid=762
0309: dt=82.944000, rms=0.515 (0.006%), neg=0, invalid=762
0310: dt=82.944000, rms=0.515 (0.031%), neg=0, invalid=762
0311: dt=82.944000, rms=0.515 (0.030%), neg=0, invalid=762
0312: dt=82.944000, rms=0.515 (-0.030%), neg=0, invalid=762
0313: dt=20.571429, rms=0.515 (0.003%), neg=0, invalid=762
0314: dt=9.072000, rms=0.515 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.525, neg=0, invalid=762
0315: dt=11.200000, rms=0.524 (0.149%), neg=0, invalid=762
0316: dt=11.200000, rms=0.524 (0.052%), neg=0, invalid=762
0317: dt=25.600000, rms=0.523 (0.070%), neg=0, invalid=762
0318: dt=44.800000, rms=0.523 (0.139%), neg=0, invalid=762
0319: dt=76.800000, rms=0.521 (0.321%), neg=0, invalid=762
0320: dt=38.400000, rms=0.519 (0.302%), neg=0, invalid=762
0321: dt=32.000000, rms=0.518 (0.204%), neg=0, invalid=762
0322: dt=44.800000, rms=0.517 (0.248%), neg=0, invalid=762
0323: dt=32.000000, rms=0.516 (0.151%), neg=0, invalid=762
0324: dt=44.800000, rms=0.515 (0.216%), neg=0, invalid=762
0325: dt=32.000000, rms=0.514 (0.143%), neg=0, invalid=762
0326: dt=44.800000, rms=0.513 (0.184%), neg=0, invalid=762
0327: dt=25.600000, rms=0.513 (0.122%), neg=0, invalid=762
0328: dt=102.400000, rms=0.512 (0.234%), neg=0, invalid=762
0329: dt=25.600000, rms=0.511 (0.193%), neg=0, invalid=762
0330: dt=128.000000, rms=0.509 (0.305%), neg=0, invalid=762
0331: dt=32.000000, rms=0.508 (0.150%), neg=0, invalid=762
0332: dt=44.800000, rms=0.508 (0.139%), neg=0, invalid=762
0333: dt=44.800000, rms=0.507 (0.102%), neg=0, invalid=762
0334: dt=38.400000, rms=0.507 (0.078%), neg=0, invalid=762
0335: dt=44.800000, rms=0.506 (0.103%), neg=0, invalid=762
0336: dt=32.000000, rms=0.506 (0.062%), neg=0, invalid=762
0337: dt=38.400000, rms=0.505 (0.071%), neg=0, invalid=762
0338: dt=25.600000, rms=0.505 (0.054%), neg=0, invalid=762
0339: dt=44.800000, rms=0.505 (0.092%), neg=0, invalid=762
0340: dt=11.200000, rms=0.505 (0.018%), neg=0, invalid=762
0341: dt=11.200000, rms=0.504 (0.027%), neg=0, invalid=762
0342: dt=11.200000, rms=0.504 (0.028%), neg=0, invalid=762
0343: dt=11.200000, rms=0.504 (0.044%), neg=0, invalid=762
0344: dt=11.200000, rms=0.504 (0.071%), neg=0, invalid=762
0345: dt=11.200000, rms=0.503 (0.078%), neg=0, invalid=762
0346: dt=11.200000, rms=0.503 (0.087%), neg=0, invalid=762
0347: dt=11.200000, rms=0.503 (0.011%), neg=0, invalid=762
0348: dt=11.200000, rms=0.503 (0.026%), neg=0, invalid=762
0349: dt=11.200000, rms=0.503 (0.020%), neg=0, invalid=762
0350: dt=11.200000, rms=0.503 (0.014%), neg=0, invalid=762
0351: dt=2.800000, rms=0.503 (0.001%), neg=0, invalid=762
0352: dt=1.400000, rms=0.503 (0.003%), neg=0, invalid=762
0353: dt=0.350000, rms=0.503 (0.001%), neg=0, invalid=762
0354: dt=0.175000, rms=0.503 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.503, neg=0, invalid=762
0355: dt=81.777778, rms=0.500 (0.623%), neg=0, invalid=762
0356: dt=32.000000, rms=0.499 (0.195%), neg=0, invalid=762
0357: dt=32.000000, rms=0.498 (0.076%), neg=0, invalid=762
0358: dt=25.600000, rms=0.498 (0.043%), neg=0, invalid=762
0359: dt=25.600000, rms=0.498 (0.061%), neg=0, invalid=762
0360: dt=25.600000, rms=0.498 (0.073%), neg=0, invalid=762
0361: dt=25.600000, rms=0.497 (0.073%), neg=0, invalid=762
0362: dt=25.600000, rms=0.497 (0.105%), neg=0, invalid=762
0363: dt=25.600000, rms=0.496 (0.105%), neg=0, invalid=762
0364: dt=25.600000, rms=0.496 (0.103%), neg=0, invalid=762
0365: dt=25.600000, rms=0.495 (0.111%), neg=0, invalid=762
0366: dt=25.600000, rms=0.494 (0.121%), neg=0, invalid=762
0367: dt=25.600000, rms=0.494 (0.143%), neg=0, invalid=762
0368: dt=25.600000, rms=0.493 (0.144%), neg=0, invalid=762
0369: dt=25.600000, rms=0.492 (0.170%), neg=0, invalid=762
0370: dt=25.600000, rms=0.491 (0.159%), neg=0, invalid=762
0371: dt=25.600000, rms=0.491 (0.170%), neg=0, invalid=762
0372: dt=25.600000, rms=0.490 (0.144%), neg=0, invalid=762
0373: dt=25.600000, rms=0.489 (0.134%), neg=0, invalid=762
0374: dt=25.600000, rms=0.489 (0.138%), neg=0, invalid=762
0375: dt=25.600000, rms=0.488 (0.118%), neg=0, invalid=762
0376: dt=25.600000, rms=0.488 (0.095%), neg=0, invalid=762
0377: dt=25.600000, rms=0.487 (0.090%), neg=0, invalid=762
0378: dt=25.600000, rms=0.487 (0.073%), neg=0, invalid=762
0379: dt=25.600000, rms=0.486 (0.077%), neg=0, invalid=762
0380: dt=25.600000, rms=0.486 (0.078%), neg=0, invalid=762
0381: dt=25.600000, rms=0.486 (0.021%), neg=0, invalid=762
0382: dt=25.600000, rms=0.486 (-0.007%), neg=0, invalid=762
0383: dt=1.600000, rms=0.486 (0.000%), neg=0, invalid=762
0384: dt=11.200000, rms=0.486 (-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=0.506, neg=0, invalid=762
0385: dt=0.000000, rms=0.505 (0.086%), neg=0, invalid=762
0386: dt=0.000000, rms=0.505 (0.000%), neg=0, invalid=762
0387: dt=0.150000, rms=0.505 (-0.017%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.506, neg=0, invalid=762
0388: dt=0.000000, rms=0.505 (0.086%), neg=0, invalid=762
0389: dt=0.000000, rms=0.505 (0.000%), neg=0, invalid=762
0390: dt=0.150000, rms=0.505 (-0.016%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.544, neg=0, invalid=762
0391: dt=1.280000, rms=0.541 (0.605%), neg=0, invalid=762
0392: dt=0.192000, rms=0.541 (0.008%), neg=0, invalid=762
0393: dt=0.192000, rms=0.541 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.541, neg=0, invalid=762
0394: dt=0.448000, rms=0.540 (0.150%), neg=0, invalid=762
0395: dt=0.384000, rms=0.540 (0.018%), neg=0, invalid=762
0396: dt=0.384000, rms=0.540 (-0.012%), 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=0.496, neg=0, invalid=762
0397: dt=0.448000, rms=0.485 (2.385%), neg=0, invalid=762
0398: dt=0.448000, rms=0.482 (0.524%), neg=0, invalid=762
0399: dt=0.448000, rms=0.481 (0.299%), neg=0, invalid=762
0400: dt=0.448000, rms=0.480 (0.187%), neg=0, invalid=762
0401: dt=0.448000, rms=0.479 (0.135%), neg=0, invalid=762
0402: dt=0.448000, rms=0.479 (0.099%), neg=0, invalid=762
0403: dt=0.448000, rms=0.478 (0.077%), neg=0, invalid=762
0404: dt=0.448000, rms=0.478 (0.060%), neg=0, invalid=762
0405: dt=0.448000, rms=0.478 (0.051%), neg=0, invalid=762
0406: dt=0.448000, rms=0.477 (0.040%), neg=0, invalid=762
0407: dt=0.448000, rms=0.477 (0.038%), neg=0, invalid=762
0408: dt=0.448000, rms=0.477 (0.057%), neg=0, invalid=762
0409: dt=0.448000, rms=0.477 (0.022%), neg=0, invalid=762
0410: dt=0.448000, rms=0.477 (0.037%), neg=0, invalid=762
0411: dt=0.448000, rms=0.477 (0.015%), neg=0, invalid=762
0412: dt=0.448000, rms=0.477 (0.023%), neg=0, invalid=762
0413: dt=0.448000, rms=0.476 (0.033%), neg=0, invalid=762
0414: dt=0.448000, rms=0.476 (0.034%), neg=0, invalid=762
0415: dt=0.448000, rms=0.476 (0.004%), neg=0, invalid=762
0416: dt=0.448000, rms=0.476 (0.001%), neg=0, invalid=762
0417: dt=0.384000, rms=0.476 (0.006%), neg=0, invalid=762
0418: dt=0.384000, rms=0.476 (0.001%), neg=0, invalid=762
0419: dt=0.384000, rms=0.476 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.477, neg=0, invalid=762
0420: dt=0.448000, rms=0.472 (0.989%), neg=0, invalid=762
0421: dt=0.384000, rms=0.472 (0.103%), neg=0, invalid=762
0422: dt=0.448000, rms=0.471 (0.050%), neg=0, invalid=762
0423: dt=0.448000, rms=0.471 (0.015%), neg=0, invalid=762
0424: dt=0.448000, rms=0.471 (0.016%), neg=0, invalid=762
0425: dt=0.448000, rms=0.471 (-0.004%), 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=0.470, neg=0, invalid=762
0426: dt=0.000000, rms=0.469 (0.114%), neg=0, invalid=762
0427: dt=0.000000, rms=0.469 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.470, neg=0, invalid=762
0428: dt=221.952000, rms=0.469 (0.174%), neg=0, invalid=762
0429: dt=92.480000, rms=0.469 (0.017%), neg=0, invalid=762
0430: dt=92.480000, rms=0.469 (0.010%), neg=0, invalid=762
0431: dt=92.480000, rms=0.469 (0.012%), neg=0, invalid=762
0432: dt=92.480000, rms=0.469 (0.018%), neg=0, invalid=762
0433: dt=92.480000, rms=0.468 (0.018%), neg=0, invalid=762
0434: dt=92.480000, rms=0.468 (0.022%), neg=0, invalid=762
0435: dt=92.480000, rms=0.468 (0.008%), neg=0, invalid=762
0436: dt=92.480000, rms=0.468 (0.018%), neg=0, invalid=762
0437: dt=92.480000, rms=0.468 (0.014%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.469, neg=0, invalid=762
0438: dt=9.072000, rms=0.468 (0.124%), neg=0, invalid=762
0439: dt=7.776000, rms=0.468 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.469, neg=0, invalid=762
0440: dt=145.152000, rms=0.467 (0.409%), neg=0, invalid=762
0441: dt=82.944000, rms=0.466 (0.116%), neg=0, invalid=762
0442: dt=82.944000, rms=0.466 (0.001%), neg=0, invalid=762
0443: dt=82.944000, rms=0.465 (0.256%), neg=0, invalid=762
0444: dt=82.944000, rms=0.464 (0.149%), neg=0, invalid=762
0445: dt=82.944000, rms=0.464 (0.170%), neg=0, invalid=762
0446: dt=82.944000, rms=0.463 (0.166%), neg=0, invalid=762
0447: dt=82.944000, rms=0.462 (0.113%), neg=0, invalid=762
0448: dt=82.944000, rms=0.462 (0.116%), neg=0, invalid=762
0449: dt=82.944000, rms=0.461 (0.130%), neg=0, invalid=762
0450: dt=82.944000, rms=0.461 (0.081%), neg=0, invalid=762
0451: dt=82.944000, rms=0.460 (0.076%), neg=0, invalid=762
0452: dt=36.288000, rms=0.460 (0.038%), neg=0, invalid=762
0453: dt=36.288000, rms=0.460 (0.008%), neg=0, invalid=762
0454: dt=36.288000, rms=0.460 (0.014%), neg=0, invalid=762
0455: dt=36.288000, rms=0.460 (0.019%), neg=0, invalid=762
0456: dt=36.288000, rms=0.460 (0.022%), neg=0, invalid=762
0457: dt=36.288000, rms=0.460 (0.022%), neg=0, invalid=762
0458: dt=36.288000, rms=0.460 (0.020%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.461, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0459: dt=24.049689, rms=0.460 (0.263%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0460: dt=38.400000, rms=0.459 (0.141%), neg=0, invalid=762
0461: dt=38.400000, rms=0.458 (0.126%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0462: dt=38.400000, rms=0.458 (0.183%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 9 iterations, nbhd size=1, neg = 0
0463: dt=38.400000, rms=0.457 (0.118%), neg=0, invalid=762
iter 0, gcam->neg = 21
after 7 iterations, nbhd size=0, neg = 0
0464: dt=38.400000, rms=0.457 (0.026%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0465: dt=38.400000, rms=0.456 (0.244%), neg=0, invalid=762
0466: dt=11.200000, rms=0.456 (0.056%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0467: dt=11.200000, rms=0.455 (0.059%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0468: dt=11.200000, rms=0.455 (0.046%), neg=0, invalid=762
0469: dt=11.200000, rms=0.455 (0.086%), neg=0, invalid=762
0470: dt=11.200000, rms=0.454 (0.113%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0471: dt=11.200000, rms=0.454 (0.102%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.454, neg=0, invalid=762
0472: dt=70.857143, rms=0.449 (1.075%), neg=0, invalid=762
0473: dt=25.583960, rms=0.447 (0.408%), neg=0, invalid=762
0474: dt=25.528090, rms=0.447 (0.119%), neg=0, invalid=762
0475: dt=25.528090, rms=0.446 (0.126%), neg=0, invalid=762
0476: dt=25.528090, rms=0.446 (0.148%), neg=0, invalid=762
0477: dt=25.528090, rms=0.445 (0.097%), neg=0, invalid=762
0478: dt=25.528090, rms=0.444 (0.170%), neg=0, invalid=762
0479: dt=25.528090, rms=0.444 (0.116%), neg=0, invalid=762
0480: dt=25.528090, rms=0.444 (0.100%), neg=0, invalid=762
0481: dt=25.600000, rms=0.443 (0.045%), neg=0, invalid=762
0482: dt=25.600000, rms=0.443 (0.028%), neg=0, invalid=762
0483: dt=25.600000, rms=0.443 (0.056%), neg=0, invalid=762
0484: dt=25.600000, rms=0.443 (0.045%), neg=0, invalid=762
0485: dt=25.600000, rms=0.442 (0.082%), neg=0, invalid=762
0486: dt=25.600000, rms=0.442 (0.046%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.447, neg=0, invalid=762
0487: dt=0.252000, rms=0.446 (0.092%), neg=0, invalid=762
0488: dt=0.180000, rms=0.446 (0.002%), neg=0, invalid=762
0489: dt=0.180000, rms=0.446 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.447, neg=0, invalid=762
0490: dt=3.733333, rms=0.446 (0.131%), neg=0, invalid=762
0491: dt=2.880000, rms=0.446 (0.020%), neg=0, invalid=762
0492: dt=2.880000, rms=0.446 (0.005%), neg=0, invalid=762
0493: dt=2.880000, rms=0.446 (-0.007%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.453, neg=0, invalid=762
0494: dt=0.000000, rms=0.453 (0.113%), neg=0, invalid=762
0495: dt=0.000000, rms=0.453 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.453, neg=0, invalid=762
0496: dt=1.280000, rms=0.452 (0.207%), neg=0, invalid=762
0497: dt=0.448000, rms=0.452 (0.006%), neg=0, invalid=762
0498: dt=0.448000, rms=0.452 (0.003%), neg=0, invalid=762
0499: dt=0.448000, rms=0.452 (-0.020%), 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=0.445, neg=0, invalid=762
iter 0, gcam->neg = 257
after 12 iterations, nbhd size=1, neg = 0
0500: dt=2.183908, rms=0.420 (5.583%), neg=0, invalid=762
0501: dt=0.080000, rms=0.420 (0.061%), neg=0, invalid=762
0502: dt=0.080000, rms=0.420 (-0.047%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0503: dt=0.080000, rms=0.420 (0.203%), neg=0, invalid=762
0504: dt=0.007000, rms=0.420 (0.002%), neg=0, invalid=762
0505: dt=0.007000, rms=0.420 (0.001%), neg=0, invalid=762
0506: dt=0.007000, rms=0.420 (0.001%), neg=0, invalid=762
0507: dt=0.007000, rms=0.420 (-0.007%), 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=0.408, neg=0, invalid=762
0508: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.408, neg=0, invalid=762
0509: dt=32.368000, rms=0.408 (0.001%), neg=0, invalid=762
0510: dt=23.120000, rms=0.408 (0.000%), neg=0, invalid=762
0511: dt=23.120000, rms=0.408 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.408, neg=0, invalid=762
0512: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.408, neg=0, invalid=762
0513: dt=62.208000, rms=0.408 (0.029%), neg=0, invalid=762
0514: dt=145.152000, rms=0.407 (0.045%), neg=0, invalid=762
0515: dt=82.944000, rms=0.407 (0.014%), neg=0, invalid=762
0516: dt=82.944000, rms=0.407 (0.024%), neg=0, invalid=762
0517: dt=82.944000, rms=0.407 (0.030%), neg=0, invalid=762
0518: dt=82.944000, rms=0.407 (0.019%), neg=0, invalid=762
0519: dt=82.944000, rms=0.407 (0.032%), neg=0, invalid=762
0520: dt=82.944000, rms=0.407 (0.023%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.407, neg=0, invalid=762
0521: dt=6.400000, rms=0.407 (0.015%), neg=0, invalid=762
0522: dt=1.200000, rms=0.407 (0.001%), neg=0, invalid=762
0523: dt=1.200000, rms=0.407 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.407, neg=0, invalid=762
0524: dt=113.543529, rms=0.405 (0.625%), neg=0, invalid=762
0525: dt=23.967611, rms=0.404 (0.255%), neg=0, invalid=762
0526: dt=38.400000, rms=0.403 (0.068%), neg=0, invalid=762
0527: dt=38.400000, rms=0.403 (0.081%), neg=0, invalid=762
0528: dt=38.400000, rms=0.403 (0.153%), neg=0, invalid=762
0529: dt=38.400000, rms=0.402 (0.147%), neg=0, invalid=762
0530: dt=38.400000, rms=0.401 (0.203%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0531: dt=38.400000, rms=0.400 (0.164%), neg=0, invalid=762
0532: dt=38.400000, rms=0.400 (0.176%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0533: dt=38.400000, rms=0.399 (0.129%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0534: dt=38.400000, rms=0.399 (0.124%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0535: dt=38.400000, rms=0.398 (0.105%), neg=0, invalid=762
0536: dt=11.200000, rms=0.398 (0.006%), neg=0, invalid=762
0537: dt=11.200000, rms=0.398 (0.002%), neg=0, invalid=762
0538: dt=11.200000, rms=0.398 (0.003%), neg=0, invalid=762
0539: dt=11.200000, rms=0.398 (0.003%), neg=0, invalid=762
0540: dt=11.200000, rms=0.398 (0.004%), neg=0, invalid=762
0541: dt=11.200000, rms=0.398 (0.004%), neg=0, invalid=762
0542: dt=11.200000, rms=0.398 (0.003%), neg=0, invalid=762
0543: dt=11.200000, rms=0.398 (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=0.402, neg=0, invalid=762
0544: dt=0.000000, rms=0.402 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.402, neg=0, invalid=762
0545: dt=4.032000, rms=0.402 (0.019%), neg=0, invalid=762
0546: dt=2.304000, rms=0.402 (0.005%), neg=0, invalid=762
0547: dt=2.304000, rms=0.402 (0.002%), neg=0, invalid=762
0548: dt=2.304000, rms=0.402 (-0.009%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0549: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0550: dt=0.000000, rms=0.409 (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=0.397, neg=0, invalid=762
iter 0, gcam->neg = 387
after 12 iterations, nbhd size=1, neg = 0
0551: dt=1.401379, rms=0.388 (2.351%), neg=0, invalid=762
0552: dt=0.000023, rms=0.388 (0.000%), neg=0, invalid=762
0553: dt=0.000023, rms=0.388 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.388, neg=0, invalid=762
0554: dt=0.096000, rms=0.388 (0.045%), neg=0, invalid=762
0555: dt=0.028000, rms=0.388 (0.005%), neg=0, invalid=762
0556: dt=0.028000, rms=0.388 (0.002%), neg=0, invalid=762
0557: dt=0.028000, rms=0.388 (-0.005%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 3 hours, 10 minutes and 25 seconds.
mri_ca_register utimesec    12213.410279
mri_ca_register stimesec    7.524856
mri_ca_register ru_maxrss   1347784
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4218403
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63064
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3535
mri_ca_register ru_nivcsw   33542
FSRUNTIME@ mri_ca_register  3.1736 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 21:53:03 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-584
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-6.0.0/0050008/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 2 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 7.26
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 = 0.21836 (23)
Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (2017 voxels, overlap=0.528)
Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (2017 voxels, peak = 22), gca=22.1
gca peak = 0.17677 (13)
mri peak = 0.17821 (23)
Right_Lateral_Ventricle (43): linear fit = 1.60 x + 0.0 (2572 voxels, overlap=0.262)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2572 voxels, peak = 21), gca=19.5
gca peak = 0.28129 (95)
mri peak = 0.13000 (99)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (598 voxels, overlap=0.953)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (598 voxels, peak = 97), gca=97.4
gca peak = 0.16930 (96)
mri peak = 0.15373 (98)
Left_Pallidum (13): linear fit = 1.03 x + 0.0 (648 voxels, overlap=0.745)
Left_Pallidum (13): linear fit = 1.03 x + 0.0 (648 voxels, peak = 99), gca=99.4
gca peak = 0.24553 (55)
mri peak = 0.09091 (67)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (944 voxels, overlap=0.064)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (944 voxels, peak = 66), gca=66.3
gca peak = 0.30264 (59)
mri peak = 0.10244 (68)
Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (980 voxels, overlap=0.018)
Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (980 voxels, peak = 68), gca=67.6
gca peak = 0.07580 (103)
mri peak = 0.12023 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (48443 voxels, overlap=0.595)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (48443 voxels, peak = 105), gca=104.5
gca peak = 0.07714 (104)
mri peak = 0.11825 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (49031 voxels, overlap=0.612)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (49031 voxels, peak = 106), gca=105.6
gca peak = 0.09712 (58)
mri peak = 0.04199 (70)
Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (34320 voxels, overlap=0.357)
Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (34320 voxels, peak = 69), gca=68.7
gca peak = 0.11620 (58)
mri peak = 0.04482 (68)
Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (33035 voxels, overlap=0.432)
Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (33035 voxels, peak = 67), gca=67.0
gca peak = 0.30970 (66)
mri peak = 0.16969 (79)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (1047 voxels, overlap=0.013)
Right_Caudate (50): linear fit = 1.14 x + 0.0 (1047 voxels, peak = 76), gca=75.6
gca peak = 0.15280 (69)
mri peak = 0.14365 (78)
Left_Caudate (11): linear fit = 1.05 x + 0.0 (899 voxels, overlap=0.569)
Left_Caudate (11): linear fit = 1.05 x + 0.0 (899 voxels, peak = 73), gca=72.8
gca peak = 0.13902 (56)
mri peak = 0.04453 (56)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (28350 voxels, overlap=0.993)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (28350 voxels, peak = 59), gca=58.5
gca peak = 0.14777 (55)
mri peak = 0.04544 (56)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (30058 voxels, overlap=0.996)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (30058 voxels, peak = 59), gca=58.6
gca peak = 0.16765 (84)
mri peak = 0.09588 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (6459 voxels, overlap=0.810)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (6459 voxels, peak = 87), gca=86.9
gca peak = 0.18739 (84)
mri peak = 0.09321 (85)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6523 voxels, overlap=0.862)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6523 voxels, peak = 87), gca=86.9
gca peak = 0.29869 (57)
mri peak = 0.08865 (72)
Left_Amygdala (18): linear fit = 1.24 x + 0.0 (564 voxels, overlap=0.057)
Left_Amygdala (18): linear fit = 1.24 x + 0.0 (564 voxels, peak = 70), gca=70.4
gca peak = 0.33601 (57)
mri peak = 0.10806 (70)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (542 voxels, overlap=0.049)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (542 voxels, peak = 68), gca=67.5
gca peak = 0.11131 (90)
mri peak = 0.09773 (91)
Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5007 voxels, overlap=0.787)
Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5007 voxels, peak = 93), gca=93.1
gca peak = 0.11793 (83)
mri peak = 0.10258 (90)
Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (4870 voxels, overlap=0.679)
Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (4870 voxels, peak = 89), gca=89.2
gca peak = 0.08324 (81)
mri peak = 0.09380 (84)
Left_Putamen (12): linear fit = 1.07 x + 0.0 (1316 voxels, overlap=0.566)
Left_Putamen (12): linear fit = 1.07 x + 0.0 (1316 voxels, peak = 86), gca=86.3
gca peak = 0.10360 (77)
mri peak = 0.09695 (83)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (1427 voxels, overlap=0.547)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (1427 voxels, peak = 83), gca=82.8
gca peak = 0.08424 (78)
mri peak = 0.09983 (90)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (13737 voxels, overlap=0.414)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (13737 voxels, peak = 86), gca=86.2
gca peak = 0.12631 (89)
mri peak = 0.09461 (92)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1801 voxels, overlap=0.560)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1801 voxels, peak = 97), gca=96.6
gca peak = 0.14500 (87)
mri peak = 0.08165 (95)
Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1919 voxels, overlap=0.724)
Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1919 voxels, peak = 94), gca=93.5
gca peak = 0.14975 (24)
mri peak = 0.12121 (20)
gca peak = 0.19357 (14)
mri peak = 0.13703 (19)
Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (338 voxels, overlap=0.630)
Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (338 voxels, peak = 18), gca=17.6
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 1.18 x + 0.0
estimating mean wm scale to be 1.01 x + 0.0
estimating mean csf scale to be 1.29 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.16156 (20)
mri peak = 0.21836 (23)
Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (2017 voxels, overlap=0.679)
Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (2017 voxels, peak = 22), gca=21.5
gca peak = 0.13422 (19)
mri peak = 0.17821 (23)
Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (2572 voxels, overlap=0.537)
Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (2572 voxels, peak = 21), gca=20.6
gca peak = 0.26998 (98)
mri peak = 0.13000 (99)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (598 voxels, overlap=1.004)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (598 voxels, peak = 98), gca=98.0
gca peak = 0.15652 (100)
mri peak = 0.15373 (98)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (648 voxels, overlap=1.000)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (648 voxels, peak = 100), gca=100.5
gca peak = 0.28157 (67)
mri peak = 0.09091 (67)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (944 voxels, overlap=1.003)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (944 voxels, peak = 66), gca=66.0
gca peak = 0.22435 (64)
mri peak = 0.10244 (68)
Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (980 voxels, overlap=1.003)
Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (980 voxels, peak = 65), gca=65.0
gca peak = 0.07771 (104)
mri peak = 0.12023 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (48443 voxels, overlap=0.645)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (48443 voxels, peak = 104), gca=104.0
gca peak = 0.07820 (106)
mri peak = 0.11825 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49031 voxels, overlap=0.670)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49031 voxels, peak = 106), gca=106.0
gca peak = 0.08218 (69)
mri peak = 0.04199 (70)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (34320 voxels, overlap=0.952)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (34320 voxels, peak = 69), gca=69.0
gca peak = 0.10163 (67)
mri peak = 0.04482 (68)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (33035 voxels, overlap=0.955)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (33035 voxels, peak = 67), gca=67.0
gca peak = 0.24442 (76)
mri peak = 0.16969 (79)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1047 voxels, overlap=0.999)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1047 voxels, peak = 76), gca=76.0
gca peak = 0.15188 (72)
mri peak = 0.14365 (78)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (899 voxels, overlap=0.838)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (899 voxels, peak = 71), gca=70.9
gca peak = 0.13187 (57)
mri peak = 0.04453 (56)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (28350 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (28350 voxels, peak = 58), gca=58.4
gca peak = 0.13829 (58)
mri peak = 0.04544 (56)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (30058 voxels, overlap=1.000)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (30058 voxels, peak = 57), gca=57.1
gca peak = 0.15882 (87)
mri peak = 0.09588 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6459 voxels, overlap=0.929)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6459 voxels, peak = 87), gca=86.6
gca peak = 0.18134 (87)
mri peak = 0.09321 (85)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6523 voxels, overlap=0.963)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6523 voxels, peak = 87), gca=86.6
gca peak = 0.28278 (70)
mri peak = 0.08865 (72)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (564 voxels, overlap=1.012)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (564 voxels, peak = 71), gca=71.0
gca peak = 0.30102 (68)
mri peak = 0.10806 (70)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (542 voxels, overlap=1.007)
Right_Amygdala (54): linear fit = 1.01 x + 0.0 (542 voxels, peak = 69), gca=69.0
gca peak = 0.11162 (93)
mri peak = 0.09773 (91)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5007 voxels, overlap=0.889)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5007 voxels, peak = 93), gca=92.5
gca peak = 0.10250 (87)
mri peak = 0.10258 (90)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4870 voxels, overlap=0.887)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4870 voxels, peak = 87), gca=86.6
gca peak = 0.08593 (80)
mri peak = 0.09380 (84)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (1316 voxels, overlap=0.838)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (1316 voxels, peak = 81), gca=81.2
gca peak = 0.10530 (81)
mri peak = 0.09695 (83)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (1427 voxels, overlap=0.847)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (1427 voxels, peak = 82), gca=82.2
gca peak = 0.07103 (89)
mri peak = 0.09983 (90)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (13737 voxels, overlap=0.756)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (13737 voxels, peak = 89), gca=88.6
gca peak = 0.11726 (95)
mri peak = 0.09461 (92)
Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1801 voxels, overlap=0.825)
Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1801 voxels, peak = 93), gca=92.6
gca peak = 0.17263 (92)
mri peak = 0.08165 (95)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1919 voxels, overlap=0.914)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1919 voxels, peak = 91), gca=90.6
gca peak = 0.12335 (33)
mri peak = 0.12121 (20)
gca peak = 0.16541 (20)
mri peak = 0.13703 (19)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (338 voxels, overlap=0.760)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (338 voxels, peak = 20), gca=20.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.17958 (37)
gca peak Left_Thalamus = 0.36646 (103)
gca peak Third_Ventricle = 0.12335 (33)
gca peak CSF = 0.20391 (47)
gca peak Left_Accumbens_area = 0.65110 (66)
gca peak Left_undetermined = 0.98573 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.11916 (35)
gca peak Right_Inf_Lat_Vent = 0.24202 (28)
gca peak Right_Accumbens_area = 0.29779 (74)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14509 (37)
gca peak Fifth_Ventricle = 0.75707 (40)
gca peak WM_hypointensities = 0.07886 (78)
gca peak non_WM_hypointensities = 0.09744 (44)
gca peak Optic_Chiasm = 0.70867 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.06 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
64627 voxels changed in iteration 0 of unlikely voxel relabeling
222 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
49076 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels)
392 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 68523 changed. image ll: -2.122, PF=0.500
pass 2: 18385 changed. image ll: -2.122, PF=0.500
pass 3: 5284 changed.
pass 4: 1847 changed.
47975 voxels changed in iteration 0 of unlikely voxel relabeling
291 voxels changed in iteration 1 of unlikely voxel relabeling
5 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6945 voxels changed in iteration 0 of unlikely voxel relabeling
81 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
5881 voxels changed in iteration 0 of unlikely voxel relabeling
54 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
4646 voxels changed in iteration 0 of unlikely voxel relabeling
42 voxels changed in iteration 1 of unlikely voxel relabeling
6 voxels changed in iteration 2 of unlikely voxel relabeling
5 voxels changed in iteration 3 of unlikely voxel relabeling
8 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    3999.184031
mri_ca_label stimesec    2.924555
mri_ca_label ru_maxrss   2094184
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   778881
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63056
mri_ca_label ru_oublock  488
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    265
mri_ca_label ru_nivcsw   9662
auto-labeling took 65 minutes and 55 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/transforms/cc_up.lta 0050008 

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-6.0.0/0050008/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/norm.mgz
39848 voxels in left wm, 71343 in right wm, xrange [118, 130]
searching rotation angles z=[-8  6], y=[-10  4]

searching scale 1 Z rot -7.8  
searching scale 1 Z rot -7.5  
searching scale 1 Z rot -7.3  
searching scale 1 Z rot -7.0  
searching scale 1 Z rot -6.8  
searching scale 1 Z rot -6.5  
searching scale 1 Z rot -6.3  
searching scale 1 Z rot -6.0  
searching scale 1 Z rot -5.8  
searching scale 1 Z rot -5.5  
searching scale 1 Z rot -5.3  
searching scale 1 Z rot -5.0  
searching scale 1 Z rot -4.8  
searching scale 1 Z rot -4.5  
searching scale 1 Z rot -4.3  
searching scale 1 Z rot -4.0  
searching scale 1 Z rot -3.8  
searching scale 1 Z rot -3.5  
searching scale 1 Z rot -3.3  
searching scale 1 Z rot -3.0  
searching scale 1 Z rot -2.8  
searching scale 1 Z rot -2.5  
searching scale 1 Z rot -2.3  
searching scale 1 Z rot -2.0  
searching scale 1 Z rot -1.8  
searching scale 1 Z rot -1.5  
searching scale 1 Z rot -1.3  
searching scale 1 Z rot -1.0  
searching scale 1 Z rot -0.8  
searching scale 1 Z rot -0.5  
searching scale 1 Z rot -0.3  
searching scale 1 Z rot -0.0  
searching scale 1 Z rot 0.2  
searching scale 1 Z rot 0.5  
searching scale 1 Z rot 0.7  
searching scale 1 Z rot 1.0  
searching scale 1 Z rot 1.2  
searching scale 1 Z rot 1.5  
searching scale 1 Z rot 1.7  
searching scale 1 Z rot 2.0  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.5  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 3.0  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.5  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 4.0  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.5  
searching scale 1 Z rot 4.7  
searching scale 1 Z rot 5.0  
searching scale 1 Z rot 5.2  
searching scale 1 Z rot 5.5  
searching scale 1 Z rot 5.7  
searching scale 1 Z rot 6.0  
searching scale 1 Z rot 6.2  
searching scale 1 Z rot 6.5  
searching scale 1 Z rot 6.7  global minimum found at slice 125.0, rotations (-2.74, -0.01)
final transformation (x=125.0, yr=-2.740, zr=-0.013):
 0.99886   0.00023  -0.04780   7.89533;
-0.00023   1.00000   0.00001   8.02739;
 0.04780   0.00000   0.99886   22.13954;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [127, 132] in xformed coordinates
best xformed slice 129
cc center is found at 129 120 100
eigenvectors:
-0.00025  -0.00038   1.00000;
-0.27495  -0.96146  -0.00044;
 0.96146  -0.27495   0.00013;
error in mid anterior detected - correcting...
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/aseg.auto.mgz...
corpus callosum segmentation took 1.2 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 23:00:09 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 23:00:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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...
299 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 74 (74), valley at 33 (33)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 74 (74), valley at 32 (32)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 7 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 23:03:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1758786 voxels in mask (pct= 10.48)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 23:03:19 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (102.0): 102.2 +- 7.0 [79.0 --> 125.0]
GM (73.0) : 71.3 +- 10.4 [30.0 --> 95.0]
setting bottom of white matter range to 81.7
setting top of gray matter range to 92.0
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...
4672 sparsely connected voxels removed...
thickening thin strands....
20 segments, 3524 filled
2528 bright non-wm voxels segmented.
2048 diagonally connected voxels added...
white matter segmentation took 1.6 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE

 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz 

preserving editing changes in input volume...
auto filling took 0.44 minutes
reading wm segmentation from wm.seg.mgz...
4 voxels added to wm to prevent paths from MTL structures to cortex
2376 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 44530 voxels turned on, 41809 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 110   new 110
115,126,128 old 110   new 110
writing edited volume to wm.asegedit.mgz....

 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  13 found -  13 modified     |    TOTAL:  13
pass   2 (xy+):   0 found -  13 modified     |    TOTAL:  13
pass   1 (xy-):  14 found -  14 modified     |    TOTAL:  27
pass   2 (xy-):   0 found -  14 modified     |    TOTAL:  27
pass   1 (yz+):  24 found -  24 modified     |    TOTAL:  51
pass   2 (yz+):   0 found -  24 modified     |    TOTAL:  51
pass   1 (yz-):  13 found -  13 modified     |    TOTAL:  64
pass   2 (yz-):   0 found -  13 modified     |    TOTAL:  64
pass   1 (xz+):  14 found -  14 modified     |    TOTAL:  78
pass   2 (xz+):   0 found -  14 modified     |    TOTAL:  78
pass   1 (xz-):   8 found -   8 modified     |    TOTAL:  86
pass   2 (xz-):   0 found -   8 modified     |    TOTAL:  86
Iteration Number : 1
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  10
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  10
pass   1 (+++):  15 found -  15 modified     |    TOTAL:  25
pass   2 (+++):   0 found -  15 modified     |    TOTAL:  25
pass   1 (+++):  14 found -  14 modified     |    TOTAL:  39
pass   2 (+++):   0 found -  14 modified     |    TOTAL:  39
pass   1 (+++):  15 found -  15 modified     |    TOTAL:  54
pass   2 (+++):   0 found -  15 modified     |    TOTAL:  54
Iteration Number : 1
pass   1 (++):  51 found -  51 modified     |    TOTAL:  51
pass   2 (++):   0 found -  51 modified     |    TOTAL:  51
pass   1 (+-):  46 found -  46 modified     |    TOTAL:  97
pass   2 (+-):   0 found -  46 modified     |    TOTAL:  97
pass   1 (--):  72 found -  72 modified     |    TOTAL: 169
pass   2 (--):   0 found -  72 modified     |    TOTAL: 169
pass   1 (-+):  35 found -  35 modified     |    TOTAL: 204
pass   2 (-+):   0 found -  35 modified     |    TOTAL: 204
Iteration Number : 2
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   6 found -   6 modified     |    TOTAL:   9
pass   2 (xy-):   0 found -   6 modified     |    TOTAL:   9
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:  11
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:  11
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:  13
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:  13
pass   1 (xz+):   4 found -   4 modified     |    TOTAL:  17
pass   2 (xz+):   0 found -   4 modified     |    TOTAL:  17
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  18
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  18
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   5
pass   1 (--):   0 found -   0 modified     |    TOTAL:   5
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   5
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   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 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 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 = 371 (out of 614806: 0.060344)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 23:05:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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
 1.08277   0.00976  -0.02822  -8.71204;
 0.00155   0.97809   0.40210  -53.89828;
 0.03506  -0.36858   0.88757   55.43580;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.08277   0.00976  -0.02822  -8.71204;
 0.00155   0.97809   0.40210  -53.89828;
 0.03506  -0.36858   0.88757   55.43580;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1290 (min = 350, max = 1400), aspect = 0.54 (min = 0.10, max = 0.75)
no need to search
using seed (126, 113, 91), TAL = (2.0, -37.0, 15.0)
talairach voxel to voxel transform
 0.92263   0.00158   0.02862   6.53664;
 0.01155   0.87333  -0.39528   69.08411;
-0.03165   0.36260   0.96140  -34.02811;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (126,  113,  91) --> (2.0, -37.0, 15.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (2.00, -37.00, 15.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, -37.00, 15.00) SRC: (108.96, 133.05, 91.01)
search lh wm seed point around talairach space (-16.00, -37.00, 15.00), SRC: (142.18, 133.46, 89.87)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sat Oct  7 23:06:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   3 found -   3 modified     |    TOTAL:   5
pass   2 (xy-):   0 found -   3 modified     |    TOTAL:   5
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:   9
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:   9
pass   1 (yz-):   6 found -   6 modified     |    TOTAL:  15
pass   2 (yz-):   0 found -   6 modified     |    TOTAL:  15
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  17
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  17
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  18
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  18
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   3
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 21 (out of 297244: 0.007065)
Ambiguous edge configurations... 

mri_pretess done


 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 2915 vertices, 3147 faces
slice 50: 13015 vertices, 13414 faces
slice 60: 25758 vertices, 26219 faces
slice 70: 39142 vertices, 39604 faces
slice 80: 51375 vertices, 51804 faces
slice 90: 62382 vertices, 62819 faces
slice 100: 74236 vertices, 74662 faces
slice 110: 85746 vertices, 86165 faces
slice 120: 96583 vertices, 97000 faces
slice 130: 107757 vertices, 108159 faces
slice 140: 117942 vertices, 118341 faces
slice 150: 127877 vertices, 128250 faces
slice 160: 136138 vertices, 136426 faces
slice 170: 142748 vertices, 143037 faces
slice 180: 148181 vertices, 148389 faces
slice 190: 151234 vertices, 151350 faces
slice 200: 151656 vertices, 151714 faces
slice 210: 151656 vertices, 151714 faces
slice 220: 151656 vertices, 151714 faces
slice 230: 151656 vertices, 151714 faces
slice 240: 151656 vertices, 151714 faces
slice 250: 151656 vertices, 151714 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...
   151656 voxel in cpt #1: X=-58 [v=151656,e=455142,f=303428] located at (-23.451778, -25.203850, -0.575566)
For the whole surface: X=-58 [v=151656,e=455142,f=303428]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 23:06:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:   5
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:   5
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:   8
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:   8
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   9
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   9
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:  12
pass   2 (xz-):   0 found -   3 modified     |    TOTAL:  12
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   1 found -   1 modified     |    TOTAL:   2
pass   2 (--):   0 found -   1 modified     |    TOTAL:   2
pass   1 (-+):   4 found -   4 modified     |    TOTAL:   6
pass   2 (-+):   0 found -   4 modified     |    TOTAL:   6
Iteration Number : 2
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   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 : 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
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 21 (out of 295481: 0.007107)
Ambiguous edge configurations... 

mri_pretess done


 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 1330 vertices, 1471 faces
slice 50: 8565 vertices, 8870 faces
slice 60: 19198 vertices, 19662 faces
slice 70: 32084 vertices, 32490 faces
slice 80: 44022 vertices, 44429 faces
slice 90: 55825 vertices, 56218 faces
slice 100: 67936 vertices, 68372 faces
slice 110: 79409 vertices, 79842 faces
slice 120: 91194 vertices, 91633 faces
slice 130: 102861 vertices, 103335 faces
slice 140: 113692 vertices, 114125 faces
slice 150: 124920 vertices, 125346 faces
slice 160: 133859 vertices, 134213 faces
slice 170: 141057 vertices, 141375 faces
slice 180: 146688 vertices, 146944 faces
slice 190: 150616 vertices, 150806 faces
slice 200: 151530 vertices, 151612 faces
slice 210: 151530 vertices, 151612 faces
slice 220: 151530 vertices, 151612 faces
slice 230: 151530 vertices, 151612 faces
slice 240: 151530 vertices, 151612 faces
slice 250: 151530 vertices, 151612 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...
   151530 voxel in cpt #1: X=-82 [v=151530,e=454836,f=303224] located at (29.544586, -20.671181, 1.691031)
For the whole surface: X=-82 [v=151530,e=454836,f=303224]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 23:06:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 23:06:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

Waiting for PID 32285 of (32285 32288) to complete...
Waiting for PID 32288 of (32285 32288) 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 (32285 32288) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 23:06:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 23:06:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Waiting for PID 32331 of (32331 32334) to complete...
Waiting for PID 32334 of (32331 32334) to complete...

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 49.2 mm, total surface area = 79217 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.157 (target=0.015)   
step 005: RMS=0.117 (target=0.015)   
step 010: RMS=0.088 (target=0.015)   
step 015: RMS=0.074 (target=0.015)   
step 020: RMS=0.063 (target=0.015)   
step 025: RMS=0.055 (target=0.015)   
step 030: RMS=0.050 (target=0.015)   
step 035: RMS=0.046 (target=0.015)   
step 040: RMS=0.044 (target=0.015)   
step 045: RMS=0.042 (target=0.015)   
step 050: RMS=0.040 (target=0.015)   
step 055: RMS=0.040 (target=0.015)   
step 060: RMS=0.039 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    47.172828
mris_inflate stimesec    0.150977
mris_inflate ru_maxrss   221032
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31688
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  10688
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2396
mris_inflate ru_nivcsw   3444

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 47.8 mm, total surface area = 78781 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.160 (target=0.015)   
step 005: RMS=0.120 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.077 (target=0.015)   
step 020: RMS=0.068 (target=0.015)   
step 025: RMS=0.060 (target=0.015)   
step 030: RMS=0.056 (target=0.015)   
step 035: RMS=0.052 (target=0.015)   
step 040: RMS=0.050 (target=0.015)   
step 045: RMS=0.048 (target=0.015)   
step 050: RMS=0.047 (target=0.015)   
step 055: RMS=0.047 (target=0.015)   
step 060: RMS=0.047 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    47.238818
mris_inflate stimesec    0.111982
mris_inflate ru_maxrss   221072
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31697
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  10680
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2286
mris_inflate ru_nivcsw   3316
PIDs (32331 32334) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 23:07:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 

#--------------------------------------------
#@# QSphere rh Sat Oct  7 23:07:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 

Waiting for PID 32400 of (32400 32403) to complete...
Waiting for PID 32403 of (32400 32403) to complete...

 mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.93 +- 0.57 (0.00-->6.16) (max @ vno 115610 --> 116611)
face area 0.03 +- 0.04 (-0.11-->0.66)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.312...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.308, avgs=0
005/300: dt: 0.9000, rms radial error=175.055, avgs=0
010/300: dt: 0.9000, rms radial error=174.508, avgs=0
015/300: dt: 0.9000, rms radial error=173.783, avgs=0
020/300: dt: 0.9000, rms radial error=172.959, avgs=0
025/300: dt: 0.9000, rms radial error=172.077, avgs=0
030/300: dt: 0.9000, rms radial error=171.163, avgs=0
035/300: dt: 0.9000, rms radial error=170.231, avgs=0
040/300: dt: 0.9000, rms radial error=169.292, avgs=0
045/300: dt: 0.9000, rms radial error=168.350, avgs=0
050/300: dt: 0.9000, rms radial error=167.407, avgs=0
055/300: dt: 0.9000, rms radial error=166.467, avgs=0
060/300: dt: 0.9000, rms radial error=165.529, avgs=0
065/300: dt: 0.9000, rms radial error=164.596, avgs=0
070/300: dt: 0.9000, rms radial error=163.667, avgs=0
075/300: dt: 0.9000, rms radial error=162.742, avgs=0
080/300: dt: 0.9000, rms radial error=161.822, avgs=0
085/300: dt: 0.9000, rms radial error=160.907, avgs=0
090/300: dt: 0.9000, rms radial error=159.996, avgs=0
095/300: dt: 0.9000, rms radial error=159.095, avgs=0
100/300: dt: 0.9000, rms radial error=158.202, avgs=0
105/300: dt: 0.9000, rms radial error=157.313, avgs=0
110/300: dt: 0.9000, rms radial error=156.430, avgs=0
115/300: dt: 0.9000, rms radial error=155.551, avgs=0
120/300: dt: 0.9000, rms radial error=154.677, avgs=0
125/300: dt: 0.9000, rms radial error=153.809, avgs=0
130/300: dt: 0.9000, rms radial error=152.945, avgs=0
135/300: dt: 0.9000, rms radial error=152.085, avgs=0
140/300: dt: 0.9000, rms radial error=151.230, avgs=0
145/300: dt: 0.9000, rms radial error=150.380, avgs=0
150/300: dt: 0.9000, rms radial error=149.534, avgs=0
155/300: dt: 0.9000, rms radial error=148.692, avgs=0
160/300: dt: 0.9000, rms radial error=147.856, avgs=0
165/300: dt: 0.9000, rms radial error=147.024, avgs=0
170/300: dt: 0.9000, rms radial error=146.197, avgs=0
175/300: dt: 0.9000, rms radial error=145.374, avgs=0
180/300: dt: 0.9000, rms radial error=144.556, avgs=0
185/300: dt: 0.9000, rms radial error=143.743, avgs=0
190/300: dt: 0.9000, rms radial error=142.934, avgs=0
195/300: dt: 0.9000, rms radial error=142.130, avgs=0
200/300: dt: 0.9000, rms radial error=141.331, avgs=0
205/300: dt: 0.9000, rms radial error=140.536, avgs=0
210/300: dt: 0.9000, rms radial error=139.745, avgs=0
215/300: dt: 0.9000, rms radial error=138.959, avgs=0
220/300: dt: 0.9000, rms radial error=138.177, avgs=0
225/300: dt: 0.9000, rms radial error=137.400, avgs=0
230/300: dt: 0.9000, rms radial error=136.627, avgs=0
235/300: dt: 0.9000, rms radial error=135.858, avgs=0
240/300: dt: 0.9000, rms radial error=135.093, avgs=0
245/300: dt: 0.9000, rms radial error=134.332, avgs=0
250/300: dt: 0.9000, rms radial error=133.576, avgs=0
255/300: dt: 0.9000, rms radial error=132.824, avgs=0
260/300: dt: 0.9000, rms radial error=132.077, avgs=0
265/300: dt: 0.9000, rms radial error=131.333, avgs=0
270/300: dt: 0.9000, rms radial error=130.594, avgs=0
275/300: dt: 0.9000, rms radial error=129.858, avgs=0
280/300: dt: 0.9000, rms radial error=129.127, avgs=0
285/300: dt: 0.9000, rms radial error=128.401, avgs=0
290/300: dt: 0.9000, rms radial error=127.678, avgs=0
295/300: dt: 0.9000, rms radial error=126.959, avgs=0
300/300: dt: 0.9000, rms radial error=126.244, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 17812.32
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
epoch 2 (K=40.0), pass 1, starting sse = 3051.59
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00027
epoch 3 (K=160.0), pass 1, starting sse = 329.50
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00365
epoch 4 (K=640.0), pass 1, starting sse = 28.85
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.13/12 = 0.01047
final distance error %28.60
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    272.647551
mris_sphere stimesec    0.256960
mris_sphere ru_maxrss   221240
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   31750
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  10672
mris_sphere ru_oublock  10712
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8855
mris_sphere ru_nivcsw   19407
FSRUNTIME@ mris_sphere  0.0758 hours 1 threads

 mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.94 +- 0.57 (0.00-->6.54) (max @ vno 115312 --> 115319)
face area 0.03 +- 0.03 (-0.16-->0.75)

== 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=175.905, avgs=0
005/300: dt: 0.9000, rms radial error=175.647, avgs=0
010/300: dt: 0.9000, rms radial error=175.093, avgs=0
015/300: dt: 0.9000, rms radial error=174.365, avgs=0
020/300: dt: 0.9000, rms radial error=173.535, avgs=0
025/300: dt: 0.9000, rms radial error=172.646, avgs=0
030/300: dt: 0.9000, rms radial error=171.723, avgs=0
035/300: dt: 0.9000, rms radial error=170.783, avgs=0
040/300: dt: 0.9000, rms radial error=169.835, avgs=0
045/300: dt: 0.9000, rms radial error=168.884, avgs=0
050/300: dt: 0.9000, rms radial error=167.934, avgs=0
055/300: dt: 0.9000, rms radial error=166.985, avgs=0
060/300: dt: 0.9000, rms radial error=166.041, avgs=0
065/300: dt: 0.9000, rms radial error=165.100, avgs=0
070/300: dt: 0.9000, rms radial error=164.165, avgs=0
075/300: dt: 0.9000, rms radial error=163.236, avgs=0
080/300: dt: 0.9000, rms radial error=162.319, avgs=0
085/300: dt: 0.9000, rms radial error=161.408, avgs=0
090/300: dt: 0.9000, rms radial error=160.502, avgs=0
095/300: dt: 0.9000, rms radial error=159.601, avgs=0
100/300: dt: 0.9000, rms radial error=158.706, avgs=0
105/300: dt: 0.9000, rms radial error=157.815, avgs=0
110/300: dt: 0.9000, rms radial error=156.930, avgs=0
115/300: dt: 0.9000, rms radial error=156.049, avgs=0
120/300: dt: 0.9000, rms radial error=155.173, avgs=0
125/300: dt: 0.9000, rms radial error=154.305, avgs=0
130/300: dt: 0.9000, rms radial error=153.442, avgs=0
135/300: dt: 0.9000, rms radial error=152.583, avgs=0
140/300: dt: 0.9000, rms radial error=151.729, avgs=0
145/300: dt: 0.9000, rms radial error=150.879, avgs=0
150/300: dt: 0.9000, rms radial error=150.034, avgs=0
155/300: dt: 0.9000, rms radial error=149.193, avgs=0
160/300: dt: 0.9000, rms radial error=148.357, avgs=0
165/300: dt: 0.9000, rms radial error=147.526, avgs=0
170/300: dt: 0.9000, rms radial error=146.700, avgs=0
175/300: dt: 0.9000, rms radial error=145.877, avgs=0
180/300: dt: 0.9000, rms radial error=145.060, avgs=0
185/300: dt: 0.9000, rms radial error=144.247, avgs=0
190/300: dt: 0.9000, rms radial error=143.438, avgs=0
195/300: dt: 0.9000, rms radial error=142.635, avgs=0
200/300: dt: 0.9000, rms radial error=141.835, avgs=0
205/300: dt: 0.9000, rms radial error=141.040, avgs=0
210/300: dt: 0.9000, rms radial error=140.250, avgs=0
215/300: dt: 0.9000, rms radial error=139.464, avgs=0
220/300: dt: 0.9000, rms radial error=138.682, avgs=0
225/300: dt: 0.9000, rms radial error=137.905, avgs=0
230/300: dt: 0.9000, rms radial error=137.132, avgs=0
235/300: dt: 0.9000, rms radial error=136.363, avgs=0
240/300: dt: 0.9000, rms radial error=135.599, avgs=0
245/300: dt: 0.9000, rms radial error=134.838, avgs=0
250/300: dt: 0.9000, rms radial error=134.082, avgs=0
255/300: dt: 0.9000, rms radial error=133.330, avgs=0
260/300: dt: 0.9000, rms radial error=132.583, avgs=0
265/300: dt: 0.9000, rms radial error=131.839, avgs=0
270/300: dt: 0.9000, rms radial error=131.099, avgs=0
275/300: dt: 0.9000, rms radial error=130.364, avgs=0
280/300: dt: 0.9000, rms radial error=129.633, avgs=0
285/300: dt: 0.9000, rms radial error=128.905, avgs=0
290/300: dt: 0.9000, rms radial error=128.182, avgs=0
295/300: dt: 0.9000, rms radial error=127.463, avgs=0
300/300: dt: 0.9000, rms radial error=126.747, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 17809.56
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
epoch 2 (K=40.0), pass 1, starting sse = 3035.42
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00002
epoch 3 (K=160.0), pass 1, starting sse = 326.73
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00271
epoch 4 (K=640.0), pass 1, starting sse = 29.73
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/12 = 0.00603
final distance error %27.92
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    273.049490
mris_sphere stimesec    0.240963
mris_sphere ru_maxrss   221272
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   32260
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  10664
mris_sphere ru_oublock  10704
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8827
mris_sphere ru_nivcsw   19779
FSRUNTIME@ mris_sphere  0.0759 hours 1 threads
PIDs (32400 32403) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 23:11:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 cp ../surf/lh.orig.nofix ../surf/lh.orig 


 cp ../surf/lh.inflated.nofix ../surf/lh.inflated 

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 23:11:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 cp ../surf/rh.orig.nofix ../surf/rh.orig 


 cp ../surf/rh.inflated.nofix ../surf/rh.inflated 

#@# Fix Topology lh Sat Oct  7 23:11:46 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050008 lh 

#@# Fix Topology rh Sat Oct  7 23:11:46 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050008 rh 

Waiting for PID 32616 of (32616 32619) to complete...
Waiting for PID 32619 of (32616 32619) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050008 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=-58 (nv=151656, nf=303428, ne=455142, g=30)
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...
10136 ambiguous faces found in tessellation
segmenting defects...
26 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 16 into 10
25 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -8.9714  (-4.4857)
      -vertex     loglikelihood: -5.8960  (-2.9480)
      -normal dot loglikelihood: -3.5883  (-3.5883)
      -quad curv  loglikelihood: -6.4949  (-3.2474)
      Total Loglikelihood : -24.9506

CORRECTING DEFECT 0 (vertices=22, convex hull=25, v0=1716)
After retessellation of defect 0 (v0=1716), euler #=-23 (145913,436281,290345) : difference with theory (-22) = 1 

CORRECTING DEFECT 1 (vertices=70, convex hull=96, v0=2160)
After retessellation of defect 1 (v0=2160), euler #=-22 (145931,436376,290423) : difference with theory (-21) = 1 

CORRECTING DEFECT 2 (vertices=23, convex hull=59, v0=6644)
After retessellation of defect 2 (v0=6644), euler #=-21 (145939,436421,290461) : difference with theory (-20) = 1 

CORRECTING DEFECT 3 (vertices=142, convex hull=138, v0=10607)
After retessellation of defect 3 (v0=10607), euler #=-20 (145967,436569,290582) : difference with theory (-19) = 1 

CORRECTING DEFECT 4 (vertices=25, convex hull=59, v0=17754)
After retessellation of defect 4 (v0=17754), euler #=-19 (145978,436623,290626) : difference with theory (-18) = 1 

CORRECTING DEFECT 5 (vertices=61, convex hull=57, v0=17780)
After retessellation of defect 5 (v0=17780), euler #=-18 (145987,436672,290667) : difference with theory (-17) = 1 

CORRECTING DEFECT 6 (vertices=109, convex hull=69, v0=31876)
After retessellation of defect 6 (v0=31876), euler #=-17 (146007,436763,290739) : difference with theory (-16) = 1 

CORRECTING DEFECT 7 (vertices=27, convex hull=68, v0=51062)
After retessellation of defect 7 (v0=51062), euler #=-16 (146016,436816,290784) : difference with theory (-15) = 1 

CORRECTING DEFECT 8 (vertices=33, convex hull=71, v0=57595)
After retessellation of defect 8 (v0=57595), euler #=-15 (146036,436906,290855) : difference with theory (-14) = 1 

CORRECTING DEFECT 9 (vertices=282, convex hull=188, v0=60815)
After retessellation of defect 9 (v0=60815), euler #=-14 (146066,437088,291008) : difference with theory (-13) = 1 

CORRECTING DEFECT 10 (vertices=1029, convex hull=589, v0=71573)
L defect detected...
After retessellation of defect 10 (v0=71573), euler #=-12 (146222,437861,291627) : difference with theory (-12) = 0 

CORRECTING DEFECT 11 (vertices=211, convex hull=100, v0=72500)
After retessellation of defect 11 (v0=72500), euler #=-11 (146240,437961,291710) : difference with theory (-11) = 0 

CORRECTING DEFECT 12 (vertices=5, convex hull=28, v0=76022)
After retessellation of defect 12 (v0=76022), euler #=-10 (146242,437974,291722) : difference with theory (-10) = 0 

CORRECTING DEFECT 13 (vertices=2754, convex hull=806, v0=78184)
XL defect detected...
After retessellation of defect 13 (v0=78184), euler #=-9 (146496,439151,292646) : difference with theory (-9) = 0 

CORRECTING DEFECT 14 (vertices=29, convex hull=55, v0=79156)
After retessellation of defect 14 (v0=79156), euler #=-8 (146517,439237,292712) : difference with theory (-8) = 0 

CORRECTING DEFECT 15 (vertices=76, convex hull=29, v0=81966)
After retessellation of defect 15 (v0=81966), euler #=-7 (146521,439257,292729) : difference with theory (-7) = 0 

CORRECTING DEFECT 16 (vertices=24, convex hull=37, v0=95151)
After retessellation of defect 16 (v0=95151), euler #=-6 (146529,439295,292760) : difference with theory (-6) = 0 

CORRECTING DEFECT 17 (vertices=42, convex hull=24, v0=95170)
After retessellation of defect 17 (v0=95170), euler #=-5 (146534,439316,292777) : difference with theory (-5) = 0 

CORRECTING DEFECT 18 (vertices=21, convex hull=24, v0=101678)
After retessellation of defect 18 (v0=101678), euler #=-4 (146537,439331,292790) : difference with theory (-4) = 0 

CORRECTING DEFECT 19 (vertices=44, convex hull=40, v0=102549)
After retessellation of defect 19 (v0=102549), euler #=-3 (146550,439385,292832) : difference with theory (-3) = 0 

CORRECTING DEFECT 20 (vertices=227, convex hull=112, v0=108398)
After retessellation of defect 20 (v0=108398), euler #=-2 (146603,439597,292992) : difference with theory (-2) = 0 

CORRECTING DEFECT 21 (vertices=306, convex hull=157, v0=118243)
After retessellation of defect 21 (v0=118243), euler #=-1 (146657,439829,293171) : difference with theory (-1) = 0 

CORRECTING DEFECT 22 (vertices=34, convex hull=80, v0=134053)
After retessellation of defect 22 (v0=134053), euler #=0 (146672,439911,293239) : difference with theory (0) = 0 

CORRECTING DEFECT 23 (vertices=133, convex hull=162, v0=136078)
After retessellation of defect 23 (v0=136078), euler #=1 (146708,440097,293390) : difference with theory (1) = 0 

CORRECTING DEFECT 24 (vertices=16, convex hull=57, v0=149343)
After retessellation of defect 24 (v0=149343), euler #=2 (146716,440142,293428) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.25 (0.10-->13.41) (max @ vno 121475 --> 128868)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.25 (0.10-->13.41) (max @ vno 121475 --> 128868)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
97 mutations (35.0%), 180 crossovers (65.0%), 729 vertices were eliminated
building final representation...
4940 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=146716, nf=293428, ne=440142, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 42.3 minutes
0 defective edges
removing intersecting faces
000: 495 intersecting
001: 5 intersecting
mris_fix_topology utimesec    2540.622766
mris_fix_topology stimesec    0.309952
mris_fix_topology ru_maxrss   521576
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   62855
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  10672
mris_fix_topology ru_oublock  14056
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    389
mris_fix_topology ru_nivcsw   4197
FSRUNTIME@ mris_fix_topology lh  0.7054 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050008 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=-82 (nv=151530, nf=303224, ne=454836, g=42)
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 13 iterations
marking ambiguous vertices...
11802 ambiguous faces found in tessellation
segmenting defects...
25 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 21 into 20
24 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -8.9425  (-4.4713)
      -vertex     loglikelihood: -5.8712  (-2.9356)
      -normal dot loglikelihood: -3.5783  (-3.5783)
      -quad curv  loglikelihood: -6.0286  (-3.0143)
      Total Loglikelihood : -24.4206

CORRECTING DEFECT 0 (vertices=32, convex hull=65, v0=4366)
After retessellation of defect 0 (v0=4366), euler #=-19 (144627,431869,287223) : difference with theory (-21) = -2 

CORRECTING DEFECT 1 (vertices=300, convex hull=239, v0=22683)
After retessellation of defect 1 (v0=22683), euler #=-18 (144759,432374,287597) : difference with theory (-20) = -2 

CORRECTING DEFECT 2 (vertices=34, convex hull=48, v0=34858)
After retessellation of defect 2 (v0=34858), euler #=-17 (144774,432434,287643) : difference with theory (-19) = -2 

CORRECTING DEFECT 3 (vertices=36, convex hull=70, v0=41350)
After retessellation of defect 3 (v0=41350), euler #=-16 (144799,432540,287725) : difference with theory (-18) = -2 

CORRECTING DEFECT 4 (vertices=22, convex hull=32, v0=47387)
After retessellation of defect 4 (v0=47387), euler #=-15 (144804,432565,287746) : difference with theory (-17) = -2 

CORRECTING DEFECT 5 (vertices=199, convex hull=139, v0=61179)
After retessellation of defect 5 (v0=61179), euler #=-14 (144880,432870,287976) : difference with theory (-16) = -2 

CORRECTING DEFECT 6 (vertices=402, convex hull=232, v0=61313)
After retessellation of defect 6 (v0=61313), euler #=-13 (145018,433401,288370) : difference with theory (-15) = -2 

CORRECTING DEFECT 7 (vertices=726, convex hull=379, v0=69944)
After retessellation of defect 7 (v0=69944), euler #=-13 (145230,434250,289007) : difference with theory (-14) = -1 

CORRECTING DEFECT 8 (vertices=45, convex hull=66, v0=71856)
After retessellation of defect 8 (v0=71856), euler #=-12 (145252,434343,289079) : difference with theory (-13) = -1 

CORRECTING DEFECT 9 (vertices=2678, convex hull=1386, v0=73169)
XL defect detected...
After retessellation of defect 9 (v0=73169), euler #=-12 (146076,437573,291485) : difference with theory (-12) = 0 

CORRECTING DEFECT 10 (vertices=37, convex hull=62, v0=92959)
After retessellation of defect 10 (v0=92959), euler #=-11 (146094,437651,291546) : difference with theory (-11) = 0 

CORRECTING DEFECT 11 (vertices=23, convex hull=21, v0=93172)
After retessellation of defect 11 (v0=93172), euler #=-10 (146097,437666,291559) : difference with theory (-10) = 0 

CORRECTING DEFECT 12 (vertices=502, convex hull=364, v0=94409)
After retessellation of defect 12 (v0=94409), euler #=-10 (146302,438466,292154) : difference with theory (-9) = 1 

CORRECTING DEFECT 13 (vertices=38, convex hull=76, v0=96498)
After retessellation of defect 13 (v0=96498), euler #=-9 (146326,438574,292239) : difference with theory (-8) = 1 

CORRECTING DEFECT 14 (vertices=50, convex hull=27, v0=99195)
After retessellation of defect 14 (v0=99195), euler #=-8 (146333,438603,292262) : difference with theory (-7) = 1 

CORRECTING DEFECT 15 (vertices=52, convex hull=23, v0=108962)
After retessellation of defect 15 (v0=108962), euler #=-7 (146342,438635,292286) : difference with theory (-6) = 1 

CORRECTING DEFECT 16 (vertices=37, convex hull=41, v0=108967)
After retessellation of defect 16 (v0=108967), euler #=-6 (146354,438687,292327) : difference with theory (-5) = 1 

CORRECTING DEFECT 17 (vertices=1010, convex hull=300, v0=110181)
After retessellation of defect 17 (v0=110181), euler #=-5 (146426,439048,292617) : difference with theory (-4) = 1 

CORRECTING DEFECT 18 (vertices=406, convex hull=169, v0=114736)
After retessellation of defect 18 (v0=114736), euler #=-4 (146499,439352,292849) : difference with theory (-3) = 1 

CORRECTING DEFECT 19 (vertices=6, convex hull=11, v0=116615)
After retessellation of defect 19 (v0=116615), euler #=-3 (146499,439354,292852) : difference with theory (-2) = 1 

CORRECTING DEFECT 20 (vertices=131, convex hull=110, v0=117423)
After retessellation of defect 20 (v0=117423), euler #=-1 (146528,439497,292968) : difference with theory (-1) = 0 

CORRECTING DEFECT 21 (vertices=14, convex hull=31, v0=121498)
After retessellation of defect 21 (v0=121498), euler #=0 (146530,439512,292982) : difference with theory (0) = 0 

CORRECTING DEFECT 22 (vertices=85, convex hull=102, v0=145145)
After retessellation of defect 22 (v0=145145), euler #=1 (146557,439638,293082) : difference with theory (1) = 0 

CORRECTING DEFECT 23 (vertices=42, convex hull=66, v0=150418)
After retessellation of defect 23 (v0=150418), euler #=2 (146577,439725,293150) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.24 (0.05-->10.87) (max @ vno 109597 --> 148723)
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 (0.05-->10.87) (max @ vno 109597 --> 148723)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
58 mutations (33.9%), 113 crossovers (66.1%), 401 vertices were eliminated
building final representation...
4953 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=146577, nf=293150, ne=439725, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 56.4 minutes
0 defective edges
removing intersecting faces
000: 404 intersecting
001: 42 intersecting
002: 2 intersecting
mris_fix_topology utimesec    3383.769588
mris_fix_topology stimesec    0.600908
mris_fix_topology ru_maxrss   550936
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   63806
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  21328
mris_fix_topology ru_oublock  14024
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    629
mris_fix_topology ru_nivcsw   9368
FSRUNTIME@ mris_fix_topology rh  0.9398 hours 1 threads
PIDs (32616 32619) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 146716 - 440142 + 293428 = 2 --> 0 holes
      F =2V-4:          293428 = 293432-4 (0)
      2E=3F:            880284 = 880284 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 146577 - 439725 + 293150 = 2 --> 0 holes
      F =2V-4:          293150 = 293154-4 (0)
      2E=3F:            879450 = 879450 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_remove_intersection ../surf/lh.orig ../surf/lh.orig 

intersection removal took 0.00 hours
removing intersecting faces
000: 140 intersecting
001: 3 intersecting
expanding nbhd size to 2
002: 4 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_remove_intersection ../surf/rh.orig ../surf/rh.orig 

intersection removal took 0.00 hours
removing intersecting faces
000: 159 intersecting
001: 5 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 00:08:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050008 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 00:08:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050008 rh 

Waiting for PID 2293 of (2293 2296) to complete...
Waiting for PID 2296 of (2293 2296) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050008 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-6.0.0/0050008/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
18652 bright wm thresholded.
3064 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.orig...
computing class statistics...
border white:    277438 voxels (1.65%)
border gray      311012 voxels (1.85%)
WM (99.0): 98.9 +- 7.4 [70.0 --> 110.0]
GM (77.0) : 75.5 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.0 (was 70)
setting MAX_BORDER_WHITE to 110.4 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 52.0 (was 40)
setting MAX_GRAY to 95.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.1 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.23 (0.02-->6.67) (max @ vno 115001 --> 146422)
face area 0.28 +- 0.13 (0.00-->14.14)
mean absolute distance = 0.78 +- 0.97
3601 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=103+-5.2,    GM=72+-7.8
mean inside = 94.8, mean outside = 79.1
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=83.0, 62 (62) missing vertices, mean dist 0.3 [0.7 (%37.3)->0.8 (%62.7))]
%63 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.12-->8.18) (max @ vno 115001 --> 146422)
face area 0.28 +- 0.13 (0.00-->10.74)
mean absolute distance = 0.40 +- 0.68
3647 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2987170.5, rms=9.199
001: dt: 0.5000, sse=1783539.0, rms=6.529 (29.033%)
002: dt: 0.5000, sse=1216414.4, rms=4.758 (27.117%)
003: dt: 0.5000, sse=954515.4, rms=3.655 (23.192%)
004: dt: 0.5000, sse=832578.5, rms=3.005 (17.765%)
005: dt: 0.5000, sse=786615.8, rms=2.720 (9.483%)
006: dt: 0.5000, sse=768586.6, rms=2.584 (5.008%)
rms = 2.55, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=762131.5, rms=2.545 (1.500%)
008: dt: 0.2500, sse=664695.8, rms=1.597 (37.241%)
009: dt: 0.2500, sse=650376.9, rms=1.419 (11.156%)
rms = 1.37, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=647280.8, rms=1.371 (3.417%)
rms = 1.34, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=644650.9, rms=1.339 (2.309%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=85.7, 52 (14) missing vertices, mean dist -0.2 [0.5 (%69.8)->0.2 (%30.2))]
%72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.24 (0.08-->8.57) (max @ vno 115001 --> 146422)
face area 0.36 +- 0.17 (0.00-->13.15)
mean absolute distance = 0.30 +- 0.44
3584 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1252309.8, rms=4.212
012: dt: 0.5000, sse=944957.0, rms=2.630 (37.558%)
013: dt: 0.5000, sse=882734.3, rms=2.197 (16.470%)
014: dt: 0.5000, sse=861128.2, rms=2.040 (7.151%)
rms = 2.14, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=816224.4, rms=1.541 (24.438%)
016: dt: 0.2500, sse=796292.1, rms=1.264 (17.953%)
017: dt: 0.2500, sse=791468.3, rms=1.186 (6.238%)
rms = 1.15, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=789967.0, rms=1.155 (2.606%)
rms = 1.13, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=788607.4, rms=1.131 (2.046%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=88.0, 31 (2) missing vertices, mean dist -0.2 [0.3 (%71.7)->0.2 (%28.3))]
%83 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 +- 0.24 (0.07-->8.76) (max @ vno 115001 --> 146422)
face area 0.34 +- 0.17 (0.00-->12.31)
mean absolute distance = 0.24 +- 0.34
3678 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1028315.6, rms=3.282
020: dt: 0.5000, sse=835250.1, rms=1.950 (40.568%)
021: dt: 0.5000, sse=821064.2, rms=1.844 (5.460%)
rms = 1.85, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=777954.6, rms=1.345 (27.036%)
023: dt: 0.2500, sse=766095.4, rms=1.070 (20.456%)
rms = 1.03, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=757469.5, rms=1.031 (3.658%)
rms = 1.01, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=756556.7, rms=1.014 (1.618%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=88.9, 49 (2) missing vertices, mean dist -0.1 [0.3 (%58.4)->0.2 (%41.6))]
%88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=779487.7, rms=1.560
026: dt: 0.5000, sse=754457.8, rms=1.221 (21.749%)
rms = 1.50, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=735449.6, rms=0.925 (24.254%)
028: dt: 0.2500, sse=730366.5, rms=0.839 (9.241%)
rms = 0.81, time step reduction 2 of 3 to 0.125...
029: dt: 0.2500, sse=729848.2, rms=0.811 (3.434%)
rms = 0.81, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=727382.6, rms=0.808 (0.345%)
positioning took 0.6 minutes
generating cortex label...
10 non-cortical segments detected
only using segment with 7394 vertices
erasing segment 0 (vno[0] = 43417)
erasing segment 2 (vno[0] = 60054)
erasing segment 3 (vno[0] = 85376)
erasing segment 4 (vno[0] = 110337)
erasing segment 5 (vno[0] = 112347)
erasing segment 6 (vno[0] = 113195)
erasing segment 7 (vno[0] = 113228)
erasing segment 8 (vno[0] = 116497)
erasing segment 9 (vno[0] = 122242)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.02-->8.85) (max @ vno 115001 --> 146422)
face area 0.34 +- 0.16 (0.00-->11.67)
refinement took 5.5 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050008 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-6.0.0/0050008/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
18652 bright wm thresholded.
3064 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.orig...
computing class statistics...
border white:    277438 voxels (1.65%)
border gray      311012 voxels (1.85%)
WM (99.0): 98.9 +- 7.4 [70.0 --> 110.0]
GM (77.0) : 75.5 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 63.0 (was 70)
setting MAX_BORDER_WHITE to 110.4 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 53.0 (was 40)
setting MAX_GRAY to 95.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 63.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 43.1 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->6.77) (max @ vno 109597 --> 145942)
face area 0.28 +- 0.13 (0.00-->7.03)
mean absolute distance = 0.73 +- 0.90
3657 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=103+-5.2,    GM=73+-7.0
mean inside = 94.9, mean outside = 79.5
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=83.7, 71 (71) missing vertices, mean dist 0.2 [0.6 (%38.9)->0.8 (%61.1))]
%67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.05-->7.43) (max @ vno 145653 --> 145722)
face area 0.28 +- 0.13 (0.00-->6.33)
mean absolute distance = 0.37 +- 0.62
3809 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2904667.5, rms=9.032
001: dt: 0.5000, sse=1721393.4, rms=6.360 (29.582%)
002: dt: 0.5000, sse=1178182.0, rms=4.615 (27.445%)
003: dt: 0.5000, sse=935754.1, rms=3.574 (22.553%)
004: dt: 0.5000, sse=830512.9, rms=2.982 (16.575%)
005: dt: 0.5000, sse=784089.4, rms=2.715 (8.934%)
006: dt: 0.5000, sse=771389.0, rms=2.598 (4.304%)
rms = 2.56, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=762478.1, rms=2.559 (1.525%)
008: dt: 0.2500, sse=664133.1, rms=1.616 (36.853%)
009: dt: 0.2500, sse=649034.1, rms=1.432 (11.385%)
rms = 1.39, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=645676.9, rms=1.388 (3.084%)
rms = 1.36, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=644154.2, rms=1.359 (2.095%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=86.2, 79 (10) missing vertices, mean dist -0.2 [0.4 (%70.3)->0.3 (%29.7))]
%75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.08-->7.55) (max @ vno 145653 --> 145722)
face area 0.35 +- 0.16 (0.00-->8.25)
mean absolute distance = 0.29 +- 0.43
4642 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1213609.8, rms=4.058
012: dt: 0.5000, sse=928914.0, rms=2.484 (38.784%)
013: dt: 0.5000, sse=872117.8, rms=2.134 (14.090%)
014: dt: 0.5000, sse=860916.8, rms=2.022 (5.250%)
rms = 2.15, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=812199.6, rms=1.533 (24.173%)
016: dt: 0.2500, sse=795071.5, rms=1.291 (15.773%)
rms = 1.24, time step reduction 2 of 3 to 0.125...
017: dt: 0.2500, sse=792380.5, rms=1.244 (3.699%)
rms = 1.21, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=789338.0, rms=1.209 (2.749%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=88.5, 75 (3) missing vertices, mean dist -0.2 [0.3 (%71.7)->0.2 (%28.3))]
%85 local maxima, %10 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 0.89 +- 0.24 (0.06-->7.76) (max @ vno 145653 --> 145722)
face area 0.34 +- 0.16 (0.00-->8.02)
mean absolute distance = 0.23 +- 0.33
3671 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1001030.2, rms=3.140
019: dt: 0.5000, sse=836022.9, rms=1.965 (37.415%)
020: dt: 0.5000, sse=846912.8, rms=1.884 (4.145%)
rms = 1.88, time step reduction 1 of 3 to 0.250...
021: dt: 0.5000, sse=826914.5, rms=1.881 (0.138%)
022: dt: 0.2500, sse=765581.0, rms=1.185 (37.019%)
023: dt: 0.2500, sse=769274.2, rms=1.088 (8.197%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=758291.2, rms=1.078 (0.869%)
rms = 1.06, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=755716.4, rms=1.057 (2.013%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=89.3, 99 (3) missing vertices, mean dist -0.1 [0.2 (%58.1)->0.2 (%41.9))]
%89 local maxima, % 6 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-6.0.0/0050008/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=770827.9, rms=1.508
026: dt: 0.5000, sse=752668.7, rms=1.207 (20.017%)
rms = 1.51, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=733005.3, rms=0.940 (22.116%)
028: dt: 0.2500, sse=733422.6, rms=0.877 (6.632%)
rms = 0.85, time step reduction 2 of 3 to 0.125...
029: dt: 0.2500, sse=726451.5, rms=0.846 (3.594%)
rms = 0.84, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=725534.8, rms=0.843 (0.388%)
positioning took 0.6 minutes
generating cortex label...
11 non-cortical segments detected
only using segment with 7047 vertices
erasing segment 1 (vno[0] = 74024)
erasing segment 2 (vno[0] = 75015)
erasing segment 3 (vno[0] = 77284)
erasing segment 4 (vno[0] = 80832)
erasing segment 5 (vno[0] = 106912)
erasing segment 6 (vno[0] = 106958)
erasing segment 7 (vno[0] = 107053)
erasing segment 8 (vno[0] = 107852)
erasing segment 9 (vno[0] = 108740)
erasing segment 10 (vno[0] = 110694)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.area
vertex spacing 0.89 +- 0.25 (0.03-->7.64) (max @ vno 145653 --> 145722)
face area 0.33 +- 0.16 (0.00-->7.91)
refinement took 5.4 minutes
PIDs (2293 2296) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 00:13:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm 

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 00:13:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm 

Waiting for PID 2517 of (2517 2520) to complete...
Waiting for PID 2520 of (2517 2520) 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 (2517 2520) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 00:13:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 00:13:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 2564 of (2564 2567) to complete...
Waiting for PID 2567 of (2564 2567) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 49.7 mm, total surface area = 88621 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.177 (target=0.015)   
step 005: RMS=0.123 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.073 (target=0.015)   
step 020: RMS=0.060 (target=0.015)   
step 025: RMS=0.049 (target=0.015)   
step 030: RMS=0.041 (target=0.015)   
step 035: RMS=0.035 (target=0.015)   
step 040: RMS=0.030 (target=0.015)   
step 045: RMS=0.027 (target=0.015)   
step 050: RMS=0.024 (target=0.015)   
step 055: RMS=0.022 (target=0.015)   
step 060: RMS=0.021 (target=0.015)   
inflation complete.
inflation took 0.7 minutes
mris_inflate utimesec    43.802341
mris_inflate stimesec    0.128980
mris_inflate ru_maxrss   214288
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31152
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11496
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5658
mris_inflate ru_nivcsw   3347

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 48.4 mm, total surface area = 87951 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.179 (target=0.015)   
step 005: RMS=0.125 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.074 (target=0.015)   
step 020: RMS=0.060 (target=0.015)   
step 025: RMS=0.051 (target=0.015)   
step 030: RMS=0.042 (target=0.015)   
step 035: RMS=0.036 (target=0.015)   
step 040: RMS=0.031 (target=0.015)   
step 045: RMS=0.027 (target=0.015)   
step 050: RMS=0.024 (target=0.015)   
step 055: RMS=0.022 (target=0.015)   
step 060: RMS=0.021 (target=0.015)   
inflation complete.
inflation took 0.7 minutes
mris_inflate utimesec    44.301265
mris_inflate stimesec    0.128980
mris_inflate ru_maxrss   214232
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31137
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11480
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2359
mris_inflate ru_nivcsw   5178
PIDs (2564 2567) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 00:14:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 00:14:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 2668 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...
Waiting for PID 2671 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...
Waiting for PID 2674 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...
Waiting for PID 2677 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...
Waiting for PID 2680 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...
Waiting for PID 2683 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...
Waiting for PID 2686 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...
Waiting for PID 2689 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...
Waiting for PID 2692 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...
Waiting for PID 2695 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...
Waiting for PID 2698 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...
Waiting for PID 2703 of (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 2.809*4pi (35.305) --> -2 handles
ICI = 176.0, FI = 1806.0, variation=28542.289
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
179 vertices thresholded to be in k1 ~ [-0.18 0.39], k2 ~ [-0.09 0.07]
total integrated curvature = 0.444*4pi (5.574) --> 1 handles
ICI = 1.5, FI = 8.5, variation=152.600
128 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
154 vertices thresholded to be in [-0.12 0.16]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.020
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 7.157*4pi (89.943) --> -6 handles
ICI = 184.8, FI = 1896.0, variation=29901.525
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
166 vertices thresholded to be in k1 ~ [-0.20 0.38], k2 ~ [-0.10 0.05]
total integrated curvature = 0.534*4pi (6.713) --> 0 handles
ICI = 1.5, FI = 8.5, variation=151.220
116 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
151 vertices thresholded to be in [-0.12 0.20]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.021
done.
PIDs (2668 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 2703) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 00:16:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050008 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      [ 0050008/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                      [ 287 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.176482
WARN:    S explicit min:                          0.000000	vertex = 331

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 00:16:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050008 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      [ 0050008/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                      [ 268 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.490174
WARN:    S explicit min:                          0.000000	vertex = 169
#--------------------------------------------
#@# Sphere lh Sun Oct  8 00:16:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 00:16:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 2861 of (2861 2864) to complete...
Waiting for PID 2864 of (2861 2864) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0.292...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.14
pass 1: epoch 2 of 3 starting distance error %20.14
unfolding complete - removing small folds...
starting distance error %20.03
removing remaining folds...
final distance error %20.05
MRISunfold() return, current seed 1234
-01: dt=0.0000, 66 negative triangles
204: dt=0.9900, 66 negative triangles
205: dt=0.9900, 42 negative triangles
206: dt=0.9900, 42 negative triangles
207: dt=0.9900, 36 negative triangles
208: dt=0.9900, 31 negative triangles
209: dt=0.9900, 26 negative triangles
210: dt=0.9900, 26 negative triangles
211: dt=0.9900, 23 negative triangles
212: dt=0.9900, 23 negative triangles
213: dt=0.9900, 21 negative triangles
214: dt=0.9900, 19 negative triangles
215: dt=0.9900, 21 negative triangles
216: dt=0.9900, 21 negative triangles
217: dt=0.9900, 20 negative triangles
218: dt=0.9900, 20 negative triangles
219: dt=0.9900, 19 negative triangles
220: dt=0.9900, 24 negative triangles
221: dt=0.9900, 19 negative triangles
222: dt=0.9900, 18 negative triangles
223: dt=0.9900, 19 negative triangles
224: dt=0.9900, 16 negative triangles
225: dt=0.9900, 15 negative triangles
226: dt=0.9900, 17 negative triangles
227: dt=0.9900, 13 negative triangles
228: dt=0.9900, 14 negative triangles
229: dt=0.9900, 17 negative triangles
230: dt=0.9900, 14 negative triangles
231: dt=0.9900, 18 negative triangles
232: dt=0.9900, 15 negative triangles
233: dt=0.9900, 12 negative triangles
234: dt=0.9900, 19 negative triangles
235: dt=0.9900, 10 negative triangles
236: dt=0.9900, 10 negative triangles
237: dt=0.9900, 6 negative triangles
238: dt=0.9900, 6 negative triangles
239: dt=0.9900, 5 negative triangles
240: dt=0.9900, 2 negative triangles
241: dt=0.9900, 2 negative triangles
242: dt=0.9900, 1 negative triangles
243: dt=0.9900, 1 negative triangles
244: dt=0.9900, 1 negative triangles
245: dt=0.9900, 2 negative triangles
246: dt=0.9900, 3 negative triangles
247: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.85 hours
mris_sphere utimesec    3182.773144
mris_sphere stimesec    1.776729
mris_sphere ru_maxrss   302020
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   53234
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10368
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    116074
mris_sphere ru_nivcsw   238510
FSRUNTIME@ mris_sphere  0.8456 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0.291...
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 %42.12
pass 1: epoch 2 of 3 starting distance error %19.81
unfolding complete - removing small folds...
starting distance error %19.72
removing remaining folds...
final distance error %19.73
MRISunfold() return, current seed 1234
-01: dt=0.0000, 179 negative triangles
129: dt=0.9900, 179 negative triangles
130: dt=0.9900, 120 negative triangles
131: dt=0.9900, 93 negative triangles
132: dt=0.9900, 74 negative triangles
133: dt=0.9900, 75 negative triangles
134: dt=0.9900, 64 negative triangles
135: dt=0.9900, 56 negative triangles
136: dt=0.9900, 53 negative triangles
137: dt=0.9900, 54 negative triangles
138: dt=0.9900, 58 negative triangles
139: dt=0.9900, 47 negative triangles
140: dt=0.9900, 46 negative triangles
141: dt=0.9900, 57 negative triangles
142: dt=0.9900, 48 negative triangles
143: dt=0.9900, 50 negative triangles
144: dt=0.9900, 56 negative triangles
145: dt=0.9900, 51 negative triangles
146: dt=0.9900, 43 negative triangles
147: dt=0.9900, 50 negative triangles
148: dt=0.9900, 52 negative triangles
149: dt=0.9900, 51 negative triangles
150: dt=0.9900, 40 negative triangles
151: dt=0.9900, 50 negative triangles
152: dt=0.9900, 46 negative triangles
153: dt=0.9900, 49 negative triangles
154: dt=0.9900, 48 negative triangles
155: dt=0.9900, 54 negative triangles
156: dt=0.9900, 51 negative triangles
157: dt=0.9900, 52 negative triangles
158: dt=0.9900, 50 negative triangles
159: dt=0.9900, 50 negative triangles
160: dt=0.9405, 43 negative triangles
161: dt=0.9405, 44 negative triangles
162: dt=0.9405, 44 negative triangles
163: dt=0.9405, 43 negative triangles
164: dt=0.9405, 50 negative triangles
165: dt=0.9405, 48 negative triangles
166: dt=0.9405, 49 negative triangles
167: dt=0.9405, 51 negative triangles
168: dt=0.9405, 53 negative triangles
169: dt=0.9405, 50 negative triangles
170: dt=0.8935, 43 negative triangles
171: dt=0.8935, 53 negative triangles
172: dt=0.8935, 51 negative triangles
173: dt=0.8935, 50 negative triangles
174: dt=0.8935, 46 negative triangles
175: dt=0.8935, 49 negative triangles
176: dt=0.8935, 49 negative triangles
177: dt=0.8935, 50 negative triangles
178: dt=0.8935, 42 negative triangles
179: dt=0.8935, 47 negative triangles
180: dt=0.8488, 50 negative triangles
181: dt=0.8488, 46 negative triangles
182: dt=0.8488, 49 negative triangles
183: dt=0.8488, 48 negative triangles
184: dt=0.8488, 45 negative triangles
185: dt=0.8488, 44 negative triangles
186: dt=0.8488, 44 negative triangles
187: dt=0.8488, 44 negative triangles
188: dt=0.8488, 43 negative triangles
189: dt=0.8488, 45 negative triangles
190: dt=0.8064, 47 negative triangles
191: dt=0.8064, 47 negative triangles
192: dt=0.8064, 45 negative triangles
193: dt=0.8064, 42 negative triangles
194: dt=0.8064, 45 negative triangles
195: dt=0.8064, 45 negative triangles
196: dt=0.8064, 43 negative triangles
197: dt=0.8064, 47 negative triangles
198: dt=0.8064, 45 negative triangles
199: dt=0.8064, 44 negative triangles
200: dt=0.7660, 42 negative triangles
expanding nbhd size to 1
201: dt=0.9900, 46 negative triangles
202: dt=0.9900, 42 negative triangles
203: dt=0.9900, 37 negative triangles
204: dt=0.9900, 39 negative triangles
205: dt=0.9900, 35 negative triangles
206: dt=0.9900, 37 negative triangles
207: dt=0.9900, 34 negative triangles
208: dt=0.9900, 38 negative triangles
209: dt=0.9900, 34 negative triangles
210: dt=0.9900, 39 negative triangles
211: dt=0.9900, 36 negative triangles
212: dt=0.9900, 38 negative triangles
213: dt=0.9900, 37 negative triangles
214: dt=0.9900, 33 negative triangles
215: dt=0.9900, 35 negative triangles
216: dt=0.9900, 33 negative triangles
217: dt=0.9900, 32 negative triangles
218: dt=0.9900, 35 negative triangles
219: dt=0.9900, 32 negative triangles
220: dt=0.9900, 34 negative triangles
221: dt=0.9900, 31 negative triangles
222: dt=0.9900, 34 negative triangles
223: dt=0.9900, 32 negative triangles
224: dt=0.9900, 30 negative triangles
225: dt=0.9900, 32 negative triangles
226: dt=0.9900, 32 negative triangles
227: dt=0.9900, 31 negative triangles
228: dt=0.9900, 29 negative triangles
229: dt=0.9900, 31 negative triangles
230: dt=0.9900, 30 negative triangles
231: dt=0.9900, 33 negative triangles
232: dt=0.9900, 31 negative triangles
233: dt=0.9900, 30 negative triangles
234: dt=0.9900, 32 negative triangles
235: dt=0.9900, 28 negative triangles
236: dt=0.9900, 30 negative triangles
237: dt=0.9900, 28 negative triangles
238: dt=0.9900, 31 negative triangles
239: dt=0.9900, 28 negative triangles
240: dt=0.9900, 29 negative triangles
241: dt=0.9900, 27 negative triangles
242: dt=0.9900, 30 negative triangles
243: dt=0.9900, 27 negative triangles
244: dt=0.9900, 27 negative triangles
245: dt=0.9900, 23 negative triangles
246: dt=0.9900, 27 negative triangles
247: dt=0.9900, 25 negative triangles
248: dt=0.9900, 25 negative triangles
249: dt=0.9900, 25 negative triangles
250: dt=0.9900, 23 negative triangles
251: dt=0.9900, 26 negative triangles
252: dt=0.9900, 24 negative triangles
253: dt=0.9900, 26 negative triangles
254: dt=0.9900, 23 negative triangles
255: dt=0.9405, 24 negative triangles
256: dt=0.9405, 22 negative triangles
257: dt=0.9405, 21 negative triangles
258: dt=0.9405, 22 negative triangles
259: dt=0.9405, 21 negative triangles
260: dt=0.9405, 23 negative triangles
261: dt=0.9405, 25 negative triangles
262: dt=0.9405, 23 negative triangles
263: dt=0.9405, 21 negative triangles
264: dt=0.9405, 21 negative triangles
265: dt=0.9405, 22 negative triangles
266: dt=0.9405, 21 negative triangles
267: dt=0.8935, 23 negative triangles
268: dt=0.8935, 20 negative triangles
269: dt=0.8935, 23 negative triangles
270: dt=0.8935, 25 negative triangles
271: dt=0.8935, 22 negative triangles
272: dt=0.8935, 23 negative triangles
273: dt=0.8935, 19 negative triangles
274: dt=0.8935, 22 negative triangles
275: dt=0.8935, 22 negative triangles
276: dt=0.8935, 20 negative triangles
277: dt=0.8935, 20 negative triangles
278: dt=0.8935, 21 negative triangles
279: dt=0.8935, 18 negative triangles
280: dt=0.8935, 22 negative triangles
281: dt=0.8935, 18 negative triangles
282: dt=0.8935, 18 negative triangles
283: dt=0.8935, 18 negative triangles
284: dt=0.8935, 16 negative triangles
285: dt=0.8935, 22 negative triangles
286: dt=0.8935, 19 negative triangles
287: dt=0.8935, 16 negative triangles
288: dt=0.8935, 21 negative triangles
289: dt=0.8935, 18 negative triangles
290: dt=0.8935, 16 negative triangles
291: dt=0.8935, 19 negative triangles
292: dt=0.8935, 18 negative triangles
293: dt=0.8935, 15 negative triangles
294: dt=0.8935, 19 negative triangles
295: dt=0.8935, 14 negative triangles
296: dt=0.8935, 18 negative triangles
297: dt=0.8935, 16 negative triangles
298: dt=0.8935, 15 negative triangles
299: dt=0.8935, 17 negative triangles
300: dt=0.8935, 16 negative triangles
301: dt=0.8935, 16 negative triangles
302: dt=0.8935, 18 negative triangles
303: dt=0.8935, 12 negative triangles
304: dt=0.8935, 14 negative triangles
305: dt=0.8935, 15 negative triangles
306: dt=0.8935, 15 negative triangles
307: dt=0.8935, 12 negative triangles
308: dt=0.8935, 12 negative triangles
309: dt=0.8935, 15 negative triangles
310: dt=0.8935, 15 negative triangles
311: dt=0.8935, 14 negative triangles
312: dt=0.8935, 12 negative triangles
313: dt=0.8488, 15 negative triangles
314: dt=0.8488, 14 negative triangles
315: dt=0.8488, 12 negative triangles
316: dt=0.8488, 12 negative triangles
317: dt=0.8488, 13 negative triangles
318: dt=0.8488, 12 negative triangles
319: dt=0.8488, 11 negative triangles
320: dt=0.8488, 12 negative triangles
321: dt=0.8488, 12 negative triangles
322: dt=0.8488, 12 negative triangles
323: dt=0.8488, 11 negative triangles
324: dt=0.8488, 10 negative triangles
325: dt=0.8488, 10 negative triangles
326: dt=0.8488, 13 negative triangles
327: dt=0.8488, 10 negative triangles
328: dt=0.8488, 10 negative triangles
329: dt=0.8488, 12 negative triangles
330: dt=0.8488, 11 negative triangles
331: dt=0.8488, 11 negative triangles
332: dt=0.8488, 12 negative triangles
333: dt=0.8488, 12 negative triangles
334: dt=0.8064, 10 negative triangles
335: dt=0.8064, 9 negative triangles
336: dt=0.8064, 9 negative triangles
337: dt=0.8064, 12 negative triangles
338: dt=0.8064, 11 negative triangles
339: dt=0.8064, 10 negative triangles
340: dt=0.8064, 10 negative triangles
341: dt=0.8064, 10 negative triangles
342: dt=0.8064, 8 negative triangles
343: dt=0.8064, 9 negative triangles
344: dt=0.8064, 8 negative triangles
345: dt=0.8064, 6 negative triangles
346: dt=0.8064, 8 negative triangles
347: dt=0.8064, 7 negative triangles
348: dt=0.8064, 7 negative triangles
349: dt=0.8064, 8 negative triangles
350: dt=0.8064, 10 negative triangles
351: dt=0.8064, 7 negative triangles
352: dt=0.8064, 7 negative triangles
353: dt=0.8064, 6 negative triangles
354: dt=0.8064, 5 negative triangles
355: dt=0.8064, 8 negative triangles
356: dt=0.8064, 5 negative triangles
357: dt=0.8064, 5 negative triangles
358: dt=0.8064, 6 negative triangles
359: dt=0.8064, 6 negative triangles
360: dt=0.8064, 5 negative triangles
361: dt=0.8064, 4 negative triangles
362: dt=0.8064, 2 negative triangles
363: dt=0.8064, 4 negative triangles
364: dt=0.8064, 7 negative triangles
365: dt=0.8064, 5 negative triangles
366: dt=0.8064, 2 negative triangles
367: dt=0.8064, 2 negative triangles
368: dt=0.8064, 1 negative triangles
369: dt=0.8064, 1 negative triangles
370: dt=0.8064, 4 negative triangles
371: dt=0.8064, 5 negative triangles
372: dt=0.8064, 3 negative triangles
373: dt=0.8064, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.79 hours
mris_sphere utimesec    2863.195728
mris_sphere stimesec    1.736735
mris_sphere ru_maxrss   301776
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   53169
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10528
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    107005
mris_sphere ru_nivcsw   237099
FSRUNTIME@ mris_sphere  0.7945 hours 1 threads
PIDs (2861 2864) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 01:07:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 01:07:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 4570 of (4570 4573) to complete...
Waiting for PID 4573 of (4570 4573) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 = 5.460
curvature mean = 0.043, std = 0.826
curvature mean = 0.023, std = 0.850
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, -16.00) sse = 369079.2, tmin=1.1018
  d=32.00 min @ (-8.00, -8.00, 8.00) sse = 243096.7, tmin=2.2379
  d=8.00 min @ (0.00, 2.00, -2.00) sse = 233859.0, tmin=4.5285
  d=4.00 min @ (0.00, -1.00, 0.00) sse = 232470.5, tmin=5.6877
  d=1.00 min @ (0.00, 0.25, 0.25) sse = 232369.9, tmin=8.0098
  d=0.50 min @ (0.12, 0.00, -0.12) sse = 232318.0, tmin=9.2036
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.20 min
curvature mean = 0.003, std = 0.829
curvature mean = 0.007, std = 0.939
curvature mean = -0.007, std = 0.831
curvature mean = 0.003, std = 0.973
curvature mean = -0.010, std = 0.831
curvature mean = 0.000, std = 0.988
2 Reading smoothwm
curvature mean = -0.027, std = 0.281
curvature mean = 0.039, std = 0.244
curvature mean = 0.062, std = 0.355
curvature mean = 0.036, std = 0.301
curvature mean = 0.030, std = 0.555
curvature mean = 0.035, std = 0.326
curvature mean = 0.017, std = 0.704
curvature mean = 0.035, std = 0.337
curvature mean = 0.006, std = 0.813
MRISregister() return, current seed 0
-01: dt=0.0000, 14 negative triangles
130: dt=0.9900, 14 negative triangles
expanding nbhd size to 1
131: dt=0.9900, 22 negative triangles
132: dt=0.9900, 8 negative triangles
133: dt=0.9900, 10 negative triangles
134: dt=0.9900, 9 negative triangles
135: dt=0.9900, 5 negative triangles
136: dt=0.9900, 3 negative triangles
137: dt=0.9900, 4 negative triangles
138: dt=0.9900, 2 negative triangles
139: dt=0.9900, 1 negative triangles
140: dt=0.9900, 2 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.38 hours
mris_register utimesec    5210.099944
mris_register stimesec    4.225357
mris_register ru_maxrss   269120
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   39618
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10400
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    379266
mris_register ru_nivcsw   223933
FSRUNTIME@ mris_register  1.3844 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 = 5.483
curvature mean = 0.025, std = 0.816
curvature mean = 0.022, std = 0.850
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 388449.9, tmin=1.1009
  d=32.00 min @ (8.00, 8.00, -8.00) sse = 268117.3, tmin=2.2275
  d=16.00 min @ (0.00, 0.00, 4.00) sse = 246224.7, tmin=3.3736
  d=8.00 min @ (0.00, -2.00, 0.00) sse = 245456.7, tmin=4.5202
  d=4.00 min @ (1.00, 1.00, -1.00) sse = 241529.3, tmin=5.6770
  d=2.00 min @ (-0.50, 0.00, 0.50) sse = 241131.0, tmin=6.8432
  d=1.00 min @ (0.00, 0.00, -0.25) sse = 241013.3, tmin=8.0118
  d=0.50 min @ (0.12, 0.12, 0.00) sse = 240961.7, tmin=9.2057
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.21 min
curvature mean = -0.008, std = 0.830
curvature mean = 0.009, std = 0.944
curvature mean = -0.014, std = 0.837
curvature mean = 0.003, std = 0.978
curvature mean = -0.015, std = 0.838
curvature mean = 0.001, std = 0.992
2 Reading smoothwm
curvature mean = -0.026, std = 0.288
curvature mean = 0.032, std = 0.241
curvature mean = 0.062, std = 0.352
curvature mean = 0.029, std = 0.297
curvature mean = 0.030, std = 0.555
curvature mean = 0.029, std = 0.323
curvature mean = 0.015, std = 0.701
curvature mean = 0.029, std = 0.334
curvature mean = 0.005, std = 0.804
MRISregister() return, current seed 0
-01: dt=0.0000, 37 negative triangles
122: dt=0.9900, 37 negative triangles
expanding nbhd size to 1
123: dt=0.9900, 59 negative triangles
124: dt=0.9900, 41 negative triangles
125: dt=0.9900, 38 negative triangles
126: dt=0.9900, 39 negative triangles
127: dt=0.9900, 40 negative triangles
128: dt=0.9900, 43 negative triangles
129: dt=0.9900, 42 negative triangles
130: dt=0.9405, 37 negative triangles
131: dt=0.9405, 31 negative triangles
132: dt=0.9405, 35 negative triangles
133: dt=0.9405, 37 negative triangles
134: dt=0.9405, 30 negative triangles
135: dt=0.9405, 31 negative triangles
136: dt=0.9405, 27 negative triangles
137: dt=0.9405, 26 negative triangles
138: dt=0.9405, 28 negative triangles
139: dt=0.9405, 23 negative triangles
140: dt=0.9405, 23 negative triangles
141: dt=0.9405, 20 negative triangles
142: dt=0.9405, 22 negative triangles
143: dt=0.9405, 22 negative triangles
144: dt=0.9405, 19 negative triangles
145: dt=0.9405, 20 negative triangles
146: dt=0.9405, 19 negative triangles
147: dt=0.9405, 18 negative triangles
148: dt=0.9405, 17 negative triangles
149: dt=0.9405, 16 negative triangles
150: dt=0.9405, 19 negative triangles
151: dt=0.9405, 17 negative triangles
152: dt=0.9405, 17 negative triangles
153: dt=0.9405, 16 negative triangles
154: dt=0.9405, 17 negative triangles
155: dt=0.9405, 15 negative triangles
156: dt=0.9405, 11 negative triangles
157: dt=0.9405, 10 negative triangles
158: dt=0.9405, 8 negative triangles
159: dt=0.9405, 8 negative triangles
160: dt=0.9405, 6 negative triangles
161: dt=0.9405, 6 negative triangles
162: dt=0.9405, 8 negative triangles
163: dt=0.9405, 8 negative triangles
164: dt=0.9405, 5 negative triangles
165: dt=0.9405, 5 negative triangles
166: dt=0.9405, 4 negative triangles
167: dt=0.9405, 4 negative triangles
168: dt=0.9405, 2 negative triangles
169: dt=0.9405, 2 negative triangles
170: dt=0.9405, 2 negative triangles
171: dt=0.9405, 2 negative triangles
172: dt=0.9405, 2 negative triangles
173: dt=0.9405, 2 negative triangles
174: dt=0.9405, 2 negative triangles
175: dt=0.9405, 1 negative triangles
176: dt=0.9405, 1 negative triangles
177: dt=0.9405, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.28 hours
mris_register utimesec    4608.670375
mris_register stimesec    3.951399
mris_register ru_maxrss   269776
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   38834
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10424
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    345814
mris_register ru_nivcsw   225311
FSRUNTIME@ mris_register  1.2798 hours 1 threads
PIDs (4570 4573) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 02:30:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white 

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 02:30:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white 

Waiting for PID 8214 of (8214 8217) to complete...
Waiting for PID 8217 of (8214 8217) 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 (8214 8217) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 02:30:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv 

#--------------------------------------------
#@# AvgCurv rh Sun Oct  8 02:30:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 8258 of (8258 8261) to complete...
Waiting for PID 8261 of (8258 8261) 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 (8258 8261) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 02:30:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot 

#-----------------------------------------
#@# Cortical Parc rh Sun Oct  8 02:30:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 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 8305 of (8305 8308) to complete...
Waiting for PID 8308 of (8305 8308) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 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...
1243 labels changed using aseg
relabeling using gibbs priors...
000:   3155 changed, 146716 examined...
001:    705 changed, 13396 examined...
002:    198 changed, 3941 examined...
003:     64 changed, 1174 examined...
004:     17 changed, 363 examined...
005:      6 changed, 118 examined...
006:      2 changed, 37 examined...
007:      0 changed, 9 examined...
279 labels changed using aseg
000: 117 total segments, 70 labels (233 vertices) changed
001: 50 total segments, 10 labels (30 vertices) changed
002: 40 total segments, 1 labels (7 vertices) changed
003: 39 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 10 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2121 vertices marked for relabeling...
2121 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 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...
887 labels changed using aseg
relabeling using gibbs priors...
000:   2946 changed, 146577 examined...
001:    667 changed, 12659 examined...
002:    163 changed, 3856 examined...
003:     53 changed, 977 examined...
004:     22 changed, 328 examined...
005:     17 changed, 137 examined...
006:      3 changed, 91 examined...
007:      2 changed, 24 examined...
008:      0 changed, 12 examined...
174 labels changed using aseg
000: 97 total segments, 50 labels (213 vertices) changed
001: 49 total segments, 2 labels (2 vertices) changed
002: 47 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1802 vertices marked for relabeling...
1802 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 16 seconds.
PIDs (8305 8308) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 02:30:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050008 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 02:30:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050008 rh 

Waiting for PID 8372 of (8372 8375) to complete...
Waiting for PID 8375 of (8372 8375) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050008 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-6.0.0/0050008/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
18652 bright wm thresholded.
3064 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.orig...
computing class statistics...
border white:    277438 voxels (1.65%)
border gray      311012 voxels (1.85%)
WM (99.0): 98.9 +- 7.4 [70.0 --> 110.0]
GM (77.0) : 75.5 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.0 (was 70)
setting MAX_BORDER_WHITE to 110.4 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 52.0 (was 40)
setting MAX_GRAY to 95.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.1 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-5.2,    GM=72+-7.8
mean inside = 94.8, mean outside = 79.1
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.02-->8.85) (max @ vno 115001 --> 146422)
face area 0.33 +- 0.16 (0.00-->11.53)
mean absolute distance = 0.70 +- 0.94
2678 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 47 points - only 0.00% unknown
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 5 with 132 points - only 0.00% unknown
deleting segment 6 with 22 points - only 0.00% unknown
deleting segment 7 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
deleting segment 9 with 6 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
deleting segment 11 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
mean border=82.9, 50 (50) missing vertices, mean dist 0.4 [1.0 (%14.9)->0.7 (%85.1))]
%61 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.25 (0.11-->9.05) (max @ vno 115001 --> 146422)
face area 0.33 +- 0.16 (0.00-->10.13)
mean absolute distance = 0.39 +- 0.67
3218 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2356124.8, rms=7.668
001: dt: 0.5000, sse=1332132.1, rms=4.744 (38.129%)
002: dt: 0.5000, sse=976723.3, rms=3.161 (33.361%)
003: dt: 0.5000, sse=872819.9, rms=2.538 (19.732%)
004: dt: 0.5000, sse=835848.8, rms=2.274 (10.375%)
rms = 2.28, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=784807.2, rms=1.762 (22.524%)
006: dt: 0.2500, sse=761456.6, rms=1.474 (16.343%)
007: dt: 0.2500, sse=754967.7, rms=1.386 (5.956%)
rms = 1.34, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=753685.5, rms=1.343 (3.133%)
rms = 1.32, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=750628.2, rms=1.316 (2.015%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 60 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 4 with 79 points - only 0.00% unknown
deleting segment 5 with 21 points - only 0.00% unknown
deleting segment 6 with 5 points - only 0.00% unknown
deleting segment 7 with 10 points - only 0.00% unknown
deleting segment 8 with 6 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
mean border=85.6, 51 (13) missing vertices, mean dist -0.2 [0.5 (%68.9)->0.2 (%31.1))]
%71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.25 (0.09-->9.13) (max @ vno 115001 --> 146422)
face area 0.36 +- 0.18 (0.00-->10.86)
mean absolute distance = 0.30 +- 0.45
3637 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1217605.5, rms=4.034
010: dt: 0.5000, sse=935128.4, rms=2.508 (37.837%)
011: dt: 0.5000, sse=874813.6, rms=2.057 (17.963%)
012: dt: 0.5000, sse=857767.9, rms=1.928 (6.284%)
rms = 2.04, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=814816.0, rms=1.423 (26.189%)
014: dt: 0.2500, sse=797052.6, rms=1.152 (19.050%)
015: dt: 0.2500, sse=793930.4, rms=1.099 (4.603%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=793101.8, rms=1.092 (0.606%)
rms = 1.08, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=794065.8, rms=1.077 (1.363%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 40 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 3 with 83 points - only 0.00% unknown
deleting segment 4 with 22 points - only 0.00% unknown
deleting segment 5 with 10 points - only 0.00% unknown
deleting segment 6 with 16 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 8 with 4 points - only 0.00% unknown
mean border=88.0, 51 (5) missing vertices, mean dist -0.2 [0.3 (%71.9)->0.2 (%28.1))]
%83 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 (0.07-->9.23) (max @ vno 146430 --> 146437)
face area 0.34 +- 0.17 (0.00-->11.14)
mean absolute distance = 0.24 +- 0.34
3817 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1032903.0, rms=3.273
018: dt: 0.5000, sse=839274.4, rms=1.931 (41.011%)
019: dt: 0.5000, sse=824669.6, rms=1.818 (5.816%)
rms = 1.83, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=781378.9, rms=1.317 (27.560%)
021: dt: 0.2500, sse=763740.1, rms=1.043 (20.785%)
rms = 1.01, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=762473.4, rms=1.011 (3.134%)
rms = 0.99, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=760574.8, rms=0.994 (1.691%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 39 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 3 with 83 points - only 0.00% unknown
deleting segment 4 with 22 points - only 0.00% unknown
deleting segment 5 with 10 points - only 0.00% unknown
deleting segment 6 with 27 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 8 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
mean border=88.9, 52 (4) missing vertices, mean dist -0.1 [0.3 (%58.5)->0.2 (%41.5))]
%88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=783314.2, rms=1.557
024: dt: 0.5000, sse=759008.6, rms=1.212 (22.186%)
rms = 1.48, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=739344.2, rms=0.913 (24.665%)
026: dt: 0.2500, sse=736606.6, rms=0.829 (9.193%)
rms = 0.80, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=733143.7, rms=0.796 (3.927%)
rms = 0.79, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=732708.3, rms=0.793 (0.462%)
positioning took 0.6 minutes
generating cortex label...
11 non-cortical segments detected
only using segment with 7384 vertices
erasing segment 0 (vno[0] = 44562)
erasing segment 2 (vno[0] = 60054)
erasing segment 3 (vno[0] = 85376)
erasing segment 4 (vno[0] = 110337)
erasing segment 5 (vno[0] = 110556)
erasing segment 6 (vno[0] = 112347)
erasing segment 7 (vno[0] = 113195)
erasing segment 8 (vno[0] = 113228)
erasing segment 9 (vno[0] = 122242)
erasing segment 10 (vno[0] = 125541)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.area
vertex spacing 0.89 +- 0.26 (0.02-->9.33) (max @ vno 115001 --> 146422)
face area 0.34 +- 0.17 (0.00-->11.10)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 32 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
deleting segment 3 with 25 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=60.7, 46 (46) missing vertices, mean dist 1.7 [0.2 (%0.0)->2.7 (%100.0))]
%16 local maxima, %43 large gradients and %36 min vals, 221 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=24117300.0, rms=28.894
001: dt: 0.0500, sse=21671662.0, rms=27.344 (5.365%)
002: dt: 0.0500, sse=19911512.0, rms=26.172 (4.288%)
003: dt: 0.0500, sse=18553056.0, rms=25.229 (3.600%)
004: dt: 0.0500, sse=17445018.0, rms=24.434 (3.153%)
005: dt: 0.0500, sse=16504471.0, rms=23.737 (2.850%)
006: dt: 0.0500, sse=15682353.0, rms=23.112 (2.637%)
007: dt: 0.0500, sse=14947484.0, rms=22.537 (2.485%)
008: dt: 0.0500, sse=14280206.0, rms=22.003 (2.371%)
009: dt: 0.0500, sse=13667220.0, rms=21.500 (2.285%)
010: dt: 0.0500, sse=13098818.0, rms=21.023 (2.218%)
positioning took 1.0 minutes
mean border=60.5, 39 (18) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.2 (%100.0))]
%17 local maxima, %43 large gradients and %35 min vals, 177 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=13783876.0, rms=21.598
011: dt: 0.0500, sse=13251482.0, rms=21.153 (2.057%)
012: dt: 0.0500, sse=12752708.0, rms=20.729 (2.009%)
013: dt: 0.0500, sse=12283436.0, rms=20.320 (1.968%)
014: dt: 0.0500, sse=11840591.0, rms=19.928 (1.933%)
015: dt: 0.0500, sse=11422136.0, rms=19.549 (1.899%)
016: dt: 0.0500, sse=11026568.0, rms=19.185 (1.865%)
017: dt: 0.0500, sse=10652053.0, rms=18.833 (1.834%)
018: dt: 0.0500, sse=10297434.0, rms=18.493 (1.802%)
019: dt: 0.0500, sse=9961489.0, rms=18.166 (1.771%)
020: dt: 0.0500, sse=9643325.0, rms=17.850 (1.738%)
positioning took 1.0 minutes
mean border=60.4, 58 (10) missing vertices, mean dist 1.2 [0.1 (%0.4)->1.8 (%99.6))]
%18 local maxima, %43 large gradients and %35 min vals, 189 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=9741372.0, rms=17.954
021: dt: 0.0500, sse=9433950.0, rms=17.645 (1.720%)
022: dt: 0.0500, sse=9142763.0, rms=17.347 (1.686%)
023: dt: 0.0500, sse=8865720.0, rms=17.059 (1.660%)
024: dt: 0.0500, sse=8603365.0, rms=16.782 (1.626%)
025: dt: 0.0500, sse=8355016.5, rms=16.515 (1.591%)
026: dt: 0.0500, sse=8119224.5, rms=16.257 (1.560%)
027: dt: 0.0500, sse=7894081.0, rms=16.008 (1.537%)
028: dt: 0.0500, sse=7677192.0, rms=15.763 (1.528%)
029: dt: 0.0500, sse=7468347.0, rms=15.524 (1.518%)
030: dt: 0.0500, sse=7267188.5, rms=15.290 (1.508%)
positioning took 1.0 minutes
mean border=60.3, 93 (8) missing vertices, mean dist 1.0 [0.1 (%6.3)->1.6 (%93.7))]
%18 local maxima, %44 large gradients and %34 min vals, 193 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=7351495.5, rms=15.389
031: dt: 0.5000, sse=5894413.0, rms=13.587 (11.710%)
032: dt: 0.5000, sse=4770837.5, rms=12.008 (11.621%)
033: dt: 0.5000, sse=3850082.8, rms=10.542 (12.207%)
034: dt: 0.5000, sse=3108632.0, rms=9.187 (12.856%)
035: dt: 0.5000, sse=2522323.2, rms=7.956 (13.401%)
036: dt: 0.5000, sse=2079944.4, rms=6.878 (13.542%)
037: dt: 0.5000, sse=1764771.8, rms=5.999 (12.780%)
038: dt: 0.5000, sse=1565337.6, rms=5.361 (10.641%)
039: dt: 0.5000, sse=1441644.1, rms=4.931 (8.026%)
040: dt: 0.5000, sse=1375494.5, rms=4.676 (5.166%)
041: dt: 0.5000, sse=1333784.9, rms=4.516 (3.412%)
042: dt: 0.5000, sse=1313552.2, rms=4.428 (1.956%)
043: dt: 0.5000, sse=1299447.4, rms=4.374 (1.230%)
rms = 4.33, time step reduction 1 of 3 to 0.250...
044: dt: 0.5000, sse=1291189.9, rms=4.334 (0.911%)
045: dt: 0.2500, sse=1167341.2, rms=3.724 (14.073%)
046: dt: 0.2500, sse=1138148.1, rms=3.575 (3.990%)
rms = 3.56, time step reduction 2 of 3 to 0.125...
047: dt: 0.2500, sse=1136197.8, rms=3.561 (0.388%)
048: dt: 0.1250, sse=1123319.1, rms=3.489 (2.023%)
rms = 3.48, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1122009.6, rms=3.482 (0.203%)
positioning took 2.5 minutes
mean border=59.0, 2019 (1) missing vertices, mean dist 0.1 [0.2 (%44.7)->0.5 (%55.3))]
%31 local maxima, %33 large gradients and %30 min vals, 123 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=1401316.8, rms=4.080
050: dt: 0.5000, sse=1317811.1, rms=3.700 (9.312%)
rms = 3.81, time step reduction 1 of 3 to 0.250...
051: dt: 0.2500, sse=1219965.4, rms=3.158 (14.646%)
052: dt: 0.2500, sse=1185519.0, rms=2.951 (6.572%)
053: dt: 0.2500, sse=1176192.2, rms=2.892 (1.982%)
rms = 2.88, time step reduction 2 of 3 to 0.125...
054: dt: 0.2500, sse=1173176.9, rms=2.877 (0.516%)
055: dt: 0.1250, sse=1163180.1, rms=2.806 (2.477%)
rms = 2.80, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1162248.1, rms=2.801 (0.192%)
positioning took 1.2 minutes
mean border=58.2, 2254 (1) missing vertices, mean dist 0.1 [0.1 (%45.5)->0.3 (%54.5))]
%43 local maxima, %22 large gradients and %29 min vals, 129 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=1222704.2, rms=3.168
rms = 3.46, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1187153.9, rms=2.952 (6.804%)
058: dt: 0.2500, sse=1176147.0, rms=2.887 (2.216%)
rms = 2.87, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1172428.9, rms=2.873 (0.489%)
rms = 2.83, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1166066.9, rms=2.827 (1.594%)
positioning took 0.8 minutes
mean border=57.6, 4403 (1) missing vertices, mean dist 0.1 [0.1 (%47.5)->0.3 (%52.5))]
%48 local maxima, %17 large gradients and %28 min vals, 154 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-6.0.0/0050008/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1188853.2, rms=2.956
rms = 3.12, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1169950.5, rms=2.835 (4.103%)
062: dt: 0.2500, sse=1153867.1, rms=2.743 (3.246%)
063: dt: 0.2500, sse=1144436.6, rms=2.689 (1.938%)
rms = 2.64, time step reduction 2 of 3 to 0.125...
064: dt: 0.2500, sse=1135858.0, rms=2.641 (1.813%)
065: dt: 0.1250, sse=1129156.5, rms=2.589 (1.951%)
rms = 2.57, time step reduction 3 of 3 to 0.062...
066: dt: 0.1250, sse=1126036.9, rms=2.571 (0.690%)
positioning took 1.1 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.area.pial
vertex spacing 0.99 +- 0.42 (0.06-->8.65) (max @ vno 146430 --> 146437)
face area 0.39 +- 0.30 (0.00-->11.84)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 146716 vertices processed
25000 of 146716 vertices processed
50000 of 146716 vertices processed
75000 of 146716 vertices processed
100000 of 146716 vertices processed
125000 of 146716 vertices processed
0 of 146716 vertices processed
25000 of 146716 vertices processed
50000 of 146716 vertices processed
75000 of 146716 vertices processed
100000 of 146716 vertices processed
125000 of 146716 vertices processed
thickness calculation complete, 226:536 truncations.
36396 vertices at 0 distance
110319 vertices at 1 distance
86464 vertices at 2 distance
32785 vertices at 3 distance
9938 vertices at 4 distance
3086 vertices at 5 distance
960 vertices at 6 distance
340 vertices at 7 distance
114 vertices at 8 distance
40 vertices at 9 distance
33 vertices at 10 distance
21 vertices at 11 distance
18 vertices at 12 distance
9 vertices at 13 distance
9 vertices at 14 distance
5 vertices at 15 distance
3 vertices at 16 distance
3 vertices at 17 distance
4 vertices at 18 distance
3 vertices at 19 distance
10 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.thickness
positioning took 16.2 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050008 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-6.0.0/0050008/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
18652 bright wm thresholded.
3064 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.orig...
computing class statistics...
border white:    277438 voxels (1.65%)
border gray      311012 voxels (1.85%)
WM (99.0): 98.9 +- 7.4 [70.0 --> 110.0]
GM (77.0) : 75.5 +- 10.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 63.0 (was 70)
setting MAX_BORDER_WHITE to 110.4 (was 105)
setting MIN_BORDER_WHITE to 73.0 (was 85)
setting MAX_CSF to 53.0 (was 40)
setting MAX_GRAY to 95.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 63.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 43.1 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=103+-5.2,    GM=73+-7.0
mean inside = 94.9, mean outside = 79.5
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 0.89 +- 0.25 (0.03-->7.64) (max @ vno 145653 --> 145722)
face area 0.33 +- 0.16 (0.00-->7.81)
mean absolute distance = 0.65 +- 0.88
2671 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 1 with 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 15 points - only 0.00% unknown
deleting segment 4 with 57 points - only 0.00% unknown
deleting segment 5 with 14 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
deleting segment 7 with 20 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 11 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
deleting segment 12 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=83.6, 114 (114) missing vertices, mean dist 0.4 [0.9 (%15.1)->0.6 (%84.9))]
%65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.09-->7.35) (max @ vno 86302 --> 145722)
face area 0.33 +- 0.16 (0.00-->6.97)
mean absolute distance = 0.37 +- 0.62
3183 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2206888.0, rms=7.327
001: dt: 0.5000, sse=1255962.1, rms=4.466 (39.055%)
002: dt: 0.5000, sse=943792.4, rms=2.990 (33.046%)
003: dt: 0.5000, sse=859490.2, rms=2.458 (17.791%)
004: dt: 0.5000, sse=828079.8, rms=2.235 (9.082%)
rms = 2.25, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=779514.9, rms=1.741 (22.106%)
006: dt: 0.2500, sse=760078.4, rms=1.475 (15.247%)
007: dt: 0.2500, sse=753053.0, rms=1.400 (5.074%)
rms = 1.37, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=752794.2, rms=1.366 (2.426%)
rms = 1.34, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=749059.9, rms=1.343 (1.737%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 33.33% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 32 points - only 0.00% unknown
deleting segment 5 with 10 points - only 0.00% unknown
deleting segment 6 with 10 points - only 0.00% unknown
deleting segment 7 with 12 points - only 0.00% unknown
deleting segment 8 with 9 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
mean border=86.2, 72 (21) missing vertices, mean dist -0.2 [0.4 (%70.2)->0.2 (%29.8))]
%75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.04-->7.42) (max @ vno 86302 --> 145722)
face area 0.36 +- 0.17 (0.00-->7.76)
mean absolute distance = 0.29 +- 0.43
3683 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1177534.1, rms=3.883
010: dt: 0.5000, sse=910503.2, rms=2.358 (39.257%)
011: dt: 0.5000, sse=863838.4, rms=2.008 (14.873%)
012: dt: 0.5000, sse=850911.4, rms=1.917 (4.499%)
rms = 2.05, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=809125.9, rms=1.416 (26.123%)
014: dt: 0.2500, sse=796666.4, rms=1.179 (16.740%)
rms = 1.14, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=790828.9, rms=1.136 (3.675%)
rms = 1.12, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=789853.6, rms=1.117 (1.660%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 1 with 3 points - only 33.33% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
deleting segment 3 with 14 points - only 0.00% unknown
deleting segment 4 with 40 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 2 points - only 0.00% unknown
deleting segment 6 with 10 points - only 0.00% unknown
deleting segment 7 with 20 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
deleting segment 10 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
mean border=88.5, 83 (16) missing vertices, mean dist -0.2 [0.3 (%72.0)->0.2 (%28.0))]
%85 local maxima, %10 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 0.89 +- 0.25 (0.07-->7.41) (max @ vno 86302 --> 145722)
face area 0.34 +- 0.17 (0.00-->7.62)
mean absolute distance = 0.23 +- 0.33
3667 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1000407.6, rms=3.118
017: dt: 0.5000, sse=839128.6, rms=1.933 (38.012%)
018: dt: 0.5000, sse=831194.2, rms=1.853 (4.135%)
rms = 1.87, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=786193.6, rms=1.361 (26.546%)
020: dt: 0.2500, sse=763126.8, rms=1.090 (19.942%)
rms = 1.05, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=763954.2, rms=1.053 (3.369%)
rms = 1.03, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=759323.5, rms=1.032 (1.989%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 1 with 3 points - only 33.33% unknown
deleting segment 2 with 14 points - only 0.00% unknown
deleting segment 3 with 14 points - only 0.00% unknown
deleting segment 4 with 45 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 2 points - only 0.00% unknown
deleting segment 6 with 10 points - only 0.00% unknown
deleting segment 7 with 20 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
deleting segment 9 with 10 points - only 0.00% unknown
deleting segment 10 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
mean border=89.3, 98 (13) missing vertices, mean dist -0.1 [0.3 (%58.3)->0.2 (%41.7))]
%89 local maxima, % 6 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-6.0.0/0050008/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=775547.6, rms=1.503
023: dt: 0.5000, sse=755665.3, rms=1.201 (20.073%)
rms = 1.48, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=737621.9, rms=0.930 (22.582%)
025: dt: 0.2500, sse=734656.9, rms=0.859 (7.629%)
rms = 0.83, time step reduction 2 of 3 to 0.125...
026: dt: 0.2500, sse=731628.1, rms=0.831 (3.208%)
rms = 0.82, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=729435.3, rms=0.825 (0.828%)
positioning took 0.6 minutes
generating cortex label...
16 non-cortical segments detected
only using segment with 7043 vertices
erasing segment 0 (vno[0] = 48231)
erasing segment 2 (vno[0] = 69672)
erasing segment 3 (vno[0] = 75015)
erasing segment 4 (vno[0] = 77284)
erasing segment 5 (vno[0] = 79724)
erasing segment 6 (vno[0] = 80832)
erasing segment 7 (vno[0] = 89007)
erasing segment 8 (vno[0] = 91241)
erasing segment 9 (vno[0] = 106912)
erasing segment 10 (vno[0] = 106942)
erasing segment 11 (vno[0] = 106958)
erasing segment 12 (vno[0] = 107053)
erasing segment 13 (vno[0] = 108740)
erasing segment 14 (vno[0] = 109817)
erasing segment 15 (vno[0] = 110694)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.area
vertex spacing 0.89 +- 0.26 (0.02-->7.39) (max @ vno 86302 --> 145722)
face area 0.33 +- 0.17 (0.00-->7.48)
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
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=61.8, 142 (142) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.8 (%100.0))]
%15 local maxima, %41 large gradients and %41 min vals, 281 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=23070466.0, rms=28.235
001: dt: 0.0500, sse=20688194.0, rms=26.690 (5.473%)
002: dt: 0.0500, sse=18982578.0, rms=25.526 (4.361%)
003: dt: 0.0500, sse=17670408.0, rms=24.593 (3.655%)
004: dt: 0.0500, sse=16602401.0, rms=23.806 (3.198%)
005: dt: 0.0500, sse=15696430.0, rms=23.118 (2.891%)
006: dt: 0.0500, sse=14906545.0, rms=22.501 (2.670%)
007: dt: 0.0500, sse=14202985.0, rms=21.937 (2.509%)
008: dt: 0.0500, sse=13566363.0, rms=21.413 (2.387%)
009: dt: 0.0500, sse=12983350.0, rms=20.922 (2.294%)
010: dt: 0.0500, sse=12444789.0, rms=20.458 (2.219%)
positioning took 1.0 minutes
mean border=61.6, 95 (64) missing vertices, mean dist 1.3 [0.2 (%0.0)->2.3 (%100.0))]
%15 local maxima, %41 large gradients and %40 min vals, 261 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=13186309.0, rms=21.092
011: dt: 0.0500, sse=12682394.0, rms=20.661 (2.040%)
012: dt: 0.0500, sse=12211133.0, rms=20.251 (1.988%)
013: dt: 0.0500, sse=11768647.0, rms=19.857 (1.943%)
014: dt: 0.0500, sse=11351849.0, rms=19.479 (1.903%)
015: dt: 0.0500, sse=10958178.0, rms=19.115 (1.868%)
016: dt: 0.0500, sse=10586110.0, rms=18.765 (1.834%)
017: dt: 0.0500, sse=10233913.0, rms=18.427 (1.801%)
018: dt: 0.0500, sse=9900577.0, rms=18.101 (1.768%)
019: dt: 0.0500, sse=9584706.0, rms=17.787 (1.736%)
020: dt: 0.0500, sse=9285324.0, rms=17.484 (1.705%)
positioning took 1.0 minutes
mean border=61.5, 99 (44) missing vertices, mean dist 1.1 [0.1 (%0.4)->1.9 (%99.6))]
%16 local maxima, %41 large gradients and %39 min vals, 249 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=9392853.0, rms=17.598
021: dt: 0.0500, sse=9104241.0, rms=17.303 (1.679%)
022: dt: 0.0500, sse=8830587.0, rms=17.018 (1.647%)
023: dt: 0.0500, sse=8569748.0, rms=16.742 (1.623%)
024: dt: 0.0500, sse=8322192.5, rms=16.475 (1.592%)
025: dt: 0.0500, sse=8087014.5, rms=16.218 (1.562%)
026: dt: 0.0500, sse=7863097.5, rms=15.969 (1.535%)
027: dt: 0.0500, sse=7648986.0, rms=15.727 (1.514%)
028: dt: 0.0500, sse=7442757.5, rms=15.491 (1.504%)
029: dt: 0.0500, sse=7243746.0, rms=15.259 (1.497%)
030: dt: 0.0500, sse=7051346.0, rms=15.031 (1.492%)
positioning took 1.0 minutes
mean border=61.4, 130 (35) missing vertices, mean dist 1.0 [0.1 (%5.4)->1.7 (%94.6))]
%16 local maxima, %41 large gradients and %39 min vals, 226 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=7118575.5, rms=15.112
031: dt: 0.5000, sse=5707615.0, rms=13.335 (11.760%)
032: dt: 0.5000, sse=4618477.5, rms=11.775 (11.693%)
033: dt: 0.5000, sse=3740388.0, rms=10.350 (12.102%)
034: dt: 0.5000, sse=3042891.0, rms=9.055 (12.518%)
035: dt: 0.5000, sse=2501492.8, rms=7.907 (12.679%)
036: dt: 0.5000, sse=2094257.0, rms=6.914 (12.560%)
037: dt: 0.5000, sse=1806343.5, rms=6.118 (11.503%)
038: dt: 0.5000, sse=1614273.8, rms=5.521 (9.759%)
039: dt: 0.5000, sse=1500826.8, rms=5.138 (6.933%)
040: dt: 0.5000, sse=1435106.2, rms=4.900 (4.632%)
041: dt: 0.5000, sse=1397444.9, rms=4.760 (2.875%)
042: dt: 0.5000, sse=1376247.1, rms=4.675 (1.785%)
043: dt: 0.5000, sse=1361181.2, rms=4.617 (1.225%)
rms = 4.58, time step reduction 1 of 3 to 0.250...
044: dt: 0.5000, sse=1353310.8, rms=4.583 (0.741%)
045: dt: 0.2500, sse=1254189.5, rms=4.124 (10.018%)
046: dt: 0.2500, sse=1228951.2, rms=4.009 (2.777%)
rms = 4.00, time step reduction 2 of 3 to 0.125...
047: dt: 0.2500, sse=1227834.1, rms=4.001 (0.214%)
048: dt: 0.1250, sse=1215263.5, rms=3.939 (1.546%)
rms = 3.93, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1213349.0, rms=3.930 (0.228%)
positioning took 2.6 minutes
mean border=60.4, 2383 (6) missing vertices, mean dist 0.1 [0.2 (%45.3)->0.5 (%54.7))]
%28 local maxima, %32 large gradients and %34 min vals, 138 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=1435418.0, rms=4.214
050: dt: 0.5000, sse=1352304.1, rms=3.851 (8.630%)
rms = 3.85, time step reduction 1 of 3 to 0.250...
051: dt: 0.5000, sse=1344500.0, rms=3.849 (0.056%)
052: dt: 0.2500, sse=1241196.4, rms=3.265 (15.170%)
053: dt: 0.2500, sse=1220729.0, rms=3.149 (3.556%)
rms = 3.14, time step reduction 2 of 3 to 0.125...
054: dt: 0.2500, sse=1218822.4, rms=3.136 (0.392%)
055: dt: 0.1250, sse=1206311.4, rms=3.055 (2.581%)
rms = 3.05, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1204498.6, rms=3.046 (0.311%)
positioning took 1.1 minutes
mean border=59.7, 2900 (3) missing vertices, mean dist 0.1 [0.1 (%46.3)->0.4 (%53.7))]
%39 local maxima, %22 large gradients and %33 min vals, 173 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=1249391.4, rms=3.305
rms = 3.50, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1221119.8, rms=3.142 (4.953%)
058: dt: 0.2500, sse=1208911.4, rms=3.074 (2.142%)
rms = 3.05, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1203329.1, rms=3.049 (0.831%)
060: dt: 0.1250, sse=1195551.0, rms=2.998 (1.656%)
rms = 2.98, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1192476.5, rms=2.983 (0.522%)
positioning took 1.0 minutes
mean border=59.2, 5386 (3) missing vertices, mean dist 0.1 [0.1 (%47.8)->0.3 (%52.2))]
%43 local maxima, %17 large gradients and %32 min vals, 191 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-6.0.0/0050008/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1212790.5, rms=3.090
rms = 3.21, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1196598.8, rms=2.991 (3.197%)
063: dt: 0.2500, sse=1181477.1, rms=2.911 (2.665%)
rms = 2.86, time step reduction 2 of 3 to 0.125...
064: dt: 0.2500, sse=1172406.8, rms=2.862 (1.681%)
065: dt: 0.1250, sse=1163511.8, rms=2.802 (2.092%)
rms = 2.78, time step reduction 3 of 3 to 0.062...
066: dt: 0.1250, sse=1159628.0, rms=2.781 (0.759%)
positioning took 1.0 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.area.pial
vertex spacing 0.99 +- 0.42 (0.08-->7.34) (max @ vno 109597 --> 145942)
face area 0.39 +- 0.30 (0.00-->9.61)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 146577 vertices processed
25000 of 146577 vertices processed
50000 of 146577 vertices processed
75000 of 146577 vertices processed
100000 of 146577 vertices processed
125000 of 146577 vertices processed
0 of 146577 vertices processed
25000 of 146577 vertices processed
50000 of 146577 vertices processed
75000 of 146577 vertices processed
100000 of 146577 vertices processed
125000 of 146577 vertices processed
thickness calculation complete, 79:576 truncations.
32182 vertices at 0 distance
108036 vertices at 1 distance
89058 vertices at 2 distance
34938 vertices at 3 distance
11160 vertices at 4 distance
3469 vertices at 5 distance
1159 vertices at 6 distance
462 vertices at 7 distance
192 vertices at 8 distance
85 vertices at 9 distance
58 vertices at 10 distance
32 vertices at 11 distance
21 vertices at 12 distance
18 vertices at 13 distance
13 vertices at 14 distance
9 vertices at 15 distance
8 vertices at 16 distance
8 vertices at 17 distance
2 vertices at 18 distance
3 vertices at 19 distance
7 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.thickness
positioning took 16.3 minutes
PIDs (8372 8375) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 02:46:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0050008 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/lh.cortex.label
Total face volume 252686
Total vertex volume 249729 (mask=0)
#@# 0050008 lh 249729
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 02:46:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0050008 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/rh.cortex.label
Total face volume 253950
Total vertex volume 251427 (mask=0)
#@# 0050008 rh 251427
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 02:46:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0050008 

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 = 121
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/ribbon.mgz
mris_volmask took 14.65 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 03:01:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0050008 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 0050008 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 03:01:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0050008 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 0050008 rh pial 

Waiting for PID 10486 of (10486 10489 10492 10495) to complete...
Waiting for PID 10489 of (10486 10489 10492 10495) to complete...
Waiting for PID 10492 of (10486 10489 10492 10495) to complete...
Waiting for PID 10495 of (10486 10489 10492 10495) 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 0050008 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 252686
Total vertex volume 249729 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
 1990   1374   3579  2.570 0.464     0.113     0.022       17     1.8  bankssts
 1031    752   2156  2.509 0.647     0.148     0.025       19     1.0  caudalanteriorcingulate
 3522   2315   6138  2.508 0.482     0.115     0.023       33     3.2  caudalmiddlefrontal
 2754   1722   3098  1.786 0.419     0.149     0.038       40     4.6  cuneus
  574    405   2119  3.811 0.713     0.094     0.020        3     0.5  entorhinal
 4988   3401  10450  2.709 0.638     0.137     0.031       67     6.2  fusiform
 7261   4870  12439  2.417 0.525     0.139     0.034       91     9.6  inferiorparietal
 5384   3677  10801  2.575 0.694     0.137     0.035       88     7.4  inferiortemporal
 1604   1027   2694  2.490 0.734     0.136     0.036       25     2.1  isthmuscingulate
 8814   5746  13546  2.166 0.514     0.145     0.036      118    12.9  lateraloccipital
 4119   2750   7647  2.650 0.674     0.134     0.030       54     4.9  lateralorbitofrontal
 5046   3479   7412  1.987 0.588     0.141     0.035       67     7.3  lingual
 2925   1966   5458  2.487 0.564     0.128     0.030       41     3.2  medialorbitofrontal
 4927   3398  11930  2.855 0.675     0.136     0.034       71     6.7  middletemporal
  918    623   1731  2.491 0.565     0.088     0.016        6     0.6  parahippocampal
 2259   1390   3613  2.483 0.556     0.096     0.017       14     1.5  paracentral
 2493   1669   5145  2.773 0.490     0.130     0.027       32     2.6  parsopercularis
 1119    728   2537  2.783 0.502     0.141     0.038       16     1.6  parsorbitalis
 2086   1378   4054  2.585 0.528     0.124     0.027       25     2.2  parstriangularis
 2684   1760   2346  1.521 0.343     0.144     0.035       36     4.0  pericalcarine
 6577   4007   9143  2.061 0.595     0.106     0.023       57     6.2  postcentral
 2072   1362   3706  2.413 0.785     0.138     0.026       35     2.0  posteriorcingulate
 8535   5197  14706  2.656 0.572     0.111     0.024       79     8.2  precentral
 5574   3821   9408  2.318 0.552     0.135     0.029       71     6.4  precuneus
 1376    884   2607  2.720 0.631     0.140     0.034       26     1.9  rostralanteriorcingulate
 9445   6294  16432  2.385 0.484     0.136     0.031      130    11.5  rostralmiddlefrontal
13338   8936  28099  2.744 0.557     0.127     0.026      152    14.2  superiorfrontal
 9307   6097  13930  2.129 0.467     0.126     0.025      104     9.4  superiorparietal
 5006   3435  10991  2.810 0.666     0.121     0.025       56     5.3  superiortemporal
 5714   3805  10244  2.505 0.538     0.132     0.031       73     6.9  supramarginal
  441    289    936  2.477 0.397     0.189     0.045       11     0.8  frontalpole
  762    545   2614  3.643 0.670     0.138     0.023       10     0.8  temporalpole
  547    379    812  2.240 0.554     0.162     0.040        8     0.9  transversetemporal
 3748   2580   7172  2.941 0.917     0.129     0.036       47     5.7  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 0050008 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 252686
Total vertex volume 249729 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
 1990   1424   3579  2.570 0.464     0.127     0.029       31     2.6  bankssts
 1031    939   2156  2.509 0.647     0.162     0.036       21     1.6  caudalanteriorcingulate
 3522   2499   6138  2.508 0.482     0.120     0.024       41     3.4  caudalmiddlefrontal
 2754   1911   3098  1.786 0.419     0.125     0.030       37     3.7  cuneus
  574    699   2119  3.811 0.713     0.167     0.034        6     0.9  entorhinal
 4988   4288  10450  2.709 0.638     0.149     0.037       94     8.2  fusiform
 7261   5389  12439  2.417 0.525     0.138     0.034      100    10.2  inferiorparietal
 5384   4542  10801  2.575 0.694     0.153     0.037       92     9.4  inferiortemporal
 1604   1169   2694  2.490 0.734     0.153     0.040       31     2.8  isthmuscingulate
 8814   6818  13546  2.166 0.514     0.138     0.033      144    12.8  lateraloccipital
 4119   2963   7647  2.650 0.674     0.128     0.034       63     6.5  lateralorbitofrontal
 5046   4119   7412  1.987 0.588     0.140     0.034       64     7.8  lingual
 2925   2462   5458  2.487 0.564     0.152     0.038       48     4.9  medialorbitofrontal
 4927   4728  11930  2.855 0.675     0.149     0.030       56     6.8  middletemporal
  918    808   1731  2.491 0.565     0.128     0.028        7     1.3  parahippocampal
 2259   1550   3613  2.483 0.556     0.101     0.018       18     1.7  paracentral
 2493   2017   5145  2.773 0.490     0.148     0.033       38     3.8  parsopercularis
 1119   1062   2537  2.783 0.502     0.162     0.031       16     1.5  parsorbitalis
 2086   1710   4054  2.585 0.528     0.148     0.034       24     3.4  parstriangularis
 2684   1465   2346  1.521 0.343     0.116     0.030       46     3.7  pericalcarine
 6577   4935   9143  2.061 0.595     0.115     0.022       59     6.4  postcentral
 2072   1619   3706  2.413 0.785     0.137     0.032       32     2.9  posteriorcingulate
 8535   5878  14706  2.656 0.572     0.107     0.023       94     8.3  precentral
 5574   4239   9408  2.318 0.552     0.136     0.031       73     7.3  precuneus
 1376   1123   2607  2.720 0.631     0.158     0.040       18     2.6  rostralanteriorcingulate
 9445   7382  16432  2.385 0.484     0.137     0.028      125    12.0  rostralmiddlefrontal
13338  11042  28099  2.744 0.557     0.136     0.029      153    16.1  superiorfrontal
 9307   6965  13930  2.129 0.467     0.128     0.024      103     9.5  superiorparietal
 5006   4278  10991  2.810 0.666     0.149     0.035       66     8.2  superiortemporal
 5714   4304  10244  2.505 0.538     0.131     0.030       77     7.4  supramarginal
  441    454    936  2.477 0.397     0.183     0.035        7     0.6  frontalpole
  762    908   2614  3.643 0.670     0.171     0.030        8     1.1  temporalpole
  547    365    812  2.240 0.554     0.135     0.044       16     0.9  transversetemporal
 3748   2356   7172  2.941 0.917     0.139     0.045       67     7.3  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 0050008 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 253950
Total vertex volume 251427 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
 1351    935   2344  2.677 0.425     0.120     0.024       12     1.3  bankssts
 1008    678   1840  2.349 0.821     0.132     0.018       14     0.6  caudalanteriorcingulate
 4005   2648   7312  2.521 0.502     0.119     0.027       42     4.5  caudalmiddlefrontal
 2818   1846   3754  1.909 0.523     0.159     0.040       45     4.7  cuneus
  610    428   2112  3.327 0.937     0.107     0.020        5     0.4  entorhinal
 5328   3627  11154  2.728 0.544     0.137     0.033       77     7.2  fusiform
 6918   4623  12530  2.497 0.560     0.136     0.031       88     8.8  inferiorparietal
 5722   3818  11526  2.681 0.625     0.127     0.032       76     7.0  inferiortemporal
 1360    861   2538  2.880 0.574     0.136     0.033       19     1.6  isthmuscingulate
 7802   5111  12253  2.182 0.543     0.147     0.038      112    11.5  lateraloccipital
 3971   2661   7876  2.706 0.703     0.144     0.039      109     6.6  lateralorbitofrontal
 5017   3419   7653  2.065 0.613     0.150     0.038       71     7.8  lingual
 3398   2267   5875  2.397 0.554     0.128     0.033       47     4.6  medialorbitofrontal
 5061   3509  11357  2.762 0.575     0.136     0.031       71     6.2  middletemporal
 1009    669   1986  2.587 0.686     0.107     0.033       12     1.4  parahippocampal
 2543   1577   4198  2.488 0.549     0.107     0.022       19     2.3  paracentral
 2058   1362   4012  2.648 0.393     0.126     0.026       25     2.2  parsopercularis
 1284    839   3045  2.789 0.494     0.139     0.033       19     1.7  parsorbitalis
 2460   1678   4200  2.488 0.432     0.125     0.022       28     2.3  parstriangularis
 2610   1768   2328  1.556 0.393     0.152     0.044       34     4.7  pericalcarine
 6906   4195   9409  2.039 0.632     0.106     0.024       57     6.8  postcentral
 1793   1198   3479  2.714 0.709     0.152     0.034       33     2.2  posteriorcingulate
 8523   5285  15265  2.656 0.589     0.108     0.022       69     7.6  precentral
 6085   4125  10232  2.396 0.510     0.130     0.028       77     6.7  precuneus
  966    649   2020  2.769 0.551     0.139     0.030       15     1.2  rostralanteriorcingulate
 8059   5419  13967  2.320 0.480     0.135     0.030      109     9.4  rostralmiddlefrontal
13402   8861  27631  2.724 0.547     0.128     0.027      163    14.7  superiorfrontal
 9902   6356  15123  2.183 0.494     0.130     0.028      120    10.8  superiorparietal
 4893   3282  10731  2.980 0.601     0.121     0.027       53     5.4  superiortemporal
 6379   4235  11408  2.588 0.508     0.142     0.032       93     8.0  supramarginal
  492    310    978  2.347 0.627     0.151     0.043       10     0.9  frontalpole
  765    532   2811  3.515 0.683     0.122     0.026       12     0.9  temporalpole
  585    350    931  2.350 0.650     0.140     0.048        8     1.0  transversetemporal
 4162   2833   7522  2.849 0.792     0.141     0.052      118     9.2  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 0050008 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 253950
Total vertex volume 251427 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
 1351    826   2344  2.677 0.425     0.129     0.035       20     2.1  bankssts
 1008    824   1840  2.349 0.821     0.151     0.031       23     1.2  caudalanteriorcingulate
 4005   3063   7312  2.521 0.502     0.126     0.034       59     4.8  caudalmiddlefrontal
 2818   2196   3754  1.909 0.523     0.145     0.037       46     4.8  cuneus
  610    758   2112  3.327 0.937     0.170     0.032        9     0.9  entorhinal
 5328   4492  11154  2.728 0.544     0.141     0.032       70     7.8  fusiform
 6918   5441  12530  2.497 0.560     0.139     0.032       87    10.1  inferiorparietal
 5722   4555  11526  2.681 0.625     0.132     0.032       90     7.7  inferiortemporal
 1360    950   2538  2.880 0.574     0.163     0.053       68     2.9  isthmuscingulate
 7802   6094  12253  2.182 0.543     0.137     0.032      124    11.0  lateraloccipital
 3971   3117   7876  2.706 0.703     0.150     0.040       63     7.1  lateralorbitofrontal
 5017   4067   7653  2.065 0.613     0.147     0.038       73     8.9  lingual
 3398   2724   5875  2.397 0.554     0.146     0.033       42     5.4  medialorbitofrontal
 5061   4682  11357  2.762 0.575     0.154     0.036       81     8.8  middletemporal
 1009    822   1986  2.587 0.686     0.131     0.034       11     1.7  parahippocampal
 2543   1776   4198  2.488 0.549     0.109     0.024       25     2.7  paracentral
 2058   1675   4012  2.648 0.393     0.155     0.037       39     3.6  parsopercularis
 1284   1325   3045  2.789 0.494     0.160     0.030       14     1.8  parsorbitalis
 2460   1725   4200  2.488 0.432     0.127     0.027       36     3.1  parstriangularis
 2610   1444   2328  1.556 0.393     0.112     0.033       41     3.5  pericalcarine
 6906   5181   9409  2.039 0.632     0.120     0.026       63     7.9  postcentral
 1793   1365   3479  2.714 0.709     0.141     0.041       49     3.1  posteriorcingulate
 8523   6142  15265  2.656 0.589     0.108     0.024       90     8.7  precentral
 6085   4484  10232  2.396 0.510     0.131     0.029       80     7.7  precuneus
  966    844   2020  2.769 0.551     0.174     0.052       16     2.0  rostralanteriorcingulate
 8059   6550  13967  2.320 0.480     0.147     0.030      124    11.0  rostralmiddlefrontal
13402  11034  27631  2.724 0.547     0.140     0.029      164    17.3  superiorfrontal
 9902   7393  15123  2.183 0.494     0.131     0.029      123    12.1  superiorparietal
 4893   4000  10731  2.980 0.601     0.145     0.037       65     8.2  superiortemporal
 6379   4620  11408  2.588 0.508     0.139     0.034       94    10.0  supramarginal
  492    526    978  2.347 0.627     0.184     0.034        6     0.7  frontalpole
  765   1060   2811  3.515 0.683     0.201     0.039        7     1.4  temporalpole
  585    447    931  2.350 0.650     0.137     0.037        6     1.0  transversetemporal
 4162   2466   7522  2.849 0.792     0.141     0.061      141    11.7  insula
PIDs (10486 10489 10492 10495) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 03:03:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot 

#-----------------------------------------
#@# Cortical Parc 2 rh Sun Oct  8 03:03:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 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 10575 of (10575 10578) to complete...
Waiting for PID 10578 of (10575 10578) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 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...
65 labels changed using aseg
relabeling using gibbs priors...
000:   9809 changed, 146716 examined...
001:   2406 changed, 38027 examined...
002:    712 changed, 12491 examined...
003:    298 changed, 4049 examined...
004:    142 changed, 1663 examined...
005:     73 changed, 821 examined...
006:     36 changed, 415 examined...
007:     25 changed, 204 examined...
008:     10 changed, 128 examined...
009:      5 changed, 51 examined...
010:      4 changed, 30 examined...
011:      4 changed, 25 examined...
012:      5 changed, 26 examined...
013:      3 changed, 30 examined...
014:      0 changed, 13 examined...
1 labels changed using aseg
000: 290 total segments, 201 labels (2357 vertices) changed
001: 101 total segments, 11 labels (62 vertices) changed
002: 90 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 48 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1331 vertices marked for relabeling...
1331 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 20 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 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...
14 labels changed using aseg
relabeling using gibbs priors...
000:   9758 changed, 146577 examined...
001:   2336 changed, 38353 examined...
002:    680 changed, 12398 examined...
003:    271 changed, 3908 examined...
004:    125 changed, 1503 examined...
005:     65 changed, 686 examined...
006:     25 changed, 371 examined...
007:     13 changed, 150 examined...
008:     12 changed, 70 examined...
009:      4 changed, 71 examined...
010:      3 changed, 24 examined...
011:      0 changed, 17 examined...
2 labels changed using aseg
000: 277 total segments, 191 labels (2758 vertices) changed
001: 97 total segments, 13 labels (53 vertices) changed
002: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 55 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1224 vertices marked for relabeling...
1224 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 20 seconds.
PIDs (10575 10578) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 03:03:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0050008 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 03:03:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0050008 rh white 

Waiting for PID 10650 of (10650 10653) to complete...
Waiting for PID 10653 of (10650 10653) 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 0050008 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 252686
Total vertex volume 249729 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
 1444   1024   2420  2.264 0.527     0.152     0.036       22     2.3  G&S_frontomargin
 2153   1507   4213  2.488 0.458     0.152     0.036       28     3.2  G&S_occipital_inf
 1757    915   2831  2.497 0.516     0.093     0.021       13     1.5  G&S_paracentral
 1487    969   3022  2.710 0.393     0.142     0.034       19     1.9  G&S_subcentral
  909    618   1862  2.409 0.466     0.159     0.035       16     1.3  G&S_transv_frontopol
 2468   1698   4960  2.845 0.477     0.131     0.028       35     2.8  G&S_cingul-Ant
 1409   1017   2695  2.677 0.500     0.116     0.021       13     1.2  G&S_cingul-Mid-Ant
 1545   1075   2908  2.593 0.504     0.128     0.024       19     1.4  G&S_cingul-Mid-Post
  805    532   2039  3.031 0.577     0.165     0.046       16     1.4  G_cingul-Post-dorsal
  327    210    673  2.662 0.555     0.156     0.050        7     0.5  G_cingul-Post-ventral
 2663   1633   3155  1.753 0.460     0.149     0.039       40     4.5  G_cuneus
 1499    953   3655  2.885 0.492     0.142     0.034       27     2.0  G_front_inf-Opercular
  600    395   1445  2.801 0.507     0.151     0.037       12     0.9  G_front_inf-Orbital
  967    620   2401  2.855 0.444     0.131     0.033       13     1.3  G_front_inf-Triangul
 5388   3435  10907  2.536 0.497     0.138     0.034       87     6.6  G_front_middle
 9430   6041  21559  2.828 0.582     0.134     0.029      129    11.0  G_front_sup
  642    423   1401  2.943 0.840     0.135     0.041       10     1.0  G_Ins_lg&S_cent_ins
  702    426   2037  3.615 0.702     0.124     0.029       10     0.8  G_insular_short
 2389   1513   4573  2.405 0.401     0.152     0.037       38     3.6  G_occipital_middle
 1638   1037   2286  2.015 0.576     0.154     0.041       28     2.6  G_occipital_sup
 2159   1443   5341  2.892 0.611     0.146     0.036       36     3.1  G_oc-temp_lat-fusifor
 3488   2333   5619  2.032 0.646     0.151     0.042       55     6.0  G_oc-temp_med-Lingual
 1061    699   2844  3.161 0.844     0.095     0.020        7     0.7  G_oc-temp_med-Parahip
 2694   1712   6072  2.680 0.716     0.140     0.038       45     3.9  G_orbital
 2749   1819   5582  2.453 0.523     0.151     0.038       47     4.2  G_pariet_inf-Angular
 2728   1768   5520  2.593 0.523     0.145     0.037       44     4.1  G_pariet_inf-Supramar
 3682   2390   6467  2.227 0.471     0.126     0.029       47     4.1  G_parietal_sup
 2512   1378   3675  2.131 0.506     0.103     0.025       24     2.5  G_postcentral
 3389   1775   6627  2.939 0.523     0.104     0.026       34     3.2  G_precentral
 3047   1976   6069  2.488 0.506     0.145     0.033       54     3.8  G_precuneus
  987    645   2397  2.644 0.597     0.149     0.039       20     1.6  G_rectus
 1010    709   1518  2.468 1.173     0.126     0.048       17     1.9  G_subcallosal
  366    242    683  2.424 0.694     0.149     0.037        5     0.5  G_temp_sup-G_T_transv
 1881   1247   5265  3.001 0.710     0.156     0.041       37     3.2  G_temp_sup-Lateral
  839    569   2255  3.522 0.721     0.091     0.018        5     0.6  G_temp_sup-Plan_polar
  767    532   1464  2.554 0.449     0.117     0.025        8     0.7  G_temp_sup-Plan_tempo
 3137   2096   6952  2.566 0.757     0.151     0.048       68     6.3  G_temporal_inf
 2731   1843   7730  3.003 0.661     0.148     0.041       51     4.3  G_temporal_middle
  260    184    355  2.189 0.446     0.110     0.014        2     0.2  Lat_Fis-ant-Horizont
  353    254    522  2.644 0.483     0.146     0.027        4     0.4  Lat_Fis-ant-Vertical
  966    670   1288  2.425 0.446     0.132     0.029        9     1.1  Lat_Fis-post
 2360   1460   3088  1.890 0.500     0.146     0.041       37     4.0  Pole_occipital
 1834   1270   5965  3.478 0.641     0.144     0.032       28     2.3  Pole_temporal
 3021   2112   3041  1.693 0.504     0.139     0.032       33     4.3  S_calcarine
 3081   2112   3598  1.899 0.594     0.100     0.019       16     2.4  S_central
 1249    870   1690  2.088 0.469     0.101     0.015        8     0.8  S_cingul-Marginalis
  504    359    928  3.258 0.506     0.112     0.020        3     0.4  S_circular_insula_ant
 1207    897   1998  2.740 0.578     0.117     0.022        9     1.3  S_circular_insula_inf
 1890   1285   2876  2.798 0.570     0.114     0.025       12     2.0  S_circular_insula_sup
  917    682   1554  2.317 0.500     0.114     0.017        7     0.7  S_collat_transv_ant
  623    417    702  2.130 0.537     0.131     0.031        5     0.8  S_collat_transv_post
 2061   1409   3081  2.376 0.393     0.122     0.024       18     2.0  S_front_inf
 1303    889   1832  2.141 0.462     0.122     0.025       13     1.4  S_front_middle
 3698   2553   5752  2.396 0.392     0.104     0.019       25     2.9  S_front_sup
  266    184    434  3.026 0.553     0.140     0.039        2     0.4  S_interm_prim-Jensen
 3756   2549   4634  2.084 0.431     0.113     0.017       28     2.7  S_intrapariet&P_trans
 1040    717   1204  2.060 0.420     0.150     0.039       11     1.6  S_oc_middle&Lunatus
 1387    932   1708  2.075 0.393     0.128     0.025       13     1.4  S_oc_sup&transversal
  897    627   1225  2.181 0.336     0.121     0.020        7     0.8  S_occipital_ant
 1154    791   1829  2.494 0.439     0.136     0.028       13     1.3  S_oc-temp_lat
 2348   1694   3188  2.176 0.463     0.112     0.018       18     1.7  S_oc-temp_med&Lingual
  613    416    818  2.332 0.426     0.118     0.020        4     0.5  S_orbital_lateral
  604    442    869  2.339 0.440     0.118     0.016        5     0.3  S_orbital_med-olfact
 1532   1043   2561  2.611 0.440     0.135     0.028       18     1.6  S_orbital-H_Shaped
 1840   1246   2319  2.015 0.502     0.120     0.023       15     1.9  S_parieto_occipital
 1296    782   1092  1.844 0.744     0.145     0.022       26     1.1  S_pericallosal
 3040   2057   3840  1.984 0.429     0.119     0.023       28     2.8  S_postcentral
 2273   1533   3363  2.490 0.426     0.116     0.020       21     1.8  S_precentral-inf-part
 1545   1100   2347  2.376 0.440     0.110     0.019        9     1.2  S_precentral-sup-part
  816    565   1189  2.332 0.497     0.127     0.024        9     0.6  S_suborbital
 1052    736   1408  2.229 0.501     0.129     0.026        9     1.1  S_subparietal
 1420   1010   2017  2.437 0.436     0.121     0.018       11     1.1  S_temporal_inf
 6965   4779  11751  2.516 0.540     0.115     0.023       56     6.5  S_temporal_sup
  325    226    543  2.603 0.475     0.101     0.017        2     0.3  S_temporal_transverse

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050008 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 253950
Total vertex volume 251427 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
  829    533   1204  2.055 0.493     0.146     0.035       14     1.2  G&S_frontomargin
 1564   1059   3044  2.399 0.576     0.150     0.037       25     2.3  G&S_occipital_inf
 1681    941   2577  2.330 0.527     0.110     0.028       15     1.8  G&S_paracentral
 1482    987   2854  2.650 0.474     0.133     0.028       18     1.6  G&S_subcentral
 1191    843   2534  2.434 0.540     0.169     0.041       22     2.2  G&S_transv_frontopol
 3366   2306   6409  2.637 0.474     0.116     0.023       32     3.3  G&S_cingul-Ant
 1600   1142   3160  2.725 0.519     0.127     0.023       15     1.5  G&S_cingul-Mid-Ant
 1722   1185   3421  2.737 0.575     0.139     0.033       23     2.0  G&S_cingul-Mid-Post
  626    397   1604  3.026 0.479     0.163     0.033       12     0.8  G_cingul-Post-dorsal
  309    184    707  3.110 0.478     0.134     0.042        5     0.4  G_cingul-Post-ventral
 2708   1771   3554  1.846 0.537     0.158     0.041       41     4.6  G_cuneus
 1530    964   3459  2.774 0.417     0.131     0.031       24     2.0  G_front_inf-Opercular
  454    293   1046  2.903 0.353     0.133     0.034        7     0.5  G_front_inf-Orbital
 1028    669   2299  2.634 0.428     0.138     0.028       18     1.1  G_front_inf-Triangul
 3970   2588   8491  2.524 0.594     0.138     0.034       59     5.8  G_front_middle
 8903   5638  20170  2.818 0.579     0.131     0.030      126    10.6  G_front_sup
  835    562   1547  2.722 0.728     0.153     0.066       16     1.7  G_Ins_lg&S_cent_ins
  907    555   2035  2.895 0.825     0.156     0.080       67     3.2  G_insular_short
 2197   1429   4254  2.479 0.442     0.150     0.042       37     3.8  G_occipital_middle
 2042   1262   3201  2.146 0.512     0.142     0.036       29     2.7  G_occipital_sup
 2681   1792   6411  2.835 0.549     0.150     0.040       50     4.1  G_oc-temp_lat-fusifor
 3273   2174   5109  2.021 0.653     0.159     0.044       53     5.7  G_oc-temp_med-Lingual
 1192    793   3532  3.094 0.922     0.107     0.033       14     1.6  G_oc-temp_med-Parahip
 3038   1973   7043  2.675 0.705     0.148     0.041      106     5.3  G_orbital
 2754   1765   6150  2.724 0.562     0.144     0.034       42     3.8  G_pariet_inf-Angular
 3010   1959   6166  2.651 0.501     0.154     0.035       56     4.4  G_pariet_inf-Supramar
 3106   1977   5533  2.279 0.560     0.125     0.027       39     3.1  G_parietal_sup
 2736   1444   4021  2.154 0.589     0.105     0.028       27     3.2  G_postcentral
 3242   1747   7088  2.959 0.563     0.100     0.024       29     3.0  G_precentral
 2482   1639   4894  2.438 0.555     0.136     0.031       38     2.9  G_precuneus
  872    555   1839  2.499 0.496     0.152     0.037       17     1.3  G_rectus
  705    512   1158  2.173 1.042     0.115     0.050       11     1.2  G_subcallosal
  463    263    881  2.651 0.811     0.145     0.054        7     1.0  G_temp_sup-G_T_transv
 1585   1047   4304  3.145 0.527     0.147     0.036       25     2.2  G_temp_sup-Lateral
  859    604   2099  3.367 0.671     0.114     0.030        6     1.2  G_temp_sup-Plan_polar
  967    648   1845  2.681 0.495     0.117     0.025        9     0.9  G_temp_sup-Plan_tempo
 3082   2004   7155  2.781 0.705     0.142     0.041       56     4.8  G_temporal_inf
 2956   2047   7569  2.765 0.558     0.148     0.039       56     4.4  G_temporal_middle
  401    280    557  2.398 0.387     0.104     0.015        2     0.2  Lat_Fis-ant-Horizont
  314    233    482  2.465 0.307     0.100     0.015        2     0.1  Lat_Fis-ant-Vertical
 1481    990   2065  2.612 0.559     0.128     0.030       16     1.8  Lat_Fis-post
 3775   2371   5116  1.916 0.600     0.151     0.044       61     6.7  Pole_occipital
 2071   1373   6015  3.022 0.762     0.134     0.034       33     2.9  Pole_temporal
 2500   1767   2841  1.881 0.597     0.147     0.039       29     4.1  S_calcarine
 3268   2219   3585  1.876 0.592     0.109     0.021       22     2.8  S_central
 1449    989   2237  2.366 0.514     0.118     0.022       16     1.3  S_cingul-Marginalis
  547    387    936  3.094 0.559     0.133     0.046       17     1.4  S_circular_insula_ant
 1116    787   1765  2.896 0.590     0.114     0.026       10     1.3  S_circular_insula_inf
 1523   1049   2534  2.995 0.469     0.115     0.022        9     1.5  S_circular_insula_sup
 1089    783   2020  2.680 0.442     0.097     0.012        6     0.5  S_collat_transv_ant
  506    342    489  1.946 0.358     0.158     0.041        7     0.8  S_collat_transv_post
 2354   1626   3566  2.285 0.382     0.119     0.020       23     2.0  S_front_inf
 1843   1279   2941  2.252 0.441     0.127     0.029       22     1.9  S_front_middle
 3089   2105   5024  2.461 0.385     0.117     0.023       28     2.8  S_front_sup
  561    385    779  2.700 0.403     0.130     0.028        5     0.6  S_interm_prim-Jensen
 4080   2713   5416  2.111 0.465     0.129     0.026       47     4.2  S_intrapariet&P_trans
  662    462    781  2.150 0.528     0.145     0.033        7     0.8  S_oc_middle&Lunatus
 1762   1187   2183  2.072 0.400     0.130     0.028       17     2.1  S_oc_sup&transversal
  833    591   1263  2.308 0.398     0.121     0.022        6     0.8  S_occipital_ant
 1217    842   1939  2.613 0.323     0.120     0.025       11     1.1  S_oc-temp_lat
 2027   1466   3059  2.383 0.412     0.105     0.017       11     1.4  S_oc-temp_med&Lingual
  602    406    808  2.242 0.414     0.120     0.025        5     0.6  S_orbital_lateral
  789    540   1002  2.144 0.690     0.134     0.032        9     1.2  S_orbital_med-olfact
 1434    969   2543  2.748 0.481     0.134     0.033       14     2.0  S_orbital-H_Shaped
 2139   1441   2949  2.309 0.453     0.130     0.026       21     2.4  S_parieto_occipital
 1348    831   1322  2.152 0.764     0.148     0.026       28     1.1  S_pericallosal
 2992   1983   3614  1.994 0.400     0.117     0.022       27     2.5  S_postcentral
 2114   1420   3039  2.476 0.359     0.106     0.017       14     1.5  S_precentral-inf-part
 1689   1188   2663  2.519 0.359     0.105     0.016       10     1.2  S_precentral-sup-part
  515    350    698  2.533 0.496     0.126     0.024        4     0.5  S_suborbital
 1785   1216   2661  2.363 0.486     0.118     0.022       16     1.6  S_subparietal
 1444   1001   1998  2.472 0.497     0.121     0.019       10     1.3  S_temporal_inf
 5713   3930   9798  2.662 0.518     0.119     0.024       50     5.6  S_temporal_sup
  265    197    375  2.823 0.631     0.141     0.017        3     0.2  S_temporal_transverse
PIDs (10650 10653) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 03:04:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot 

#-----------------------------------------
#@# Cortical Parc 3 rh Sun Oct  8 03:04:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 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 10706 of (10706 10709) to complete...
Waiting for PID 10709 of (10706 10709) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 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...
1333 labels changed using aseg
relabeling using gibbs priors...
000:   2058 changed, 146716 examined...
001:    489 changed, 9654 examined...
002:    142 changed, 2752 examined...
003:     53 changed, 839 examined...
004:     28 changed, 291 examined...
005:     15 changed, 166 examined...
006:      6 changed, 87 examined...
007:      3 changed, 40 examined...
008:      3 changed, 19 examined...
009:      3 changed, 19 examined...
010:      3 changed, 17 examined...
011:      2 changed, 18 examined...
012:      0 changed, 14 examined...
244 labels changed using aseg
000: 60 total segments, 27 labels (201 vertices) changed
001: 34 total segments, 1 labels (1 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 12 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1053 vertices marked for relabeling...
1053 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050008 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...
1261 labels changed using aseg
relabeling using gibbs priors...
000:   2173 changed, 146577 examined...
001:    526 changed, 9959 examined...
002:    170 changed, 3009 examined...
003:     69 changed, 982 examined...
004:     32 changed, 401 examined...
005:     14 changed, 182 examined...
006:      8 changed, 88 examined...
007:      4 changed, 54 examined...
008:      1 changed, 24 examined...
009:      0 changed, 7 examined...
218 labels changed using aseg
000: 49 total segments, 16 labels (142 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 2 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1026 vertices marked for relabeling...
1026 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 15 seconds.
PIDs (10706 10709) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 03:04:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0050008 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 03:04:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0050008 rh white 

Waiting for PID 10770 of (10770 10773) to complete...
Waiting for PID 10773 of (10770 10773) 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 0050008 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 252686
Total vertex volume 249729 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
 1690   1217   3246  2.595 0.616     0.136     0.024       25     1.6  caudalanteriorcingulate
 3789   2479   6688  2.531 0.491     0.116     0.023       37     3.4  caudalmiddlefrontal
 3380   2148   4038  1.814 0.459     0.140     0.034       44     4.9  cuneus
  497    351   1748  3.776 0.735     0.090     0.020        3     0.3  entorhinal
 4606   3170   9227  2.629 0.595     0.138     0.031       61     5.7  fusiform
 7394   4936  12631  2.412 0.522     0.141     0.034       96     9.9  inferiorparietal
 5443   3679  11681  2.653 0.754     0.137     0.036       90     7.7  inferiortemporal
 1593   1019   2710  2.529 0.714     0.135     0.036       24     2.1  isthmuscingulate
 8753   5694  13496  2.163 0.513     0.148     0.037      123    13.3  lateraloccipital
 4827   3227   8849  2.625 0.714     0.142     0.036       74     7.1  lateralorbitofrontal
 5238   3589   7608  1.976 0.584     0.140     0.035       70     7.7  lingual
 2633   1784   4979  2.394 0.740     0.132     0.034       44     3.4  medialorbitofrontal
 7103   4861  15854  2.810 0.629     0.131     0.031       91     8.8  middletemporal
  942    650   1822  2.504 0.575     0.087     0.013        5     0.4  parahippocampal
 2716   1667   4654  2.560 0.553     0.100     0.019       18     2.1  paracentral
 2403   1592   4871  2.773 0.491     0.129     0.027       31     2.5  parsopercularis
 1029    682   2315  2.881 0.453     0.129     0.030       13     1.2  parsorbitalis
 2407   1613   4415  2.540 0.524     0.126     0.026       27     2.5  parstriangularis
 2650   1740   2316  1.522 0.342     0.144     0.035       35     4.0  pericalcarine
 7425   4555  10385  2.100 0.602     0.110     0.024       67     7.2  postcentral
 2274   1501   4027  2.404 0.766     0.139     0.027       37     2.3  posteriorcingulate
 8351   5088  14364  2.660 0.568     0.111     0.024       76     8.0  precentral
 5517   3753   9522  2.347 0.532     0.138     0.031       74     6.6  precuneus
 1805   1177   3187  2.697 0.587     0.140     0.032       30     2.2  rostralanteriorcingulate
 7057   4658  12876  2.451 0.480     0.134     0.031       94     8.4  rostralmiddlefrontal
14326   9628  29630  2.663 0.579     0.129     0.027      174    15.4  superiorfrontal
 7658   5058  11280  2.111 0.454     0.122     0.023       82     7.1  superiorparietal
 6909   4781  15646  2.858 0.714     0.120     0.025       73     7.1  superiortemporal
 5159   3451   9073  2.472 0.522     0.132     0.031       64     6.2  supramarginal
  558    388    829  2.244 0.549     0.160     0.040        8     0.9  transversetemporal
 2813   1928   5760  3.029 0.784     0.127     0.032       32     3.9  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050008 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 253950
Total vertex volume 251427 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
 1107    741   1989  2.353 0.813     0.132     0.019       15     0.7  caudalanteriorcingulate
 4144   2738   7575  2.524 0.500     0.119     0.027       44     4.7  caudalmiddlefrontal
 3495   2239   4775  1.977 0.552     0.155     0.038       52     5.6  cuneus
  550    390   1925  3.332 0.964     0.109     0.020        4     0.4  entorhinal
 4764   3286   9943  2.738 0.519     0.133     0.030       64     5.6  fusiform
 6906   4615  12554  2.502 0.555     0.137     0.032       90     8.8  inferiorparietal
 6395   4225  13114  2.678 0.637     0.131     0.035       91     8.9  inferiortemporal
 1368    860   2536  2.877 0.566     0.135     0.032       19     1.6  isthmuscingulate
 7908   5200  12164  2.159 0.529     0.147     0.038      114    11.7  lateraloccipital
 4718   3106   8996  2.602 0.725     0.145     0.044      174     9.0  lateralorbitofrontal
 4909   3348   7505  2.071 0.612     0.149     0.038       69     7.6  lingual
 2446   1631   4311  2.374 0.718     0.136     0.039       37     3.9  medialorbitofrontal
 6095   4203  13212  2.742 0.557     0.134     0.030       82     7.2  middletemporal
 1065    710   2096  2.585 0.692     0.106     0.032       13     1.5  parahippocampal
 2738   1691   4640  2.523 0.561     0.108     0.023       22     2.5  paracentral
 2387   1590   4438  2.595 0.411     0.122     0.025       27     2.4  parsopercularis
 1114    744   2664  2.814 0.509     0.128     0.029       15     1.4  parsorbitalis
 2376   1607   4275  2.495 0.444     0.130     0.025       31     2.3  parstriangularis
 2528   1723   2241  1.542 0.388     0.155     0.044       34     4.6  pericalcarine
 7658   4667  10559  2.060 0.612     0.109     0.025       67     7.7  postcentral
 1917   1291   3757  2.728 0.675     0.152     0.034       35     2.4  posteriorcingulate
 8160   5032  14720  2.676 0.594     0.109     0.022       67     7.4  precentral
 6195   4184  10536  2.391 0.517     0.132     0.030       81     7.3  precuneus
 1284    864   2419  2.650 0.575     0.129     0.027       16     1.4  rostralanteriorcingulate
 5700   3842  10127  2.348 0.485     0.134     0.029       75     6.4  rostralmiddlefrontal
16423  10950  32675  2.644 0.551     0.128     0.027      201    18.3  superiorfrontal
 8282   5342  12624  2.165 0.504     0.128     0.026       98     8.6  superiorparietal
 6704   4534  15540  3.034 0.629     0.123     0.028       76     7.7  superiortemporal
 6028   3994  10543  2.585 0.509     0.140     0.031       85     7.5  supramarginal
  553    328    906  2.356 0.669     0.134     0.049        7     1.0  transversetemporal
 3327   2276   6066  2.906 0.662     0.142     0.046       57     6.3  insula
PIDs (10770 10773) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 03:05:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 pctsurfcon --s 0050008 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 03:05:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts

 pctsurfcon --s 0050008 --rh-only 

Waiting for PID 10822 of (10822 10834) to complete...
Waiting for PID 10834 of (10822 10834) to complete...

 pctsurfcon --s 0050008 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts/pctsurfcon.log
Sun Oct  8 03:05:05 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-6.0.0/0050008/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-584 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-6.0.0/0050008/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10822/lh.wm.mgh --regheader 0050008 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00002;
 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-6.0.0/0050008/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 = 75298
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10822/lh.wm.mgh
Dim: 146716 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10822/lh.gm.mgh --projfrac 0.3 --regheader 0050008 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00002;
 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-6.0.0/0050008/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 = 90196
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10822/lh.gm.mgh
Dim: 146716 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10822/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10822/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.w-g.pct.mgh --annot 0050008 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/surf/lh.w-g.pct.mgh --annot 0050008 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-584
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/surf/lh.w-g.pct.mgh
Vertex Area is 0.664949 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 0050008 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/scripts/pctsurfcon.log
Sun Oct  8 03:05:05 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-6.0.0/0050008/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-584 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-6.0.0/0050008/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10834/rh.wm.mgh --regheader 0050008 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00002;
 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-6.0.0/0050008/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 = 74903
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10834/rh.wm.mgh
Dim: 146577 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10834/rh.gm.mgh --projfrac 0.3 --regheader 0050008 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00001;
 0.00000   0.00000   1.00000   0.00002;
 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-6.0.0/0050008/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 = 89365
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10834/rh.gm.mgh
Dim: 146577 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10834/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/tmp.pctsurfcon.10834/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.w-g.pct.mgh --annot 0050008 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/surf/rh.w-g.pct.mgh --annot 0050008 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-584
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/surf/rh.w-g.pct.mgh
Vertex Area is 0.661527 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 (10822 10834) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 03:05:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri

 mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz 

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
3136 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
2045 voxels changed to hypointensity...
5189 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 03:05:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008

 mri_aparc2aseg --s 0050008 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

#-----------------------------------------
#@# AParc-to-ASeg a2009s Sun Oct  8 03:05:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008

 mri_aparc2aseg --s 0050008 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s 

#-----------------------------------------
#@# AParc-to-ASeg DKTatlas Sun Oct  8 03:05:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008

 mri_aparc2aseg --s 0050008 --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 11002 of (11002 11005 11008) to complete...
Waiting for PID 11005 of (11002 11005 11008) to complete...
Waiting for PID 11008 of (11002 11005 11008) to complete...

 mri_aparc2aseg --s 0050008 --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 0050008
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/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-6.0.0/0050008/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.26
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 69
rescaling Left_Lateral_Ventricle from 13 --> 22
rescaling Left_Inf_Lat_Vent from 34 --> 38
rescaling Left_Cerebellum_White_Matter from 86 --> 87
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 104
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 71
rescaling Left_Putamen from 80 --> 81
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 35
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 71
rescaling CSF from 32 --> 50
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 91
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 67
rescaling Right_Lateral_Ventricle from 13 --> 21
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 57
rescaling Right_Thalamus_Proper from 85 --> 87
rescaling Right_Caudate from 62 --> 76
rescaling Right_Putamen from 80 --> 82
rescaling Right_Pallidum from 97 --> 98
rescaling Right_Hippocampus from 53 --> 66
rescaling Right_Amygdala from 55 --> 69
rescaling Right_Accumbens_area from 65 --> 74
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 42
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 497478
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 143 changed.
pass 2: 5 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050008 --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 0050008
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/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-6.0.0/0050008/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.26
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 69
rescaling Left_Lateral_Ventricle from 13 --> 22
rescaling Left_Inf_Lat_Vent from 34 --> 38
rescaling Left_Cerebellum_White_Matter from 86 --> 87
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 104
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 71
rescaling Left_Putamen from 80 --> 81
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 35
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 71
rescaling CSF from 32 --> 50
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 91
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 67
rescaling Right_Lateral_Ventricle from 13 --> 21
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 57
rescaling Right_Thalamus_Proper from 85 --> 87
rescaling Right_Caudate from 62 --> 76
rescaling Right_Putamen from 80 --> 82
rescaling Right_Pallidum from 97 --> 98
rescaling Right_Hippocampus from 53 --> 66
rescaling Right_Amygdala from 55 --> 69
rescaling Right_Accumbens_area from 65 --> 74
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 42
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 497415
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 143 changed.
pass 2: 5 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050008 --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 0050008
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/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-6.0.0/0050008/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.26
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 69
rescaling Left_Lateral_Ventricle from 13 --> 22
rescaling Left_Inf_Lat_Vent from 34 --> 38
rescaling Left_Cerebellum_White_Matter from 86 --> 87
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 104
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 71
rescaling Left_Putamen from 80 --> 81
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 35
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 71
rescaling CSF from 32 --> 50
rescaling Left_Accumbens_area from 62 --> 65
rescaling Left_VentralDC from 87 --> 91
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 67
rescaling Right_Lateral_Ventricle from 13 --> 21
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 57
rescaling Right_Thalamus_Proper from 85 --> 87
rescaling Right_Caudate from 62 --> 76
rescaling Right_Putamen from 80 --> 82
rescaling Right_Pallidum from 97 --> 98
rescaling Right_Hippocampus from 53 --> 66
rescaling Right_Amygdala from 55 --> 69
rescaling Right_Accumbens_area from 65 --> 74
rescaling Right_VentralDC from 86 --> 93
rescaling Fifth_Ventricle from 40 --> 42
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 497415
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 143 changed.
pass 2: 5 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (11002 11005 11008) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 03:14:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri

 apas2aseg --i aparc+aseg.mgz --o aseg.mgz 

Sun Oct  8 03:14:07 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-6.0.0/0050008/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-584 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-6.0.0/0050008/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-584
machine  x86_64
user     ntraut

input      aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     aseg.mgz
Binarizing based on threshold
min        -infinity
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Replacing 72
 1:  1000    3
 2:  2000   42
 3:  1001    3
 4:  2001   42
 5:  1002    3
 6:  2002   42
 7:  1003    3
 8:  2003   42
 9:  1004    3
10:  2004   42
11:  1005    3
12:  2005   42
13:  1006    3
14:  2006   42
15:  1007    3
16:  2007   42
17:  1008    3
18:  2008   42
19:  1009    3
20:  2009   42
21:  1010    3
22:  2010   42
23:  1011    3
24:  2011   42
25:  1012    3
26:  2012   42
27:  1013    3
28:  2013   42
29:  1014    3
30:  2014   42
31:  1015    3
32:  2015   42
33:  1016    3
34:  2016   42
35:  1017    3
36:  2017   42
37:  1018    3
38:  2018   42
39:  1019    3
40:  2019   42
41:  1020    3
42:  2020   42
43:  1021    3
44:  2021   42
45:  1022    3
46:  2022   42
47:  1023    3
48:  2023   42
49:  1024    3
50:  2024   42
51:  1025    3
52:  2025   42
53:  1026    3
54:  2026   42
55:  1027    3
56:  2027   42
57:  1028    3
58:  2028   42
59:  1029    3
60:  2029   42
61:  1030    3
62:  2030   42
63:  1031    3
64:  2031   42
65:  1032    3
66:  2032   42
67:  1033    3
68:  2033   42
69:  1034    3
70:  2034   42
71:  1035    3
72:  2035   42
Found 0 values in range
Counting number of voxels in first frame
Found 0 voxels in final mask
Count: 0 0.000000 16777216 0.000000
mri_binarize done
 
Started at Sun Oct 8 03:14:07 CEST 2017 
Ended   at Sun Oct  8 03:14:13 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 03:14:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008

 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 0050008 


$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 0050008 
sysname  Linux
hostname tars-584
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1558102 mm^3    (det: 1.250306 )
Computing euler number
orig.nofix lheno =  -58, rheno = -82
orig.nofix lhholes =   30, rhholes = 42
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  50 segmentations
Computing statistics for each segmentation

Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done
#-----------------------------------------
#@# WMParc Sun Oct  8 03:16:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008

 mri_aparc2aseg --s 0050008 --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 0050008
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-6.0.0/0050008/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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-6.0.0/0050008/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 7776 vertices from left hemi
Ripped 7332 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-6.0.0/0050008/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 = 997247
Used brute-force search on 21 voxels
Fixing Parahip LH WM
  Found 6 clusters
     0 k 2.000000
     1 k 12.000000
     2 k 2.000000
     3 k 1634.000000
     4 k 1.000000
     5 k 1.000000
Fixing Parahip RH WM
  Found 8 clusters
     0 k 3.000000
     1 k 1.000000
     2 k 16.000000
     3 k 4.000000
     4 k 1823.000000
     5 k 1.000000
     6 k 1.000000
     7 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 0050008 --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 0050008 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-584
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1558102 mm^3    (det: 1.250306 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
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-6.0.0/0050008/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 03:25:02 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 0050008 --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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 12531 of (12531 12537 12543 12548 12553) to complete...
Waiting for PID 12537 of (12531 12537 12543 12548 12553) to complete...
Waiting for PID 12543 of (12531 12537 12543 12548 12553) to complete...
Waiting for PID 12548 of (12531 12537 12543 12548 12553) to complete...
Waiting for PID 12553 of (12531 12537 12543 12548 12553) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 355
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4484
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 498
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8407
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 121
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4198
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 370
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6353
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 638
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6422
mri_label2label: Done

PIDs (12531 12537 12543 12548 12553) 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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 12668 of (12668 12674 12680 12686) to complete...
Waiting for PID 12674 of (12668 12674 12680 12686) to complete...
Waiting for PID 12680 of (12668 12674 12680 12686) to complete...
Waiting for PID 12686 of (12668 12674 12680 12686) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 311
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4381
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 2453
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 16042
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 511
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4692
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 821
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4243
mri_label2label: Done

PIDs (12668 12674 12680 12686) 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 0050008 --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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 12792 of (12792 12798 12804 12809 12816) to complete...
Waiting for PID 12798 of (12792 12798 12804 12809 12816) to complete...
Waiting for PID 12804 of (12792 12798 12804 12809 12816) to complete...
Waiting for PID 12809 of (12792 12798 12804 12809 12816) to complete...
Waiting for PID 12816 of (12792 12798 12804 12809 12816) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 2283
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6924
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 3611
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11725
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 865
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2883
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 66
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1356
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 33
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1232
mri_label2label: Done

PIDs (12792 12798 12804 12809 12816) 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 0050008 --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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 12916 of (12916 12922 12928 12933 12940) to complete...
Waiting for PID 12922 of (12916 12922 12928 12933 12940) to complete...
Waiting for PID 12928 of (12916 12922 12928 12933 12940) to complete...
Waiting for PID 12933 of (12916 12922 12928 12933 12940) to complete...
Waiting for PID 12940 of (12916 12922 12928 12933 12940) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 133
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1147
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 110
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2202
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 31
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1535
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 141
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2137
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 265
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2584
mri_label2label: Done

PIDs (12916 12922 12928 12933 12940) 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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 12992 of (12992 12998 13004 13010) to complete...
Waiting for PID 12998 of (12992 12998 13004 13010) to complete...
Waiting for PID 13004 of (12992 12998 13004 13010) to complete...
Waiting for PID 13010 of (12992 12998 13004 13010) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 87
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1636
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 1188
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8223
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 254
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2166
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 221
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1372
mri_label2label: Done

PIDs (12992 12998 13004 13010) 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 0050008 --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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 13085 of (13085 13091 13097 13101 13108) to complete...
Waiting for PID 13091 of (13085 13091 13097 13101 13108) to complete...
Waiting for PID 13097 of (13085 13091 13097 13101 13108) to complete...
Waiting for PID 13101 of (13085 13091 13097 13101 13108) to complete...
Waiting for PID 13108 of (13085 13091 13097 13101 13108) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 1719
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 5124
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 1824
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 5158
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 254
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 767
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 25
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 495
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146716
Number of reverse mapping hits = 11
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 461
mri_label2label: Done

PIDs (13085 13091 13097 13101 13108) completed and logs appended.

 mris_label2annot --s 0050008 --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-6.0.0/0050008/label
cmdline mris_label2annot --s 0050008 --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-584
machine  x86_64
user     ntraut

subject 0050008
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-6.0.0/0050008/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 99385 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050008 --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-6.0.0/0050008/label
cmdline mris_label2annot --s 0050008 --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-584
machine  x86_64
user     ntraut

subject 0050008
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-6.0.0/0050008/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 118532 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0050008 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 252686
Total vertex volume 249729 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
 1305    676   1888  2.196 0.517     0.112     0.031       15     1.5  BA1_exvivo
 3901   2558   5503  2.071 0.454     0.118     0.022       37     3.6  BA2_exvivo
  981    689    962  1.739 0.470     0.135     0.030        9     1.1  BA3a_exvivo
 2510   1526   3282  1.957 0.659     0.098     0.022       20     2.2  BA3b_exvivo
 1860    992   3378  2.855 0.461     0.086     0.017       10     1.4  BA4a_exvivo
 1326    826   2103  2.562 0.473     0.091     0.018        7     1.1  BA4p_exvivo
11917   7525  23964  2.770 0.581     0.118     0.025      121    11.7  BA6_exvivo
 2681   1760   5027  2.661 0.417     0.129     0.026       36     2.8  BA44_exvivo
 3214   2133   6376  2.593 0.518     0.137     0.034       45     4.0  BA45_exvivo
 4576   3024   4907  1.640 0.465     0.142     0.036       60     7.0  V1_exvivo
 9185   6001  12577  1.965 0.534     0.151     0.041      138    15.6  V2_exvivo
 2731   1843   4425  2.358 0.436     0.138     0.028       31     3.2  MT_exvivo
  591    381   1737  3.386 0.943     0.110     0.026        6     0.7  perirhinal_exvivo
  553    406   1504  3.129 0.870     0.104     0.023        4     0.5  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050008 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 252686
Total vertex volume 249729 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
  835    407   1235  2.216 0.487     0.119     0.034       11     1.0  BA1_exvivo
 1540    995   2166  2.000 0.453     0.100     0.016       11     1.1  BA2_exvivo
  835    587    755  1.683 0.383     0.142     0.029        8     0.9  BA3a_exvivo
 1562    970   1617  1.608 0.446     0.074     0.012        6     0.8  BA3b_exvivo
 1828    945   3194  2.856 0.486     0.083     0.018       11     1.4  BA4a_exvivo
 1067    687   1588  2.423 0.415     0.101     0.022        7     1.0  BA4p_exvivo
 6635   4058  13373  2.806 0.587     0.111     0.023       59     5.9  BA6_exvivo
 1711   1135   3290  2.639 0.399     0.129     0.026       24     1.7  BA44_exvivo
 1152    739   2666  2.766 0.537     0.138     0.036       16     1.6  BA45_exvivo
 4818   3178   5322  1.652 0.481     0.140     0.036       63     7.4  V1_exvivo
 4867   3164   6275  1.860 0.528     0.161     0.043       85     8.7  V2_exvivo
  751    528   1113  2.203 0.357     0.134     0.025        8     0.7  MT_exvivo
  285    180   1025  3.701 0.703     0.082     0.011        1     0.1  perirhinal_exvivo
  298    212    683  3.084 0.574     0.072     0.013        1     0.2  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 03:28:33 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 0050008 --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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 13293 of (13293 13299 13305 13310 13316) to complete...
Waiting for PID 13299 of (13293 13299 13305 13310 13316) to complete...
Waiting for PID 13305 of (13293 13299 13305 13310 13316) to complete...
Waiting for PID 13310 of (13293 13299 13305 13310 13316) to complete...
Waiting for PID 13316 of (13293 13299 13305 13310 13316) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 472
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4434
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 611
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7298
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 196
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4176
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 376
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4898
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 730
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6477
mri_label2label: Done

PIDs (13293 13299 13305 13310 13316) 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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 13362 of (13362 13368 13374 13378) to complete...
Waiting for PID 13368 of (13362 13368 13374 13378) to complete...
Waiting for PID 13374 of (13362 13368 13374 13378) to complete...
Waiting for PID 13378 of (13362 13368 13374 13378) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 356
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4829
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 2205
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14461
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 959
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7871
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 1101
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6456
mri_label2label: Done

PIDs (13362 13368 13374 13378) 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 0050008 --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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 13444 of (13444 13450 13456 13461 13468) to complete...
Waiting for PID 13450 of (13444 13450 13456 13461 13468) to complete...
Waiting for PID 13456 of (13444 13450 13456 13461 13468) to complete...
Waiting for PID 13461 of (13444 13450 13456 13461 13468) to complete...
Waiting for PID 13468 of (13444 13450 13456 13461 13468) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 2293
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 7020
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 3550
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 11566
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 514
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2446
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 92
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1130
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 88
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 840
mri_label2label: Done

PIDs (13444 13450 13456 13461 13468) 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 0050008 --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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 13551 of (13551 13557 13563 13568 13575) to complete...
Waiting for PID 13557 of (13551 13557 13563 13568 13575) to complete...
Waiting for PID 13563 of (13551 13557 13563 13568 13575) to complete...
Waiting for PID 13568 of (13551 13557 13563 13568 13575) to complete...
Waiting for PID 13575 of (13551 13557 13563 13568 13575) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 193
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1069
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 164
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2852
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 69
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1767
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 160
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2343
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 180
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1568
mri_label2label: Done

PIDs (13551 13557 13563 13568 13575) 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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 13679 of (13679 13685 13691 13696) to complete...
Waiting for PID 13685 of (13679 13685 13691 13696) to complete...
Waiting for PID 13691 of (13679 13685 13691 13696) to complete...
Waiting for PID 13696 of (13679 13685 13691 13696) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 97
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1586
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 1207
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8166
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 165
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1177
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 184
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1362
mri_label2label: Done

PIDs (13679 13685 13691 13696) 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 0050008 --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 0050008 --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 0050008 --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 0050008 --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 0050008 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 13741 of (13741 13747 13753 13758 13765) to complete...
Waiting for PID 13747 of (13741 13747 13753 13758 13765) to complete...
Waiting for PID 13753 of (13741 13747 13753 13758 13765) to complete...
Waiting for PID 13758 of (13741 13747 13753 13758 13765) to complete...
Waiting for PID 13765 of (13741 13747 13753 13758 13765) 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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 1555
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4787
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 1774
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5211
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 64
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 332
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 51
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 745
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 0050008 --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 = 0050008
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-6.0.0/0050008/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 146577
Number of reverse mapping hits = 29
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 320
mri_label2label: Done

PIDs (13741 13747 13753 13758 13765) completed and logs appended.

 mris_label2annot --s 0050008 --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-6.0.0/0050008/label
cmdline mris_label2annot --s 0050008 --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-584
machine  x86_64
user     ntraut

subject 0050008
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-6.0.0/0050008/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 99858 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050008 --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-6.0.0/0050008/label
cmdline mris_label2annot --s 0050008 --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-584
machine  x86_64
user     ntraut

subject 0050008
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-6.0.0/0050008/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 119892 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/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 0050008 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 253950
Total vertex volume 251427 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
 1243    605   1924  2.343 0.568     0.112     0.032       14     1.7  BA1_exvivo
 3541   2248   4596  2.015 0.471     0.114     0.023       32     3.1  BA2_exvivo
 1160    806   1078  1.765 0.513     0.146     0.032       14     1.5  BA3a_exvivo
 2197   1345   2586  1.749 0.577     0.094     0.021       14     1.9  BA3b_exvivo
 1920   1035   3253  2.681 0.519     0.098     0.026       14     2.0  BA4a_exvivo
 1327    881   1989  2.418 0.488     0.104     0.019        8     1.1  BA4p_exvivo
10366   6555  21270  2.770 0.562     0.112     0.023       97     9.5  BA6_exvivo
 3915   2584   7261  2.667 0.431     0.119     0.022       39     3.7  BA44_exvivo
 4550   3026   8934  2.555 0.483     0.134     0.028       64     5.1  BA45_exvivo
 4619   3068   5607  1.751 0.572     0.149     0.044       64     8.2  V1_exvivo
 8844   5818  12072  1.967 0.542     0.156     0.040      137    14.5  V2_exvivo
 2113   1442   3579  2.350 0.444     0.137     0.028       26     2.4  MT_exvivo
  535    368   2015  3.379 0.876     0.102     0.021        4     0.4  perirhinal_exvivo
  389    270    823  2.688 0.540     0.120     0.018        4     0.3  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 0050008 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050008/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 253950
Total vertex volume 251427 (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) = 1558102 mm^3    (det: 1.250306 )
lhCtxGM: 247805.000 247368.000  diff=  437.0  pctdiff= 0.176
rhCtxGM: 250086.859 249379.000  diff=  707.9  pctdiff= 0.283
lhCtxWM: 252693.228 253227.000  diff= -533.8  pctdiff=-0.211
rhCtxWM: 248821.720 249696.000  diff= -874.3  pctdiff=-0.351
SubCortGMVol  58014.000
SupraTentVol  1080417.806 (1077098.000) diff=3319.806 pctdiff=0.307
SupraTentVolNotVent  1061011.806 (1057692.000) diff=3319.806 pctdiff=0.313
BrainSegVol  1236226.000 (1233237.000) diff=2989.000 pctdiff=0.242
BrainSegVolNotVent  1212515.000 (1212136.806) diff=378.194 pctdiff=0.031
BrainSegVolNotVent  1212515.000
CerebellumVol 154708.000
VentChorVol   19406.000
3rd4th5thCSF   4305.000
CSFVol  1316.000, OptChiasmVol   115.000
MaskVol 1791794.000
  893    409   1326  2.305 0.624     0.109     0.034       11     1.3  BA1_exvivo
 2021   1273   2753  1.994 0.539     0.099     0.018       13     1.5  BA2_exvivo
 1027    707    871  1.720 0.477     0.145     0.029       12     1.1  BA3a_exvivo
 1701   1096   1730  1.585 0.445     0.088     0.018        8     1.3  BA3b_exvivo
 1236    649   2114  2.662 0.517     0.103     0.030       11     1.4  BA4a_exvivo
 1107    743   1623  2.405 0.531     0.102     0.020        6     1.0  BA4p_exvivo
 6495   4049  13404  2.823 0.541     0.110     0.023       59     5.9  BA6_exvivo
  954    621   2031  2.723 0.444     0.120     0.028       11     1.2  BA44_exvivo
 1115    747   2345  2.591 0.382     0.132     0.024       17     1.1  BA45_exvivo
 4398   2935   5206  1.740 0.570     0.147     0.043       58     7.5  V1_exvivo
 4875   3198   6444  1.864 0.534     0.165     0.042       83     9.0  V2_exvivo
  300    195    597  2.424 0.421     0.145     0.034        5     0.4  MT_exvivo
  305    202   1157  3.467 0.760     0.104     0.024        3     0.2  perirhinal_exvivo
  258    183    463  2.545 0.460     0.118     0.015        2     0.2  entorhinal_exvivo

Started at Sat Oct 7 18:13:21 CEST 2017 
Ended   at Sun Oct 8 03:32:00 CEST 2017
#@#%# recon-all-run-time-hours 9.311
recon-all -s 0050008 finished without error at Sun Oct  8 03:32:00 CEST 2017